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Iakovou, Georgios. "Simulating molecular docking with haptics." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/59468/.
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Intermolecular binding underlies various metabolic and regulatory processes of the cell, and the therapeutic and pharmacological properties of drugs. Molecular docking systems model and simulate these interactions in silico and allow the study of the binding process. In molecular docking, haptics enables the user to sense the interaction forces and intervene cognitively in the docking process. Haptics-assisted docking systems provide an immersive virtual docking environment where the user can interact with the molecules, feel the interaction forces using their sense of touch, identify visually the binding site, and guide the molecules to their binding pose. Despite a forty-year research e�ort however, the docking community has been slow to adopt this technology. Proprietary, unreleased software, expensive haptic hardware and limits on processing power are the main reasons for this. Another signi�cant factor is the size of the molecules simulated, limited to small molecules. The focus of the research described in this thesis is the development of an interactive haptics-assisted docking application that addresses the above issues, and enables the rigid docking of very large biomolecules and the study of the underlying interactions. Novel methods for computing the interaction forces of binding on the CPU and GPU, in real-time, have been developed. The force calculation methods proposed here overcome several computational limitations of previous approaches, such as precomputed force grids, and could potentially be used to model molecular exibility at haptic refresh rates. Methods for force scaling, multipoint collision response, and haptic navigation are also reported that address newfound issues, particular to the interactive docking of large systems, e.g. force stability at molecular collision. The i ii result is a haptics-assisted docking application, Haptimol RD, that runs on relatively inexpensive consumer level hardware, (i.e. there is no need for specialized/proprietary hardware).
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Atkovska, Kalina, Sergey A. Samsonov, Maciej Paszkowski-Rogacz, and M. Teresa Pisabarro. "Multipose Binding in Molecular Docking." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-147177.
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Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.
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Landaverde, Raphael J. "GPU optimizations for a production molecular docking code." Thesis, Boston University, 2014. https://hdl.handle.net/2144/21199.
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Thesis (M.Sc.Eng.) -- Boston UniversityScientists have always felt the desire to perform computationally intensive tasks that surpass the capabilities of conventional single core computers. As a result of this trend, Graphics Processing Units (GPUs) have come to be increasingly used for general computation in scientific research. This field of GPU acceleration is now a vast and mature discipline. Molecular docking, the modeling of the interactions between two molecules, is a particularly computationally intensive task that has been the subject of research for many years. It is a critical simulation tool used for the screening of protein compounds for drug design and in research of the nature of life itself. The PIPER molecular docking program was previously accelerated using GPUs, achieving a notable speedup over conventional single core implementation. Since its original release the development of the CPU based PIPER has not ceased, and it is now a mature and fast parallel code. The GPU version, however, still contains many potential points for optimization. In the current work, we present a new version of GPU PIPER that attains a 3.3x speedup over a parallel MPI version of PIPER running on an 8 core machine and using the optimized Intel Math Kernel Library. We achieve this speedup by optimizing existing kernels for modern GPU architectures and migrating critical code segments to the GPU. In particular, we both improve the runtime of the filtering and scoring stages by more than an order of magnitude, and move all molecular data permanently to the GPU to improve data locality. This new speedup is obtained while retaining a computational accuracy virtually identical to the CPU based version. We also demonstrate that, due to the algorithmic dependencies of the PIPER algorithm on the 3D Fast Fourier Transform, our GPU PIPER will likely remain proportionally faster than equivalent CPU based implementations, and with little room for further optimizations. This new GPU accelerated version of PIPER is integrated as part of the ClusPro molecular docking and analysis server at Boston University. ClusPro has over 4000 registered users and more than 50000 jobs run over the past 4 years.
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De, Youngster Dela. "An Isometry-Invariant Spectral Approach for Macro-Molecular Docking." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/30226.
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Proteins and the formation of large protein complexes are essential parts of living organisms. Proteins are present in all aspects of life processes, performing a multitude of various functions ranging from being structural components of cells, to facilitating the passage of certain molecules between various regions of cells. The 'protein docking problem' refers to the computational method of predicting the appropriate matching pair of a protein (receptor) with respect to another protein (ligand), when attempting to bind to one another to form a stable complex.
Research shows that matching the three-dimensional (3D) geometric structures of candidate proteins plays a key role in determining a so-called docking pair, which is one of the key aspects of the Computer Aided Drug Design process. However, the active sites which are responsible for binding do not always present a rigid-body shape matching problem. Rather, they may undergo sufficient deformation when docking occurs, which complicates the problem of finding a match.
To address this issue, we present an isometry-invariant and topologically robust partial shape matching method for finding complementary protein binding sites, which we call the ProtoDock algorithm. The ProtoDock algorithm comes in two variations. The first version performs a partial shape complementarity matching by initially segmenting the underlying protein object mesh into smaller portions using a spectral mesh segmentation approach. The Heat Kernel Signature (HKS), the underlying basis of our shape descriptor, is subsequently computed for the obtained segments. A final descriptor vector is constructed from the Heat Kernel Signatures and used as the basis for the segment matching. The three different descriptor methods employed are, the accepted Bag of Features (BoF) technique, and our two novel approaches, Closest Medoid Set (CMS) and Medoid Set Average (MSA).
The second variation of our ProtoDock algorithm aims to perform the partial matching by utilizing the pointwise HKS descriptors. The use of the pointwise HKS is mainly motivated by the suggestion that, at adequate times, the Heat Kernel Signature of a point on a surface sufficiently describes its neighbourhood. Hence, the HKS of a point may serve as the representative descriptor of its given region of which it forms a part. We propose three (3) sampling methods---Uniform, Random, and Segment-based Random sampling---for selecting these points for the partial matching. Random and Segment-based Random sampling both prove superior to the Uniform sampling method.
Our experimental results, run against the Protein-Protein Benchmark 4.0, demonstrate the viability of our approach, in that, it successfully returns known binding segments for known pairing proteins. Furthermore, our ProtoDock-1 algorithm still still yields good results for low resolution protein meshes. This results in even faster processing and matching times with sufficiently reduced computational requirements when obtaining the HKS.
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Tantar, Alexandru-Adrian. "Hybrid parallel metaheuristics for molecular docking on computational grids." Thesis, Lille 1, 2009. http://www.theses.fr/2009LIL10166.
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Cette thèse porte sur les méta-heuristiques hiérarchiques parallèles adaptatives pour l'échantillonnage conformationnel. Étant un problème hautement combinatoire et multlmodal, l'échantillonnage conformationnel requière la construction d'approches hybrides à large échelle. Après une analyse dei modèles mathématiques, nécessitant l'examen des différentes formulations du champ de force, nous avons proposé une étude des opérateurs de variation et des méthodes de recherche locale adaptés au problème ainsi que leur hybridation dynamique et adaptative. Cette étude nous a conduit à la proposition de mécanismes d'adaptation des paramètres des algorithmes utilisés en fonction du processus d'évolution. Dans cette thèse, nous proposons également des algorithmes adaptatifs hybndes hiérarchiques distribués, fortement extensibles. L'expérimentation, basée sur l'utilisation de multiples modèles parallèles, démontre la grande efficacité de ces algorithmes. En effet, les résultats obtenus montrent que des RMSD moyens en dessous de 1.0 A peuvent être obtenus sur des instances difficiles des problèmes de prédiction de la structure des protéines et de docking moléculaire. La validation des approches hybrides proposées a été effectuée sur Grid'5000, une grille expérimentale d'échelle nationale composée d'environ 5000 coeurs de calcul. Une image système a été développée en utilisant Globus pour permettre des déploiements distribués à large échelle. L'approche hiérarchique distribuée construite a été ainsi déployée sur plusieurs grappes, avec près de 1000 coeurs de calculThe thesis proposes an extensive analysis of adaptive hierarchical parallel metaheuristics for ab initio conformational sampling. Standing as an NP, combinatorial, highly multi-modal optimization problem, conformational sampling requires for high-performance large scale hybrid approaches to be constructed. Following an incremental definition, minimum complexity conformational sampling mathematical models are first analyzed, entailing a review of different force field formulations. A comprehensive analysis is conducted on a large set of operators and local search algorithms including adaptive and dynamic mechanisms. As determined by the analysis outcomes, complex a priori and online parameter tuning stages are designed. finally, highly scalable hierarchical hybrid distributed algorithm designs are proposed. Experimentation is carried over multiple parallelization models with afferent cooperation topologies. Expenmentations resulted in unprecedented results to be obtained. Multiple perfect conformational matches have been determined, on highly difficult protein structure prediction and molecular docking benchmarks, with RMSD average values below 1.0A. The validation of the proposed hybrid approaehes was performed on Grid'5000, a French computational grid, with almost 5000 computational cores. A Globus Toolkit hased Grid'SOOO system image has been developed, sustaining large scale distributed deployments. The constructed hierarchical hybrid distributed algorithm has been deployed on multiple clusters, with almost 1000 computing cores. Finally, a parallel AutoDock version was developed using the ParadisEO framework, integrating the developed algorithms
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BASCIU, ANDREA. "An enhanced-sampling MD-based protocol for molecular docking." Doctoral thesis, Università degli Studi di Cagliari, 2020. http://hdl.handle.net/11584/284135.
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Understanding molecular recognition of small molecules by proteins in atomistic
detail is key for drug design. Molecular docking is a widely used computational method
to mimic ligand-protein association in silico. However, predicting conformational
changes occurring in proteins upon ligand binding is still a major challenge. Ensemble
docking approaches address this issue by considering a set of different conformations of
the protein obtained either experimentally or from computer simulations, e.g. from
molecular dynamics. However, holo structures prone to host (the correct) ligands are
generally poorly sampled by standard molecular dynamics simulations of the unbound
(apo) protein. In order to address this limitation, we introduce a computational
approach based on metadynamics simulations called ensemble docking with enhanced
sampling of pocket shape (EDES) that allows holo-like conformations of proteins to be
generated by exploiting only their apo structures. This is achieved by defining a set
of collective variables able to sample different shapes of the binding site, ultimately
mimicking the steric effect due to the ligand. In this work, we assessed the method
on re-docking and cross-docking calculations. In first case, we selected three different
protein targets undergoing different extent of conformational changes upon binding and,
for each of them, we docked the experimental ligand conformation into an ensemble
of receptor structures generated by EDES. In the second case, in the contest of a
blind docking challenge, we generated the 3D structures of a set of different ligands
of the same receptor and docked them into a set of EDES-generated conformations
of that receptor. In all cases, for both re-docking and cross-docking experiments, our
protocol generates a significant fraction of structures featuring a low RMSD from the
experimental holo geometry of the receptor. Moreover, ensemble docking calculations
using those conformations yielded in almost all cases to native-like poses among the
top-ranked ones. Finally, we also tested an improved EDES recipe on a further target,
known to be extremely challenging due to its extended binding region and the large
extent of conformational changes accompanying the binding of its ligands.
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DI, DOMIZIO ALESSANDRO. "Development of methodologies for molecular docking and their applications." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2009. http://hdl.handle.net/10281/7460.
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Virtual High Throughput Screening (vHTS) has an increasingly important role in lowering both costs and time in drug discovery. The present work deals with the development (C++ programming language) of a new molecular docking software (semi-flexible model) to be used for vHTS. It would improve some of the main aspects of this type of softwares in current use, with particular reference to the program AutoDock: a particular importance is given to the calculation of the ligand conformational energy variation in passing from the unbound to the bound state, which represents a crucial term in the docking energy definition. Two real cases to which the new software modules were applied are then presented: the first belonging to drug discovery, concerning the study of new Ras oncogenic protein inhibitors; the second belonging to virtual protein engineering (VPE), concerning the design of a modified enzyme to be used in the manufacturing of semisynthetic antibiotics.
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Boyce, Sarah Emily. "Model systems for molecular docking: Understanding molecular recognition in polar and charged binding sites." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3390113.
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Salmaso, Veronica. "Exploring protein flexibility during docking to investigate ligand-target recognition." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421817.
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Ligand-protein binding models have experienced an evolution during time: from the lock-key model to induced-fit and conformational selection, the role of protein flexibility has become more and more relevant. Understanding binding mechanism is of great importance in drug-discovery, because it could help to rationalize the activity of known binders and to optimize them. The application of computational techniques to drug-discovery has been reported since the 1980s, with the advent computer-aided drug design. During the years several techniques have been developed to address the protein flexibility issue.
The present work proposes a strategy to consider protein structure variability in molecular docking, through a ligand-based/structure-based integrated approach and through the development of a fully automatic cross-docking benchmark pipeline.
Moreover, a full exploration of protein flexibility during the binding process is proposed through the Supervised Molecular Dynamics. The application of a tabu-like algorithm to classical molecular dynamics accelerates the binding process from the micro-millisecond to the nanosecond timescales. In the present work, an implementation of this algorithm has been performed to study peptide-protein recognition processes.I modelli di riconoscimento ligando-proteina si sono evoluti nel corso degli anni: dal modello chiave-serratura a quello di fit-indotto e selezione conformazionale, il ruolo della flessibilità proteica è diventato via via più importante. Capire il meccanismo di riconoscimento è di grande importanza nella progettazione di nuovi farmaci, perchè può dare la possibilità di razionalizzare l’attività di ligandi noti e di ottimizzarli. L’applicazione di tecniche computazionali alla scoperta di nuovi farmaci risale agli anni ‘80, con l’avvento del cosiddetto “Computer-Aided Drug Design”, o, tradotto, progettazione di farmaci aiutata dal computer. Negli anni sono state sviluppate molte tecniche che hanno affrontato il problema della flessibilità proteica. Questo lavoro propone una strategia per considerare la variabilità delle strutture proteiche nel docking, attraverso un approccio combinato ligand-based/structure-based e attraverso lo sviluppo di una procedura completamente automatizzata di docking incrociato. In aggiunta, viene proposta una piena esplorazione della flessibilità proteica durante il processo di legame attraverso la Dinamica Molecolare Supervisionata. L’applicazione di un algoritmo simil-tabu alla dinamica molecolare classica accelera il processo di riconoscimento dalla scala dei micro-millisecondi a quella dei nanosecondi. Nel presente lavoro è stata fatta un’implementazione di questa algoritmica per studiare il processo di riconoscimento peptide-proteina.
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Genheden, Samuel. "A fast protein-ligand docking method." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-69.
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In this dissertation a novel approach to protein-ligand docking is presented. First an existing method to predict putative active sites is employed. These predictions are then used to cut down the search space of an algorithm that uses the fast Fourier transform to calculate the geometrical and electrostatic complementarity between a protein and a small organic ligand. A simplified hydrophobicity score is also calculated for each active site. The docking method could be applied either to dock ligands in a known active site or to rank several putative active sites according to their biological feasibility. The method was evaluated on a set of 310 protein-ligand complexes. The results show that with respect to docking the method with its initial parameter settings is too coarse grained. The results also show that with respect to ranking of putative active sites the method works quite well.
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Daldrop, Peter. "Structure and molecular recognition in riboswitches." Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/db338d42-75c1-43a6-be6a-11399f04989e.
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Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking.The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identfied in silico was cofirmed to bind experimentally.The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identfied which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identi ed which fold in context of the riboswitch but do not fold in isolation. This con rms the contribution of tertiary interactions to k-turn folding. This conclusion was backed
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Alisaraie, Laleh. "Improvement of a molecular docking approach and its applications using QXP+." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=985169141.
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Sparring, Leonard. "Conquering Chemical Space : Optimization of Docking Libraries through Interconnected Molecular Features." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416977.
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Copied selected text to selection primary: The development of new pharmaceuticals is a long and ardous process that typically requires more than 10 years from target identification to approved drug. This process often relies on high throughput screening of molecular libraries. However, this is a costly and time-intensive approach and the selection of molecules to screen is not obvious, especially in relation to the size of chemical space, which has been estimated to consist of 10 60 compounds. To accelerate this exploration, molecules can be obtained from virtual chemical libraries and tested in-silico using molecular docking. Still, such methods are incapable of handling the increasingly colossal virtual libraries, currently reaching into the billions. As the libraries continue to expand, a pre-selection of compounds will be necessitated to allow accurate docking-predictions. This project aims to investigate whether the search for ligands in vast molecular libraries can be made more efficient with the aid of classifiers extended with the conformal prediction framework. This is also explored in conjunction with a fragment based approach, where information from smaller molecules are used to predict larger, lead-like molecules. The methods in this project are retrospectively tested with two clinically relevant G protein-coupled receptor targets, A 2A and D 2 . Both of these targets are involved in devastating disease, including Parkinson’s disease and cancer. The framework developed in this project has the capacity to reduce a chemical library of > 170 million tenfold, while retaining the 80 % of molecules scoring among the top 1 % of the entire library. Furthermore, it is also capable of finding known ligands. This will allow for reduction of ultra-large chemical libraries to manageable sizes, and will allow increased sampling of selected molecules. Moreover, the framework can be used as a modular extension on top of almost any classifier. The fragment-based approaches that were tested in this project performed unreliably and will be explored further.
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VERTEMARA, JACOPO. "Computational modelling of macromolecules: prediction of the 3-D structure, catalytic activity and dynamic features of proteins." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/198948.
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Durante il mio PhD ho utilizzato diverse tecniche computazionali, in particolare metodi QM e MM, per studiare la relazione struttura/attività delle proteine.
Il primo progetto consiste nella caratterizzazione strutturale del cofattore metallico FeMo-co presente nel sito attivo delle Mo-nitrogenasi. L'obbiettivo è studiare da un punto di vista strutturale l'intermedio E 4 che è attualmente ritenuto essere lo step nel quale avviene il legame con N 2 . A tale scopo sono state svolte simulazioni DFT sul FeMo-co considerando ogni possibile stato redox dei ferri proposto in letteratura ( [5FeIII:2FeII]; [3FeIII:4FeII]; [1FeIII:6FeII]) e la forma protonata e non protonata dell'omocitrato. Solo con la configurazione [3FeIII:4FeII] e con l'omocitrato protonato la struttura ottimizzata di E4 mostra la presenza di due idruri a ponte disposti in modo ortogonale tra loro e legati entrambi ai medesimi atomi di ferro (Fe6 e Fe7 ) in accordo con i dati EPR. Tramite Broken Symmetry si è studiato anche il corretto allineamento di spin dei vari atomi di ferro con particolare riguardo per i due ferri (Fe6 e Fe7) che legano gli idruri.
Un altro aspetto studiato riguardante le Mo-nistrogenasi è stata la caratterizzazione della mutazione Ar g 96→Gln . Tale sostituzione rende possibile il binding dell'acetilene al sito attivo delle nitrogenasi anche durante il resting state E0 . Per tentre di dare una spiegazione a tale fatto, si è calcolata l'energia di binding dell'acetilene sia per sito attivo wild type che per quello mutato tramite simulazioni DFT. L'energia di binding dell'acetilene risulta essere più favorevole per il mutante che per il wild type in linea con i dati sperimentali. Dalle simulazioni effettuate risulta che la sostituzione Arg 96 → Gln altera le proprietà chimico-fisiche della tasca di legame, in particolare tale mutazione ha l'effetto di aumentare le caratteristiche idrofobiche del sito di binding. Considerando la natura apolare dell'acetilene, l'aumento del carattere idrofobico dell'intorno aminoacidico del FeMo-co spiega bene il motivo del binding anche durante il resting state E0 .
Il secondo progetto è la caratterizzazione del meccanismo catalitico di un enzima di de novo design tramite simulazioni DFT e di docking molecolare. La proteina presa in considerazione è TRIL9CL23H, un analogo dell'anidrasi carbonica. Il meccanismo catalitico proposto per TRIL9CL23H risulta essere una combinazione dei meccanismi catalitici della α-anidrasi e della β-anidrasi: come accade nel α-anidrasi il sito attivo è costituito da una molecola di acqua coordinata ad un atomo di zinco, a sua volta coordinato con geometria tetraedrica a tre istidine; come accade invece nella β-anhydrase l'accettore del protone perso dalla molecola d'acqua coordinata allo zinco risulta essere un glutammato. I risultati mostrano che a differena dell'anidrasi carbonica, dove il passaggio limitante è l'attivazione della molecola d'acqua, nel caso di TRIL9CL23H il collo di bottiglia di tutto il processo catalitico risulta essere l'uscita dei prodotti dal sito attivo dell'enzima.
Nell'ultimo progetto si è studiato l'effetto della sostituzione R10T della subuità Mre11 del complesso MRX. L'obbiettivo di questo studio è quello di caratterizzare l'effetto di questa sostituzione utilizzando tecniche di simulazione di dinamica molecolare (MD). L'analisi delle dinamiche ha mostrato che la sostituzione R10T provoca una diversa disposizione spaziale del capping domain di Mre11 che ha come effetto quello di aumentare l'attività di svolgimento del DNA. Questa aumentata predisposizione di Mre11-R10T ad aprire la doppia elica di DNA garantendo così alle nucleasi un più facile accesso, spiega l'aumentata attività di resection osservata sperimentalmente.In this work I used different computational techniques, in particular QM and MM methods, to study the relation between structure and activity. The first project was the characterization under structural point of view of the FeMo-cofactor presents in the active site of nitrogenase. My work was focused on the structural characterization of the key cofactor state E4 , that is now accepted as the intermediate that bind N2 in the active site. For this purpose, DFT simulations have been performed on the FeMo-co active site considering all the iron oxidation state assignments proposed in literature ([ 5Fe III :2Fe II ]; [ 3Fe III :4Fe II ]; [ 1Fe III :6Fe II ]) with protonated and not protonated forms of homocitrate. Only in cases of [ 3F e III :4F e II ] with protonated form of homocitrate the optimized E 4 structure shows two hydrides bridged to the same iron atoms (Fe6 and Fe7 ) in an orthogonal fashion, consistently with experimental data. I have also studied the electronic properties of E 4 intermediate in order to evaluate the spin alignment of ferrous and ferric sites, with peculiar focus on the two Fe ions sharing hydride ligands. DFT broken symmetry calculations showed a parallel spin-coupling pattern for the two iron atoms (↑Fe6 : ↑Fe7 ). Another issue investigated is the effect of the substitution of Ar g 96 → Gln on the resting state of the MoFe protein. Experimental evidences show that in presence of this mutation the active site of nitrogenase is able to (non-covalently) bind acetylene even in the resting state (whereas WT protein cannot). To rationalize the observed behaviour, DFT approach has been used to evaluate the binding energy between acetylene and FeMo-co active site in the cases of mutant and wild type systems. In line with experiments, the binding energy results more favourable for the mutant than for the wild type enzyme. An explanation can be found in the different chemico-physical properties of the region available for acetylene binding in cofactor proximity: in presence of the substitution Ar g 96 → Gln the pocket environment becomes more hydrophobic than in the wild type case. Considering the nonpolar nature of acetylene, the mutated MoFe protein has therefore active site features that make it more suitable for substrate binding. The second project was the characterization of the hydrolytic mechanism of a de novo design peptide TRIL9CL23H (an analogue of carbonic anhydrase) trough DFT calculations and identification of a possible binding site for substrates using flexible docking. The mechanism proposed for TRIL9CL23H is a merge of α-anhydrase and β-anhydrase ones: as in α-anhydrase there is a zinc coordinated by three histidine residues and a water molecule, as in β-anhydrase a glutamate residue accepts the water’s proton from active site. Contrary to carbonic anhydrase, results show that the rate determining step is the release of the products from active site and not the activation of water. According to docking results the binding site is located on the side of proteins close to the active site. The last project has investigated the effect of the R10T amino acid change in the Mre11 protein which causes a rapid DSB resection. The wild type and the mutated dimer of Mre11 were studied trough molecular dynamics simulations. Results pointed out that the R10T substitution alters the mobility of the capping domain of Mre11, movement that is implicated in DNA unwinding. This mutation augments the rotation of the capping domain that can lead to a better DNA unwind activity. In this way nucleases that are involved in the DSB resection can have a better access to the DNA.
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Lima, Karine Thiers Leitão. "Polimorfismos do gene da plastoquinol oxidase (PTOX) em ecotipos de Arabidopsis thaliana (projeto 1001 genomas): correlações de expressão gênica e de variantes estruturais da proteína com a distribuição geográfica dos ecotipos." reponame:Repositório Institucional da UFC, 2017. http://www.repositorio.ufc.br/handle/riufc/22414.
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LIMA, Karine Thiers Leitão. Polimorfismos do gene da plastoquinol oxidase (PTOX) em ecotipos de Arabidopsis thaliana (projeto 1001 genomas): correlações de expressão gênica e de variantes estruturais da proteína com a distribuição geográfica dos ecotipos. 2017. 110 f. Dissertação (Mestrado em Bioquímica)-Universidade Federal do Ceará, Fortaleza, 2017.Submitted by Jairo Viana (jairo@ufc.br) on 2017-03-28T19:52:31Z No. of bitstreams: 1 2017_dis_ktllima.pdf: 4068096 bytes, checksum: f6b3738f233a7c99cf008ea14382bf0d (MD5)
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Arabidopsis thaliana was the first plant to have its entirely genome sequenced and fits as the main model for plant studies. In addition, it inhabits several environments making it an interesting target to investigate genetic variations, such as polymorphisms. The study of DNA polymorphisms is important for research because it helps to identify and develop specific molecular markers. The single nucleotide polymorphisms (SNPs) are the main types of polymorphisms explored and once identified are used to understand the adaptation and evolution of species, in addition contribute to the improvement of a particular cultivar. Plastoquinol oxidase (PTOX) is an oxidoreductase that acts on the stress response in plants. Thus, investigating the SNPs in this gene in A. thaliana may contribute to the discovery of molecular markers and suggests it as a possible target gene for plant breeding. The aim of this study was to identify the SNPs in the PTOX gene of 1190 accessions of A. thaliana, to predict the three-dimensional structures for the main polymorphisms, to analyze the gene expression in several conditions and to correlate them with the environment. We collected the genomic data and annotated the PTOX gene manually. And using the Columbia-0 ecotype as a reference all non-synonymous SNPs were identified. The coordinates of the accessions were used to classify the climate, rainfall and geographical morphology. The three-dimensional structure was predicted by the servers PHYRE2, I-TASSER and Modeller 9.16; and the polymorphic structural variants were performed by the PyMOL mutagenesis tool. The structures were submitted to molecular docking by the DockThor server. Gene expression was performed by TopHat software. In the bioinformatics analyzes 32 SNPs were found, of which 16 were non-synonyms and of these 11 changed to a different class amino acid. The amino acids from positions 13, 78, 81 and 323 were those with the highest mutation rate of all: 40%, 31%, 31% and 49%, respectively, and were found associated with rainfall and light intensity. The modified structure at position 323 seems favors a stronger interaction of the enzyme with the substrate, plastoquinol, than Columbia-0. For expression data the PTOX gene is constitutively expressed under normal conditions and induced under stress conditions, especially those involving light intensity. We concluded that the changes (SNPs) in the PTOX gene sequence suggest to be related to the environmental adaptation, that is, this influences the selection of mutant genotypes.
Arabidopsis thaliana foi a primeira planta a ter seu genoma inteiramente sequenciado e se encaixa como principal modelo para estudos de plantas. Além disso, habita vários ambientes tornando-se um alvo interessante para investigar variações genéticas, como os polimorfismos. Esse estudo de polimorfismos no DNA é importante para a pesquisa, pois ajuda a identificar e desenvolver marcadores moleculares específicos. Aqueles polimorfismos de um único nucleotídeo (SNPs) são os principais tipos de polimorfismos explorados e uma vez identificados são utilizados para compreender a adaptação e evolução da espécie, além de contribuir no melhoramento de determinado cultivar. A plastoquinol oxidase (PTOX) é uma oxidoredutase que atua na resposta ao estresse em plantas. Dessa forma, investigar os SNPs nesse gene em A. thaliana podem contribuir para descoberta de marcadores moleculares e indicá-lo como possível gene alvo para melhoramento em plantas. O objetivo deste estudo foi identificar os SNPs no gene PTOX de 1190 acessos de A. thaliana, prever as estruturas tridimensionais para os principais polimorfismos, analisar a expressão gênica em diversas condições e correlacioná-los com o ambiente. Coletamos os dados genômicos e anotamos o gene da PTOX manualmente, tomando como referência o ecotipo Columbia-0. Em seguida, todos os SNPs não-sinônimos foram identificados. As coordenadas dos acessos foram utilizadas para classificar o clima, a pluviosidade e a morfologia geográfica. A estrutura tridimensional foi predita pelo servidor PHYRE2, I-TASSER e Modeller 9.16; e as variantes estruturais polimórficas foram realizadas pela ferramenta mutagênese do PyMOL. As escolhidas foram submetidas ao “docking” molecular pelo servidor DockThor. A expressão gênica foi realizada pelo software TopHat. Nas análises de bioinformática 32 SNPs foram encontrados, dentre estes 16 foram não-sinônimos e destes 11 acarretaram a mudança para um aminoácido de classe diferente. Os aminoácidos das posições 13, 78, 81 e 323 foram aqueles que apresentaram maior taxa de mutação de todos: 40%, 31%, 31% e 49%, respectivamente, e apresentaram associação com a pluviosidade e a intensidade da luz. A estrutura modificada na posição 323 parece favorecer uma interação mais forte da enzima com o substrato, o plastoquinol, do que Columbia-0. Para os dados de expressão o gene da PTOX é expresso constitutivamente em condições normais e induzido em condições de estresse, especialmente aquelas que envolvem intensidade de luz. Concluímos que as mudanças (SNPs) na sequência do gene da PTOX sugerem estar relacionadas com a adaptação ambiental, ou seja, esta influencia a seleção de genótipos mutantes.
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RABELLO, Marcelo Montenegro. "Comparação metodológica de abordagens in silico no estudo de moléculas antiofídicas através de sua ação em toxinas isoladas de venenos de serpentes." Universidade Federal de Pernambuco, 2012. https://repositorio.ufpe.br/handle/123456789/18486.
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Este projeto pode ser resumido como uma comparação metodológica de abordagens in silico, mais precisamente de docking molecular. Foram utilizadas como alvos biológicos as fosfolipases A2 (PLA2), sendo estas um grupo de toxinas presentes abundantemente em venenos de serpentes. Foram utilizadas, como ligantes (potenciais inibidores), um total de 103 moléculas conhecidas na literatura. Um banco de dados com os ligantes e alvos foi construído, agregando-se informações sobre a atividade biológica e também suas respectivas estruturas tridimensionais. Os programas AUTODOCK, AUTODOCK VINA, GOLD, DOCK, SURFLEX e PLANTS foram utilizados para gerar os resultados de docking. O programa BINANA foi utilizado na análise das interações intermoleculares presentes nos complexos ligante-receptor, obtidos como resultados dos cálculos. Os dados gerados foram analisados com métodos multivariados, como por exemplo, a Análise de Componentes Principais (PCA) e a Análise Hierárquica de Clusters (HCA). Resíduos de aminoácidos, importantes para a estabilidade do complexo ligantereceptor, também foram identificados através de uma análise detalhada dos melhores resultados. Adicionalmente, foi reportado um artigo publicado, envolvendo PLA2s, com foco especial na molécula Quercetina como inibidor dos efeitos de veneno de serpente. Foi possível identificar os programas que apresentaram menor demanda computacional na análise comparativa de seus tempos de processamento, o que pode vir a ser muito útil em futuros estudos de docking, até mesmo com um número ainda maior de ligantes e alvos que podem ser submetidos ao procedimento de docking molecular, no intuito de aumentar o banco de dados de inibidores potenciais de PLA2s. As abordagens analíticas multivariadas utilizadas foram capazes de revelar aspectos interessantes sobre as semelhanças e diferenças entre os resultados de docking obtidos. Com a aplicação destas análises, pôde-se estabelecer uma metodologia de análise para a interpretação dos resultados nas escalas visual, numérica e gráfica, através, respectivamente, da geração das imagens para visualização molecular, das análises estatísticas (multivariadas) e da elaboração dos gráficos provenientes destas análises. Este estudo foi importante para aumentar a base de conhecimento do nosso grupo de pesquisa, e da comunidade científica como um todo, a respeito dos cálculos de modelagem molecular que envolvem os métodos de docking, e certamente serão úteis em estudos futuros com PLA2s ou outros alvos farmacológicos.
This project can be summarized as a methodological comparison of in silico approaches, more precisely between docking methods. Several phospholipase A2 (PLA2), a group of toxins abundantly present in snake venoms, were used as targets. A total number of 103 molecules were used for the definition of the ligands. It was built a database with all these ligands, adding information about their activity and also their three-dimensional structures. The programs AUTODOCK, AUTODOCK VINA, GOLD, DOCK, SURFLEX and PLANTS were used in docking calculations. The program BINANA was used to analyze the intermolecular interactions present in the ligand-receptor complexes obtained as poses from docking results. The data generated by BINANA was statistically analyzed by applying multivariate analysis methods, such as principal component analysis (PCA) and hierarchical cluster analysis (HCA). Important aminoacids residues for the stability of the complex ligandreceptor were indetified through a detailed analysis of the best results. Additionally, an article was reported, involving PLA2s, with special focus on the Quercetin molecule as an inhibitor of snake venom. In a comparative analysis of the docking calculation’s time, it was possible to identify the programs that present low computational demands. This performance analysis can be very useful in future studies of docking, even with a much larger number of ligands and targets, increasing the database of potential PLA2s inhibitors. By applying these tests, we could establish a methodological analysis for the results interpretation on visual, numerical and graphic scales, means, respectively by the generation of images for molecular visualization, statistical analysis (multivariates) and graphing from these tests. This study was important to increase the knowledge of our research group and also of the scientific community, about the molecular modeling calculations that involves docking methods, and will certainly be useful in future studies with PLA2 or other pharmacological targets.
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Silva, Luciane Sussuchi da [UNESP]. "Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/139389.
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000864119.pdf: 2517185 bytes, checksum: f66c5ecaac1008f20a8256cf9a4604ed (MD5)Esfingomielinase D (SMase D) é uma enzima conhecida por catalisar a clivagem de esfingomielina em ceramida-1-fosfato e colina, atividade presente apenas em aranhas do gênero Loxosceles (aranhas marrom) e em bactérias patogênicas do tipo Corynebacterium. A SMase D, também encontrada na literatura como fosfolipase D, é o principal componente do veneno de aranhas do gênero Loxosceles, capaz de induzir sozinha as lesões dermonecróticas características do loxoscelismo. Apesar da importância clínica, poucos detalhes sobre o mecanismo de ação destas enzimas são conhecidos. Neste trabalho, o mecanismo catalítico das SMases D de aranhas do gênero Loxosceles é estudado através de métodos computacionais como docking, dinâmica molecular clássica, simulações a pH constante e métodos híbridos QM/MM. Primeiramente são avaliadas as interações da SMase D com o íon sulfato, mio-inositol-1-fosfato, o substrato esfingomielina e o inibidor suramina, assim como os prováveis estados de protonação das histidinas 12 e 47 na presença e ausência de ligantes. A seguir, a barreira de energia livre experimental para liberação da colina é estimada em 21 kcal/mol através da teoria do estado de transição e da constante catalítica (kcat) da SMase D de Loxosceles laeta. Este valor é comparado às energias de ativação calculadas em simulações QM/MM para as vias de catálise covalente (entre 18 e 24 kcal/mol) e não covalente (25 kcal/mol), os quais correlacionam bem com o valor de 21 Kcal/mol, estimado experimentalmente. Adicionalmente, é sugerido um papel crucial para o grupo hidroxila da esfingomielina no processo de catálise. Dependendo do modo de ligação da hidroxila, a catálise pode ser covalente ou não covalente, com produtos distintos nos dois tipos de catálise. Interessante notar que os dois processos possuem energias de ativação comparáveis, em torno de 25 Kcal/mol, o que poderia supor que os dois processos são...
Sphingomyelinases D (SMase D) are enzymes that catalyze sphingomyelin in ceramida-1-fosfate and choline. This activity is only found in Loxosceles brown spiders and Corynebacterium pathogenic bacterias. SMase D, or phospholipase D, is the main component of spider venoms of the genus Loxosceles, being able to induce the characteristic dermonecrotic features of the whole venom. Despite of the clinical importance o these enzymes, their action mechanism is not completely described. In this work, the catalytic mechanism of SMases D against sphingomyelin is studied through computational methods like docking, classical molecular dynamics, constant pH simulations and hybrid methods QM/MM. First, molecular interactions of SMases D with sulfate ion, myo-inositol-1-phosphate, sphingomyelin (the substrate) and suramin inhibitor are evaluated, as well as the protonation states of the catalytic histidines, 12 and 47, in presence or absence of ligands in the active site. Then, the free energy barrier of 21 kcal/mol for choline release is estimated using the transition state theory and the catalytic constant of Loxosceles laeta activity (kcat). This value is compared to the activation energies obtained through QM/MM simulations for covalent (between 18 and 24 kcal/mol) and non-covalent (25 kcal/mol) pathways. Additionally, the hydroxyl group of sphingomyelin is proposed to play a crucial role in the catalytic mechanism. Depending on the binding way of the hydroxyl group, the catalysis may be covalent or non-covalent, with different reaction products in each case. Interestingly, the two processes showed similar activation energies, suggesting that they may be equally probable, as discussed in some experimental studies for different phospholipase D. Finally, the affinity of SMases for mimetic membranes is discussed
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Silva, Luciane Sussuchi da. "Estudos computacionais de esfingomielinases D : docking, dinâmica molecular e métodos híbridos QM/MM /." São José do Rio Preto, 2015. http://hdl.handle.net/11449/139389.
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Orientador: Jorge ChahineBanca: Ronaldo Júnio De Oliveira
Banca: José Fernando Ruggiero Bachega
Banca: Gabriel Gouvêa Slade
Banca: Fábio Rogério de Moraes
Resumo: Esfingomielinase D (SMase D) é uma enzima conhecida por catalisar a clivagem de esfingomielina em ceramida-1-fosfato e colina, atividade presente apenas em aranhas do gênero Loxosceles (aranhas marrom) e em bactérias patogênicas do tipo Corynebacterium. A SMase D, também encontrada na literatura como fosfolipase D, é o principal componente do veneno de aranhas do gênero Loxosceles, capaz de induzir sozinha as lesões dermonecróticas características do loxoscelismo. Apesar da importância clínica, poucos detalhes sobre o mecanismo de ação destas enzimas são conhecidos. Neste trabalho, o mecanismo catalítico das SMases D de aranhas do gênero Loxosceles é estudado através de métodos computacionais como docking, dinâmica molecular clássica, simulações a pH constante e métodos híbridos QM/MM. Primeiramente são avaliadas as interações da SMase D com o íon sulfato, mio-inositol-1-fosfato, o substrato esfingomielina e o inibidor suramina, assim como os prováveis estados de protonação das histidinas 12 e 47 na presença e ausência de ligantes. A seguir, a barreira de energia livre experimental para liberação da colina é estimada em 21 kcal/mol através da teoria do estado de transição e da constante catalítica (kcat) da SMase D de Loxosceles laeta. Este valor é comparado às energias de ativação calculadas em simulações QM/MM para as vias de catálise covalente (entre 18 e 24 kcal/mol) e não covalente (25 kcal/mol), os quais correlacionam bem com o valor de 21 Kcal/mol, estimado experimentalmente. Adicionalmente, é sugerido um papel crucial para o grupo hidroxila da esfingomielina no processo de catálise. Dependendo do modo de ligação da hidroxila, a catálise pode ser covalente ou não covalente, com produtos distintos nos dois tipos de catálise. Interessante notar que os dois processos possuem energias de ativação comparáveis, em torno de 25 Kcal/mol, o que poderia supor que os dois processos são...
Abstract: Sphingomyelinases D (SMase D) are enzymes that catalyze sphingomyelin in ceramida-1-fosfate and choline. This activity is only found in Loxosceles brown spiders and Corynebacterium pathogenic bacterias. SMase D, or phospholipase D, is the main component of spider venoms of the genus Loxosceles, being able to induce the characteristic dermonecrotic features of the whole venom. Despite of the clinical importance o these enzymes, their action mechanism is not completely described. In this work, the catalytic mechanism of SMases D against sphingomyelin is studied through computational methods like docking, classical molecular dynamics, constant pH simulations and hybrid methods QM/MM. First, molecular interactions of SMases D with sulfate ion, myo-inositol-1-phosphate, sphingomyelin (the substrate) and suramin inhibitor are evaluated, as well as the protonation states of the catalytic histidines, 12 and 47, in presence or absence of ligands in the active site. Then, the free energy barrier of 21 kcal/mol for choline release is estimated using the transition state theory and the catalytic constant of Loxosceles laeta activity (kcat). This value is compared to the activation energies obtained through QM/MM simulations for covalent (between 18 and 24 kcal/mol) and non-covalent (25 kcal/mol) pathways. Additionally, the hydroxyl group of sphingomyelin is proposed to play a crucial role in the catalytic mechanism. Depending on the binding way of the hydroxyl group, the catalysis may be covalent or non-covalent, with different reaction products in each case. Interestingly, the two processes showed similar activation energies, suggesting that they may be equally probable, as discussed in some experimental studies for different phospholipase D. Finally, the affinity of SMases for mimetic membranes is discussed
Doutor
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Andersson, David. "Multivariate design of molecular docking experiments : An investigation of protein-ligand interactions." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-35736.
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To be able to make informed descicions regarding the research of new drug molecules (ligands), it is crucial to have access to information regarding the chemical interaction between the drug and its biological target (protein). Computer-based methods have a given role in drug research today and, by using methods such as molecular docking, it is possible to investigate the way in which ligands and proteins interact. Despite the acceleration in computer power experienced in the last decades many problems persist in modelling these complicated interactions. The main objective of this thesis was to investigate and improve molecular modelling methods aimed to estimate protein-ligand binding. In order to do so, we have utilised chemometric tools, e.g. design of experiments (DoE) and principal component analysis (PCA), in the field of molecular modelling. More specifically, molecular docking was investigated as a tool for reproduction of ligand poses in protein 3D structures and for virtual screening. Adjustable parameters in two docking software were varied using DoE and parameter settings were identified which lead to improved results. In an additional study, we explored the nature of ligand-binding cavities in proteins since they are important factors in protein-ligand interactions, especially in the prediction of the function of newly found proteins. We developed a strategy, comprising a new set of descriptors and PCA, to map proteins based on their cavity physicochemical properties. Finally, we applied our developed strategies to design a set of glycopeptides which were used to study autoimmune arthritis. A combination of docking and statistical molecular design, synthesis and biological evaluation led to new binders for two different class II MHC proteins and recognition by a panel of T-cell hybridomas. New and interesting SAR conclusions could be drawn and the results will serve as a basis for selection of peptides to include in in vivo studies.
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Maganhi, Stella Hernandez. "Telurooxetanas : estudos cristalográficos, modelagem molecular e cálculos de docking para aplicação biológica." Universidade Federal de São Carlos, 2009. https://repositorio.ufscar.br/handle/ufscar/6445.
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Previous issue date: 2009-02-10Universidade Federal de Minas Gerais
This work is composed of 4 chapters. In Chapter 1 is a description of the problems addressed here, starting with the characteristics of the protein, its biological and social importance, and the interactions responsible for both its structure and the formation of ligand-protein complexes, there is also a brief description of Te(IV) compounds followed by the presentation of the grounds of the experimental methods used, namely crystallography and docking. In Chapter 2 the objectives of this work are presented. Chapter 3 includes the experimental procedures that were used to determine the crystal and molecular structures, the modeling of the compounds that did not have crystallographic structure, as well as the molecular docking. In Chapter 4 are described and discussed the results. The crystal structures of the telluroxetanes (3E)-2-chloro-3-(chloromethylidene)-2-(4- methoxyphenyl)-1-oxa-2 λ4- telluraspiro[3.6]decane (1) and of (3E)-2-chloro-3-(chloromethylidene)-2-(4- methoxyphenyl)-1-oxa-2 λ4- telluraspiro[3.5]nonane (2) show that the coordination polyhedron around the atom of Te is a pseudo-pentagonal bipyramid. The supramolecular synthon is different in the two cases, in spite that the Te atom makes a secondary interaction with a halide, in both cases. The docking results for all tellurium compounds have shown that these ligands form complexes with Cathepsin B through the formation of a covalent bond between the Te and S of Cys29 of the enzyme. The differences in the values of scores from the docking and the number of interactions are due, mainly, the size of the carbon chain. Finally the conclusions and outlook can be found.
Este trabalho é composto de 4 capítulos. No capítulo 1 encontra-se uma descrição dos problemas abordados aqui, começando com as características da proteína, a sua importância biológica e social, as interações responsáveis tanto pela sua estrutura como pela formação de complexos proteína-ligante; também há uma breve descrição dos compostos de telúrio seguido da apresentação dos fundamentos dos métodos experimentais utilizados, ou seja, cristalografia e docking. No capítulo 2, os objetivos deste trabalho são apresentados. O Capítulo 3 inclui os procedimentos experimentais que foram utilizados para determinar as estruturas cristalinas e moleculares, a modelagem dos compostos que não têm estrutura cristalográficas, bem como do docking molecular. No capítulo 4 são descritos e discutidos os resultados. As estruturas cristalinas das telurooxetanas (3E)-2-cloro-3-(cloromethilidene)-2-(4-metoxifenil)-1-oxa-2λ4- telluraspiro [3,6]decano (1) e de (3E)-2-cloro-3-(clorometilidene)-2 λ4- 4- telluraspiro[3,5]nonano (2), mostram que o poliedro de coordenação ao redor do átomo de Te é uma pseudo-bipirâmide pentagonal. O synthon supramolecular é diferente nos dois casos, apesar de o átomo Te, em ambos os casos, realizar uma interação secundária com um haleto. Os resultados de docking para todos os compostos de telúrio estudados monstraram que estes formam complexos com a catepsina B através da formação de uma ligação covalente entre o Te e S da Cys29 da enzima. As diferenças nos valores dos escores de docking e no número de interações são devidos, principalmente, o tamanho da cadeia de carbono. Finalmente as conclusões e as perspectivas podem ser encontrados.
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Frantz, F?bio Andr? "Smart execution of molecular docking simulations of a fully-flexible receptor model." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2012. http://tede2.pucrs.br/tede2/handle/tede/5177.
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Previous issue date: 2012-04-12Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments, providing a Reduced Fully-Flexible Receptor (RFFR) model. The main contribution of this research is to prove that P-SaMI rules can be used on Molecular Docking Simulations through a web environment integrated with an MTC middleware.
Simula??es de docagem molecular com modelos de Receptores Totalmente Flex?veis (FFR) est?o adquirindo maturidade. No entanto, isto demanda atividades computacionais de paraleliza??o para gera??o e execu??o de grande volume de dados que precisam ser analizados. Computa??o multi-tarefa ? um paradigma atrativo e que vem sendo aplicado frequentemente para executar tarefas intensivas. Neste trabalho propomos um ambiente para executar simula??es de docagem molecular no modelo FFR com pequenas mol?culas integradas a um componente MTC. Este ambiente ? baseado no padr?o M?ltiplas Inst?ncias Autoadapt?veis (P-SaMI) que possui regras para redu??o do n?mero de experimentos, provendo um modelo de Receptores Totalmente Flex?veis Reduzido (RFFR). A principal contribui??o desta pesquisa est? na comprova??o de que as regras do P-SaMI podem ser usadas em Simula??es de Docagem Molecular atrav?s de um ambiente web integrado com um componente MTC.
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Vianna, Carolina Pasa. "Identificação de ligantes da chiquimato quinase de Mycobacterium tuberculosis por docking molecular." Pontifícia Universidade Católica do Rio Grande do Sul, 2011. http://hdl.handle.net/10923/1377.
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Previous issue date: 2011Tuberculosis (TB) is the major cause of human mortality from a curable infectious disease, attacking mainly in developing countries. Among targets identified in Mycobacterium tuberculosis genome, enzymes of the shikimate pathway deserve special attention, since they are essential to the survival of the microorganism and absent in mammals. The object of our study is shikimate kinase (SK), the fifth enzyme of this pathway. We applied virtual screening methods in order to identify new potential inhibitors for this enzyme. In this work we employed MOLDOCK program in all molecular docking simulations. Accuracy of enzyme-ligand docking was validated on a set of 12 SK-ligand complexes for which crystallographic structures were available, generating root-mean square deviations below 2. 0 Å. Application of this protocol against a commercially available database allowed identification of new molecules with potential to become drugs against TB. Besides, we have identified the binding cavity residues that are essential to intermolecular interactions of this enzyme.
Entre as doenças infecciosas, a tuberculose se destaca, como sendo a principal causa de morte humana, principalmente em países em desenvolvimento. Entre os alvos identificados no genoma de Mycobacterium tuberculosis, as enzimas da via do chiquimato merecem atenção especial, pois são essenciais para a sobrevivência dos microorganismos e ausente em mamíferos. O objeto do nosso estudo é a quinta enzima desta via, a Chiquimato Quinase (SK). Foram aplicados métodos de virtual screening, a fim de identificar novos potenciais inibidores para esta enzima. Neste trabalho nós empregamos o programa MOLDOCK em todas as simulações de docking molecular. A precisão do docking enzima-ligante foi validada em um conjunto de 12 complexos de SK- ligante, para aquelas estruturas cristalográficas que estavam disponíveis, gerando um RMSD abaixo de 2,0 Å. A aplicação deste protocolo em um banco de dados comercialmente disponível permitiu a identificação de novas moléculas com potencial para se tornar drogas contra tuberculose. Além disso, foram identificados os resíduos da cavidade de ligação que são essenciais para as interações intermoleculares desta enzima.
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Frantz, Fábio André. "Smart execution of molecular docking simulations of a fully-flexible receptor model." Pontifícia Universidade Católica do Rio Grande do Sul, 2012. http://hdl.handle.net/10923/1544.
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Previous issue date: 2012Molecular docking simulations of Fully-Flexible Receptor (FFR) models are coming of age. However, they demand parallelization of computing activities for their executions and generate huge amounts of data that needs to be analyzed. Many Task Computing (MTC) is an attractive paradigm routinely applied to execute intensive tasks. In this work we propose an environment to execute molecular docking simulations of FFR models to small molecules integrated with an MTC middleware. This environment is based on a new pattern called Self-adapting Multiple Instances (P-SaMI) that provide rules to reduce the number of experiments, providing a Reduced Fully-Flexible Receptor (RFFR) model. The main contribution of this research is to prove that P-SaMI rules can be used on Molecular Docking Simulations through a web environment integrated with an MTC middleware.
Simulações de docagem molecular com modelos de Receptores Totalmente Flexíveis (FFR) estão adquirindo maturidade. No entanto, isto demanda atividades computacionais de paralelização para geração e execução de grande volume de dados que precisam ser analizados. Computação multi-tarefa é um paradigma atrativo e que vem sendo aplicado frequentemente para executar tarefas intensivas. Neste trabalho propomos um ambiente para executar simulações de docagem molecular no modelo FFR com pequenas moléculas integradas a um componente MTC. Este ambiente é baseado no padrão Múltiplas Instâncias Autoadaptáveis (P-SaMI) que possui regras para redução do número de experimentos, provendo um modelo de Receptores Totalmente Flexíveis Reduzido (RFFR). A principal contribuição desta pesquisa está na comprovação de que as regras do P-SaMI podem ser usadas em Simulações de Docagem Molecular através de um ambiente web integrado com um componente MTC.
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BORDOGNA, ANNALISA. "Predicting the binding modes of protein complexes: new strategies for molecular docking." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/19617.
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Docking approaches and homology modelling procedures have recently become protagonists in the structural prediction of protein complexes. Therefore, in the last years it raised the need of developing more and more reliable tools and defining some guidelines to obtain accurate prediction of those structures. These goals are particularly relevant when only poorly accurate information about the proteins or the interaction (e.g. no interface indication for protein-protein docking, or protein models instead of experimental structures) is available.
In this thesis several strategies based on combining different computational techniques are proposed to overcome the limitations of the sampling stage of ligand- and protein-protein docking approaches and to broaden the possibility of predicting the structure of protein complexes. In particular, in the field of protein-protein docking algorithms, the combination of two existing docking methods (HADDOCK and ZDOCK) was proposed, allowing to obtain a method (called ZADDOCK) able to overcome the limitations of the single strategies used and to sum their strengths. Moreover, both for ligand- and protein-protein docking, an analysis of the relationships between docking results and the quality of homology models was performed to assess the possibility of an a priori prediction of the accuracy of docking results on the basis of the evaluation of model quality indices.
The results obtained for ZADDOCK show on average a very good performance of the method, that produced reliable predictions without the need of any interface data to guide the sampling step. This allows its employment in the study of complexes for which no experimental information is available and bioinformatics interface prediction fails. Moreover, an accurate description of the intermolecular interactions occurring in protein complexes was obtained, which is a key information to drive subsequent experimental work. The quality of ZADDOCK results indicates that the strategy of combining different computational techniques is a very promising avenue for the development of new docking approaches.
As for the use of homology models in docking calculations, in this work it is demonstrated the possibility of a priori predicting the accuracy of ligand-protein docking results on the basis of model quality indices, with the development of a strategy based on the comparison with homologous proteins. Moreover, the results found for protein-protein docking give the bases for a future development of a general prediction strategy of docking accuracy on protein models.
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Ismail, Alexandre. "Molecular modeling of Coq6, a ubiquinone biosynthesis flavin-dependent hydroxylase. Evidence of a substrate access channel." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066044/document.
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Coq6 est une enzyme impliquée dans la biosynthèse du coenzyme Q (aussi nommé ubiquinone, ou Q), un lipide benzoquinone polyprenylé essentiel à la fonction de la chaîne respiratoire mitochondriale. Dans la levure Saccharomyces cerevisiae, cette monooxygénase flavine-dépendante putatif est proposé pour hydroxyler le noyau benzénique d' un précurseur du coenzyme Q à la position C5. Nous montrons ici à travers des études biochimiques que Coq6 est une flavoprotéine utilisant le FAD comme cofacteur. Des modèles d'homologie du complexe Coq6-FAD ont étés réalisés et étudiés par dynamique moléculaire et arrimage moléculaire du 3-hexaprenyl-4-hydroxyphényl (4-HP6), un substrat modèle hydrophobe et volumineux. Nous identifions un canal d'accès putatif pour Coq6 dans un modèle de la forme sauvage et proposons des mutations in silico positionnés à l'entrée capable de partiellement (les mutations simples G248R et L382E) ou complètement (une double-mutation G248R-L382E) bloquer l'accès du substrat au site actif via le canal d' accès. Des essais in vivo soutiennent les prédictions in silico, qui expliquent l'abrogation ou la diminution des enzymes mutées. Ce travail fournit la première information structurale détaillée d'une enzyme importante et hautement conservée de biosynthèse de l'ubiquinoneCoq6 is an enzyme involved in the biosynthesis of coenzyme Q, a polyisoprenylated benzoquinone lipid essential to the function of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, this putative flavin-dependent monooxygenase is proposed to hydroxylate the benzene ring of coenzyme Q (ubiquinone) precursor at position C5. We show here through biochemical studies that Coq6 is a flavoprotein using FAD as a cofactor. Homology models of the Coq6-FAD complex are constructed and studied through molecular dynamics and substrate docking calculations of 3-hexaprenyl-4-hydroxyphenol (4-HP6), a bulky hydrophobic model substrate. We identify a putative access channel for Coq6 in a wild type model and propose in silico mutations positioned at its entrance capable of partially (G248R and L382E single mutations) or completely (a G248R-L382E double-mutation) blocking access of the substrate to thechannel . Further in vivo assays support the computational predictions, thus explaining the decreased activities or inactivation of the mutated enzymes. This work provides the first detailed structural information of an important and highly conserved enzyme of ubiquinone biosynthesis
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Lock, Lisa S. "Recruitment specificity of Gab family docking proteins and implications for MET receptor-mediated epithelial morphogenesis." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82919.
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Activation of cell-surface receptors by extracellular signals can generate distinct biological responses. Many of these signals are coordinated through docking proteins, including those in the Gab family (Gab1, Gab2 and Gab3). Following activation of receptor tyrosine kinases (RTKs), cytokine or antigen receptors, docking proteins are recruited to the receptor complex and become phosphorylated on tyrosine residues, providing binding sites for multiple proteins involved in signal transduction. In this manner, they act to diversify and localize signals downstream from receptors by virtue of their ability to assemble multiprotein complexes.The recruitment of docking proteins to RTKs depends on the ability of the protein to interact directly or indirectly with the receptor. In chapter II, I established that Gab1 and Gab2 can be recruited to RTKs indirectly, through constitutive association of Gab1 or Gab2 with the C-terminal SH3 domain of the adapter protein Grb2. This requires two highly conserved Grb2 binding sites in Gab proteins. One site corresponds to a canonical SH3 domain binding motif, whereas the second contains an atypical PXXXRXXKP motif that I also identified in the unrelated Grb2-binding protein, Slp-76.
In contrast to the other Gab proteins, Gab1 can also interact in a Grb2-independent manner with the Met/Hepatocyte growth factor receptor. In chapter IV, I established that this interaction requires the structural integrity of the Met receptor, phosphorylation of tyrosine 1349 in the Met C-terminus, and a 13 amino acid Met binding motif (MBM) in Gab1. Instead of the expected interaction of a phosphotyrosine-binding domain in Gab1 with a phosphotyrosine-containing motif in the Met receptor, I propose that the activated kinase domain of Met and the negative charge of phosphotyrosine 1349 engage the Gab1 MBM as an extended peptide ligand.
In response to Met receptor stimulation, Gab1 overexpression promotes an invasive morphogenic program in epithelial cells. In contrast, I have shown in chapter III that Gab2 overexpression fails to induce this response. Mutation of the MBM in Gab1 abolishes the ability of Gab1 to promote morphogenesis, whereas its insertion into Gab2 increases Gab2 association with Met, but does not confer on Gab2 the ability to promote morphogenesis. This indicates that the Grb2-independent recruitment of Gab proteins to Met is necessary but not sufficient to promote epithelial morphogenesis. Overall, these studies have identified both common and unique mechanisms through which receptor tyrosine kinases can recruit Gab docking proteins, and have established that Gab1 and Gab2 do not share redundant biological functions in epithelial cells.
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Nascimento, Alessandro Silva. "Interações dos receptores nucleares com seus ligantes: Estudos estruturais do receptor de hormônio tireoidiano, do receptor de mineralocorticóide e do receptor ativado por proliferadores peroxissomais." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-13032009-124546/.
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Os receptores nucleares constituem uma superfamília de fatores de transcrição regulados pela interação com hormônios. Esta superfamília inclui, por exemplo, os receptores de hormônio tireoidiano, estrogênio, androgênio, glicocorticóide e mineralocorticóide. Neste trabalho, empregamos técnicas de biologia estrutura e bioinformática para estudar as interações entre alguns dos membros da família de receptores nucleares e seus respectivos ligantes. Para o receptor de hormônio tireoidiano, foi demonstrado, através da análise das estruturas cristalográficas das duas isoformas do receptor ligados aos tiromimético Triac, que os componentes entálpicos visíveis nas estruturas não explicam a seletividade do ligante. Dados de dinâmica molecular confirmaram que a seletividade do hormônio tem um importante componente entrópico. Empregando a técnica de dinâmica molecular, estudamos a ligação do receptor de mineralocorticóide humano à aldosterona, ao cortisol, à espironolactona e à cortisona e simulamos ainda o efeito da mutação S810L, conhecida por converter a atividade antagonista da cortisona e da espironolactona em agonista. A análise das simulações revelou um perfil de ligações de hidrogênio similar na ligação do receptor selvagem ao cortisol e à aldosterona. A cortisona perde, por conta da inserção de uma hidroxila na posição 11, uma ligação de hidrogênio importante com a Asn770 e, por isso, tem menor energia potencial de ligação. A espironolactona perde a mesma ligação de hidrogênio ao mesmo tempo em que aumenta o número de contatos de van der Waals pela inserção do grupo tioacetil na posição 7. A mutação S810L simulada no complexo com cortisona, cortisol e espironolactona não interfere no padrão de ligações de hidrogênio estabelecidas entre o receptor e os ligantes, mas altera a mobilidade de uma das regiões propostas como rota de dissociação. Propomos, portanto, que a mutação interfere na cinética de dissociação dos ligantes e não no padrão de interações estabelecidas no equilíbrio. Simulações de dissociação induzida do ligante confirmam esta proposição. Na última etapa, utilizamos os modelos experimentalmente determinados para o receptor ativado por proliferadores peroxissomais gama para a busca de novos ligantes através da técnica de docking molecular. Neste trabalho, utilizamos uma base de dados com aproximadamente um milhão de compostos. Destes, quatro foram selecionados após o docking molecular e testados experimentalmente. Um dos compostos testados se mostrou ativo neste receptor, apresentando uma atividade de 60-70% da atividade da rosiglitazona, conhecido agonista total do PPARg.Nuclear receptors are a superfamily of hormone-regulated transcriptional factors. This superfamily includes, for example, the receptor for thyroid hormone, estrogen, androgen, gluco and mineralocorticoid. In this work, we used structural biology and bioinformatic tools to study the interactions between some members of the nuclear receptor superfamily and its respective ligands. We showed by the analysis of the crystal structures of both thyroid hormone receptor isoforms bound to the thyromimetic Triac that the enthalpic components visible in the structures do not explain the ligand selectivity. Molecular dynamics simulation data confirmed later that the hormone selectivity has an important entropic component. Using the molecular dynamics simulation, we studied, in a second stage, the interaction between the human mineralocorticoid receptor bound to aldosterone, cortisol, spironolactone and cortisone and also simulated the effects of the mutations S810L, known to convert the antagonist properties of spironolactone and cortisone in an agonist activity. The analysis of the simulations showed a similar profile in hydrogen bonds established between the wild type receptor bound to cortisol and aldosterone. Cortisone looses an important hydrogen bond with Asn770 because of the insertion of a carbonyl group in the 11 position and shows a decreased binding potential energy. Spironolactone loses the same interaction but has an increased number of van der Waals contacts because of the insertion of a tioacetyl group in the 7 position. The mutant S810L simulated in complex with cortisol, cortisone and spironolactone showed that the mutation do not interfere with the hydrogen bond profile established between the receptor and the ligands but changes the mobility of a region in the receptor previously proposed as a ligand dissociation route. Ligand unbinding simulations through steered molecular dynamics (SMD) confirm that aldosterone and cortisol unbind differentially and the mutation S810L alters the unbinding profile. We then propose that the mutation changes the kinetics of ligand association/dissociation without changing the profile of the interactions established in the equilibrium. In the last stage, we used the experimentally determined structural model of the peroxissome proliferator-activated receptor gamma to search for novel ligands using the molecular docking technique. For this work, we used a database containing about 1 million compounds. Among those, four compounds were selected after the docking computation and experimentally tested. One of these compounds was found to be active in the receptor, showing about 60-70% of the agonistic activity of rosiglitzone, a known PPARg total agonist.
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PAIOTTA, ALICE. "Synthesis of Glycoderivatives as Molecular Tools in Medicinal Chemistry and Nano-Medicinal Chemistry." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2018. http://hdl.handle.net/10281/199137.
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Durante il terzo anno di dottorato mi sono occupata della sintesi finale dei glicomimetici del substrato naturale dell’enzima AGM1 GlcNAc-6P o del prodotto GlcNAc-1P.
Le sintesi messe a punto sono necessarie per ottenere prodotti finali utilizzabili come strumenti molecolari chimici per studiare il ruolo dell’HBP nella regolazione della proliferazione e la sopravvivenza delle cellule tumorali.
I prodotti presentati (caratterizzati mediante NMR (1H. COSY, HSQC e 13C) e Massa) sono stati preparati protetti (acetilati sugli ossidrili) per i test cellulari per favorire la loro diffusione attraverso la membrana cellulare e nella forma de-protetta per il test enzimatico, per poterne valutare la potenza inibitoria direttamente sull’enzima AGM1.
La messa a punto del test enzimatico ha come obiettivo la valutazione dell’effettiva capacità inibitoria dei composti sintetizzati. Il test prevede la comparazione della quantità di UDP-GlcNAc prodotto dalla reazione accoppiata dell’enzima AGM1 e AGX1, utilizzando un estratto enzimatico cellulare, in assenza e in presenza dei potenziali inibitori. La quantificazione è stata effettuata mediante l’utilizzo della tecnica cromatografica HPLC, con un metodo ion-pair a fase inversa associato ad un rilevatore UV impostato ad una lamda di 254 nm.
Inizialmente è stata preparata la retta di taratura dell’UDP-GlcNAc costruita partendo da una madre 1.5 mM e attraverso diluzioni sono state effettuate le analisi in triplicato per ogni punto della retta. Sono stati calcolati i valori del limite di rilevabilità (LOD) e di quantificazione (LOQ).
Il test messo a punto prevede la quantificazione della produzione di UDP-GlcNAc a partire dai substrati GlcNAc-6P e UTP utilizzando estratti cellulari lisati. In una prima analisi si è esaminato l’estratto enzimatico per verificare la presenza di UDP-GlcNAc endogena, che non è stata riscontrata. Quindi si è verificata l’effettiva efficacia dell’estratto nel catalizzare la produzione di UDP-GlcNAc a partire dai substrati forniti e si sono messe a punto le condizioni di reazione. Infine, si è proceduto con l’analisi degli inibitori sintetizzati. Dati preliminari non hanno evidenziato una diminuzione del segnale di UDP-GlcNAc, il che farebbe escludere una buona attività inibitoria.
Durante il periodo di Traineeship presso il CycloLab di Budapest ho potuto effettuare l'incapsulamento di un potenziale inibitore enzimatico in ciclodestrine funzionalizzate per il targeting di cellule tumorali.
Alcuni dei composti sintetizzati possiedono caratteristiche chimico-fisiche che rendono il loro passaggio attraverso la membrana cellulare molto difficile: la presenza di gruppi solfati, solfonati e fosforamidati, che possiedono cariche negative, li rendono particolarmente polari. Lo scopo del progetto è quello di sfruttare ciclodestrine (CD) opportunamente funzionalizzate come un “cavallo di Troia” per veicolare gli inibitori enzimatici all'interno delle cellule tumorali.
Al CycloLab mi sono quindi occupata della sintesi dello scaffold di interesse e dell’incapsulamento del potenziale inibitore.The project carried out during the 3 years-Ph.D. has had the objective to identify and synthesize new glycomimetics as molecular tools to study the Hexosamine Biosynthetic Pathway (HBP), which role is to regulate the proliferation and survival of cancer cells. The project has been funded by AIRC and the principal aim was to identify the Adenocarcinoma of the Pancreatic Duct (PDAC) as the target of research. The synthesis of innovative chemical tools helps the understanding of the HBP pathway and its response in PDAC: new potential inhibitors, which are similar to the natural substrate of enzyme, can be recognized but trick the enzyme and block its activity in order to decrease the UDP-GlcNAc production and consequently modify the protein glycosylation. Due to the important role of the HBP in the cells, alteration of this pathway can bring to alteration of N- and O- glycosylation and activate the Unfolded Protein Response (UPR) during the Endoplasmic Reticulum (ER) stress. The description of the research target helps the understanding of the design of molecular tools: the focus point is the inhibition of the enzyme N-acetylglucosamine-phosphate mutase (AGM1): its inhibition could represent the way to induce apoptosis in cancer cells. Through the Molecular Design, a rational design of potential inhibitors has been done. This design is based on the similarity with the structures of the natural substrate of enzyme AGM1, with some modifications. All of the drawn structures have been used for Molecular Docking in order to get a first virtual screening on the compounds library. Starting from preliminary results of theoretical approach, the synthesis of compounds have been done following three different synthetic strategies. All the steps and reaction condition are described in details and are shown the characterization (1H, 13C NMR spectra, m/z) of all the synthetized compound. The optimization of the analytical method on High Performance Liquid Chromatography is necessary in order to achieve experimental data on the ability of the designed compounds to inhibit the target enzyme, data to be compared to those obtained through a computational theoretical approach. To this aim an HPLC method has been set-up for the quantification of UDP-GlcNAc produced using the cellular extract as enzyme source, and carrying out the reaction with the natural substrates GlcNAc-6P, UTP in the presence or not of the test molecules. Using 10 and 30 µL of extract, three compounds lead to a decrease of production of UDP-GlcNAc. The computational data ”describes” the interaction between the enzyme and the molecules. The calculation of C LogP has confirmed the most apolar character of compound 3B in the acetylated form. Some preliminary evaluation of the effect of compound 2B in a Triple Negative Breast Cancer (TNBC) cell model has been carried out. In conclusion, the study of the target of this research, the HBP pathway, and the focus on the inhibition of AGM1 are the starting point for a complete project, that includes at first the design of a library of compound based on the structural properties of the natural substrate. the “in silico” evaluation of their interaction with the target enzyme, the synthesis and the screening through an enzymatic assay.. The tuning of the strategy of synthesis is important to obtain the compound for the in vitro test. The analytical method with HPLC gives results comparable to the docking scores, and then, after a calculation of C LogP, the test on cells gives the final results of potency of compound 3B (2B the acetylated form). The last part describes the collaboration with CycloLab (Budapest): some compounds of the library possess chemical-physical characteristics that make their passage through cell membrane very harsh: they are very polar and some of them possess negative charges (sulphate, sulphonates, phosphoramidate). This preliminary work is still in progress.
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Das, Biswajit. "Qsar analysis, docking & molecular dynamics simulation of several antimicrobial compounds and receptors." Thesis, University of North Bengal, 2015. http://ir.nbu.ac.in/handle/123456789/1525.
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Galanis, Alex. "Molecular mechanisms of signalling specificity to the transcription factor SAP-1." Thesis, University of Newcastle Upon Tyne, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327230.
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Ullmann, G. Matthias. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/23/index.html.
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Trindade, Antonio Carlos. "Estudo cristalino, molecular, supramolecular e de \" Docking\" de alguns compostos derivados de quinonas." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/46/46132/tde-16052007-140758/.
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Neste trabalho são apresentados os resultados das determinações cristalinas, estruturais e supramoleculares, por difração de raio X, bem como os estudos de \"docking\" , de oito compostos derivados da 1,4-quinona. As estruturas resolvidas e refinadas mostraram a existência de ligações de hidrogênio, não convencionais intra e intermoleculares. Estas últimas permitiram entender o empacotamento cristalino em cada composto. Os resultados cristalográficos foram comparados com aqueles encontrados na literatura. Mas as estruturas correspondentes aos compostos AC1 (6,7-bis-fenilsulfanil-1,4-dihidro-1,4-metano-naftaleno-5,8-diona) e AC6 (6,7-bis-metilsulfanil-1,4-dihidro-1,4-metano-naftaleno-5,8-diol) possuem esqueletos químicos ainda não descritos na cristalografia. Os estudos de \"docking\" foram realizados utilizando as conformações cristalográficas dos oito compostos e da estrutura cristalográfica da tripanotiona redutase, uma proteína, dimérica, envolvida no sistema anti-stress oxidativo no Tripanosoma cruzi, parasita responsável pela enfermidade de Chagas. Foram, então, gerados complexos proteína-ligante no sítio da interface entre monômeros. Os complexos resultantes foram agrupados de acordo com orientações preferenciais e em cada grupo, a estrutura com menor energia total foi selecionada como representante do conjunto e analisado em tela gráfica. Para cada uma das moléculas foram realizados estudos detalhados das suas interações com todos os aminoácidos que as rodeavam. Finalmente, levando em conta as energias envolvidas e as interações foi possível escolher aquela que mostra o melhor encaixe. Dentre todas as moléculas, a AC8 [4a,8a-Dicloro-6-etilsulfanil-7-(metiletil-fenil-amino)-1,4,4a,8a-tetrahidro-1,4-metano-naftaleno-5,8,-diona] foi considerada como a mais promissora, a qual apresentou melhores resultados, um maior número de interações favoráveis com menor energia.In this work the results of the crystal structure and supramolecular determination by X-ray diffraction together with docking studies, of eight compounds derived from 1,4-quinone, are presented. The solved and refined structures showed the existence of non-conventional hydrogen bonds, intra and inter-molecular. These last ones gave an insight about the crystal packing in each compound. The crystallographic results have been compared with those found in the literature. It should pointed out that structures of compounds AC1 (6,7-bis-phenylsulfanyl-1,4-dihydro-1,4-methano-naphthalene-5,8-dione) and AC6 (6,7-bis-methylsulfanyl-1,4-dihydro-1,4-methane-naphthalene-5,8-diol) have chemical skeletons which were not described before in crystallography. The docking studies have been carried out using the crystallographic conformations of the eight compounds and the crystallographic structure of trypanothione reductase, a dimmeric protein, involved in the anti-stress oxidative system of the Trypanosoma cruzi, the parasite responsible for the Chagas disease. The compounds were docked in the dimmer interface, which is the most likely binding site. The resulting complexes have been clustered together according with their orientation and of each group the one with the lowest total energy was chosen as representative of the cluster and analyzed in graphical screen. Thus, for that complex a detailed study of its interactions with all the neighbor amino acids was done. Finally, taking in account the energies and the interactions it was possible to choose the one that showed the best docking result. Amongst all molecules, the AC8 [4a,8a-dicloro-6-etilsulfanil-7-(metiletil-fenil-amino)-1,4,4a,8a-tetrahidro-1,4-methane-naftaleno-5,8,-diona] was considered as the most promising, which presented better results, a bigger number of favorable interactions with lesser energy.
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Vianna, Carolina Pasa. "Identifica??o de ligantes da chiquimato quinase de Mycobacterium tuberculosis por docking molecular." Pontif?cia Universidade Cat?lica do Rio Grande do Sul, 2011. http://tede2.pucrs.br/tede2/handle/tede/5389.
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Previous issue date: 2011-03-10Entre as doen?as infecciosas, a tuberculose se destaca, como sendo a principal causa de morte humana, principalmente em pa?ses em desenvolvimento. Entre os alvos identificados no genoma de Mycobacterium tuberculosis, as enzimas da via do chiquimato merecem aten??o especial, pois s?o essenciais para a sobreviv?ncia dos microorganismos e ausente em mam?feros. O objeto do nosso estudo ? a quinta enzima desta via, a Chiquimato Quinase (SK). Foram aplicados m?todos de virtual screening, a fim de identificar novos potenciais inibidores para esta enzima. Neste trabalho n?s empregamos o programa MOLDOCK em todas as simula??es de docking molecular. A precis?o do docking enzima-ligante foi validada em um conjunto de 12 complexos de SK- ligante, para aquelas estruturas cristalogr?ficas que estavam dispon?veis, gerando um RMSD abaixo de 2,0 ?. A aplica??o deste protocolo em um banco de dados comercialmente dispon?vel permitiu a identifica??o de novas mol?culas com potencial para se tornar drogas contra tuberculose. Al?m disso, foram identificados os res?duos da cavidade de liga??o que s?o essenciais para as intera??es intermoleculares desta enzima
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Tanczos, Anna Carroll. "Investigations of two distinct pharmacologically relevant proteins using docking studies and molecular dynamics." Thesis, University of Surrey, 2004. http://epubs.surrey.ac.uk/844408/.
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Docking of a flexible ligand to a rigid protein, followed by molecular dynamics (MD) studies to allow movement of the protein is shown to be a useful method for investigating pharmacologically relevant interactions. Studies of MMB lectins (beta-sheet proteins with shallow binding sites) reveal the importance of dimerisation to the activation of all of the carbohydrate binding sites of these lectins, finalising site III into a shape that can accommodate mannose. Aloe lectin was shown to have the overall fold of a MMB lectin and to be capable of forming a dimeric unit, shown to be stable using MD simulations in a water box. Docking shows that only two binding sites in the aloe dimer are thought to be able to bind mannose, as alterations in the residues vital for binding have occurred, and this is supported by the absence of a cluster of docked conformations in these sites. The presence of many 'sticky' patches on the exterior of aloe lectin are observed, revealing extended binding areas consistent with other members of the family. The motions of the mannose molecules in the binding areas during the molecular dynamics simulations suggest that the hydrogen bonds observed in these protein-carbohydrate complexes are dynamic in nature and can be constantly breaking and reforming. Docking of atropine to the GPCR m1AchR (an alpha-helical transmembrane protein with and enclosed binding site) indicates the presence of two key hydrogen bonds with Ser109 and Asn110. The main influences on docking seem to be shape and size of the ligand rather than charge considerations, although the negatively charged end of the binding pocket orients the molecules in the majority of the dockings in the same direction. Docking studies of atropine and selected analogues to m1AchR and two mutants, Tyr381Phe and Tyr381Ala, produce data which correlate well with experimentally determined pIC50 values and a prediction of pIC50 of previously untested antagonists for this system. Molecular dynamics studies show differential movement in the transmembrane helices for MD studies with acetylcholine, atropine and no ligand bound and rearrangement of some key hydrogen bonds. This leads to a model of inverse agonist functionality for atropine and its analogues involving the prevention of helical movement by the aromatic tail groups of these ligands.
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Fernandes, Claudia Lemelle. "Modelagem molecular e estudos de docking da enzima corismato sintase de Mycobacterium tuberculosis." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2006. http://hdl.handle.net/10183/8453.
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As enzimas da via do ácido chiquímico constituem um excelente alvo para o desenho de novos agentes antibacterianos. Esta rota é encontrada em bactérias, fungos, plantas e parasitas do filo apicomplexa, mas está ausente em mamíferos. A Corismato sintase (CS) catalisa o último passo desta rota, produto que é utilizado em outras reações biossintéticas, como biossíntese de aminoácidos aromáticos, folato, vitamina K e ubiquinona. Esta reação é a mais incomum de toda rota e é unica na natureza. Ela converte 5-enolpiruvil-chiqiuimato-3-fosfato (EPSP) em corismato na presença de uma flavina mononucleotídeo reduzida (FMNH2) como coenzima. A predição da estrutura tridimensional (3D) da enzima CS de Mycobacterium tuberculosis (Mtb) foi feita pela técnica de modelagem comparativa por homologia, utilizando a estrutura cristalográfica de CS de Streptococcus pneumoniae (PDB ID: 1QX0) como molde (≈ 42% de identidade), e o programa MODELLER6v2. Adicionalmente, com o intuito de entender as possíveis formas de ligação do substrato e da coenzima a enzima EPSP e flavina mononucleotídeo (FMN), repectivamente, foi feito um docking geométrico. A minimização de energia de todo o complexo mostrou, como esperado, que a maioria das interações ocorridas no molde são preservadas na estrutura de Mtb, exceto pela His11, Arg139 e Gln255. Entretanto, novas interações envolvendo Arg111, Gli113 e Ser317 também foram observadas. Este conhecimento poderá facilitar na busca por novos inibidores para esta enzima como fármacos alternativos no tratamento da tuberculose (Tb).The enzymes of the shikimate pathway constitute an excellent target for the design of new antibacterial agents. This pathway is found in bacteria, fungi, plants and apicomplexan parasites but is absent in mammals. Chorismate synthase (CS) catalyzes the last step of this pathway, the product of which is utilized in other enzymatic transformations like the biosynthesis of aromatic amino acids, folate, vitamin K and ubiquinone. This reaction is the most unusual of the entire pathway and is unique in nature. It converts EPSP to chorismate in the presence of a reduced FMN coenzime. Structure prediction used the comparative protein structure modeling methodology. The three-dimensional (3D) structure prediction of the enzyme CS of Mycobacterium tuberculosis was performed using the crystal structure (PDB ID: 1QX0) of CS from Streptococcus pneumoniae as template (≈ 42% identity), and the MODELLER6v2 package. Additionally, in order to understand the possible binding modes of substrate and coenzime to the enzyme, EPSP and FMN, respectively, were geometrically docked to CS. Energy minimization of the whole complex showed, as expected, that most of the template interactions are preserved in the Mtb structure, except for His11, Arg139 and Gln255. However, novel interactions involving Arg111, Gly113 and Ser317 were also observed. This knowledge should facilitate the search for inhibitors of this enzyme as alternative agents to treat tuberculosis.
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Mendes, Josiane Enevina. "Docking de herbicidas na glutationa transferase tau4-4 de soja (Glycine max)." Universidade Federal de São Carlos, 2011. https://repositorio.ufscar.br/handle/ufscar/6974.
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Previous issue date: 2011-03-30Financiadora de Estudos e Projetos
This study, based on molecular docking, describes the search for the most favorable conformations when complexes between herbicides, used in soybean cultivation, and an enzyme involved in the detoxification process are formed and based on these results some guidelines for the developing of new compounds are proposed. The glutathione transferase Tau, GmGSTU4-4, from soybean was the target protein, and diclofop, fluazifop, Clethodim, clomazone, diquat, paraquat, atrazine, diuron, bentazone, acifluorofem, fomesafem, sulfentrazone, glyphosate and clorimurom, the 14 herbicides studied. These last ones were chosen based on the list of those that are used in soybean crops and are registered with the Ministry of Agriculture and Supply of Brasil. For all of them the GmGSTU4-4-herbicide complexes were obtained. The protein binding site, analyzed by molecular visualization, presents an almost cylindrical shape, open and exposed to the solvent and is composed of two sites G and H. Three water molecules were observed in the G-site in that participate in molecular interactions with several of the studied herbicides, This finding suggests that new compounds that could, and should, be developed need to have in their structure chemical groups capable of interacting with the water, both as donors and acceptors of hydrogen bonds. Another interesting finding was that the largest herbicides may occupy both the G and H sites, and seem to be most promising in the activity of detoxification.
Este estudo, baseado em docking molecular, descreve a busca das conformações mais favoráveis para a formação dos complexos alvo-ligante com herbicidas utilizados no cultivo de soja e uma enzima envolvida no processo de desintoxicação, e baseado nestes resultados são propostas algumas diretrizes para o desenvolvimento de novos compostos. A proteína estudada foi a glutationa transferase Tau de soja, a GmGSTU4-4. Foram estudados 14 herbicidas: diclofope, fluazifope, cletodim, clomazona, diquate, paraquate, atrazina, diurom, bentazona, acifluorofem, fomesafem, sulfentrazona, clorimurom e glifosato. A escolha dos herbicidas se baseou na lista daqueles que são utilizados na cultura da soja e estão registrados no Ministério da Agricultura e Abastecimento do Brasil. Foram obtidos os complexos GmGSTU4-4-herbicidas. O sítio de ligação analisado por visualização molecular mostra uma forma quase cilíndrica, aberta e exposta ao solvente e composto de dois sítios G e H. No sítio G foram observadas três moléculas de água que participam de interações moleculares com vários dos herbicidas estudados o que sugere que novos compostos poderiam ser desenvolvidos observando a necessidade da presença de grupos químicos capazes de interagir com a água, tanto como doadores como aceptores de ligações de hidrogênio. Os herbicidas maiores podem ocupar os sítio G e H e parecem ser mais promissores na atividade de desintoxicação.
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Kinkel, Katrin. "Prediction of the binding mode of suberone-inhibitors in the p38 MAP kinase with molecular modeling studies." [S.l. : s.n.], 2008.
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Baptistini, Natália. "Análise in silico, in vitro e in vivo de compostos organocalcogênios como possíveis anti-inflamatórios." Universidade Federal de São Carlos, 2015. https://repositorio.ufscar.br/handle/ufscar/7554.
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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
In this work are presented the in silico study of the formation of complexes between organochalcogens compounds with enzymes COX-1 and COX-2 that were carried out in order to study their potential to act as selective inhibitors of COX-2 and thus as anti-inflammatories, as well as the results of in vitro and in vivo experiments of this activity. There were modeled and studied 15 organochalcogens compounds and their enantiomers, with a structure similar to that of the selective drug celecoxib. Compounds 2-(phenylseleno)-2-(2-ethyl-X)acetophenones-4’Y-substituted , with Y = H, Br, CH3, OCH3, NO2 and X = SO2, SO, S, were modeled using as starting point the crystallographic structure of the compound with Y = Br and X = SO. The three dimensional structures of the COX-1 and COX-2 enzymes were obtained from the PDB. The results of the molecular docking calculations were evaluated considering the patterns of orientations/conformations, intermolecular interactions, π interactions and scores. The results of these experiments allowed to propose a mechanism of action as well as a preferred bonding mode that would explain the activity of these compounds as possible inhibitors of COX-2, which is a condition necessary to act as anti-inflammatory. In particular, the compound where Y = OCH3 and X = SO2 (5-OCH3) being selective to COX-2 is the one with the best chances to act as an anti-inflammatory. This is because the OCH3 substituent occupied the S1 subsite of the enzyme, maintaining the interaction with His90 and the SO2 moiety interacts with the Tyr355, an important amino acid for the metabolism of the COX-2 substrate, the arachidonic acid. The other interactions made by the compound, such as π interactions, are important for fixing the ligand in the active site, although they are not directly related to its selectivity. The experiments in vitro and in vivo confirm the in silico results, as the enzyme immunoassay showed that this compound exhibits greater inhibition of COX-2 relative to COX-1. Furthermore, the activity of the 5-OCH3 compound was evaluated with the classical models of edema formation, that is the carrageenan and zymosan induced inflammation in the rat paw, resulting in a significant reduction in paw thickness after two hours and decreasing of the temperature after one hour of the application of the anti-inflammatory agent. As the best results were obtained for the model of paw edema elicited by carrageenan this suggests that the compound acts better in the case of acute inflammation.
Neste trabalho são apresentados o estudo in silico da formação de complexos entre compostos organocalcogênios e as enzimas COX-1 e COX-2 realizado com o objetivo de estudar seu potencial para atuar como inibidores seletivos da COX-2, e portanto como anti-inflamatórios, bem como os resultados dos experimentos in vitro e in vivo desta atividade. Na presente pesquisa, foram modelados e estudados 15 compostos organocalcogênios e seus enantiômeros, com estrutura similar à do fármaco seletivo celecoxibe. Os compostos da família 2-(fenilseleno)-2-(etil-X)acetofenonas-4’Y-substituídas, com Y = H, Br, CH3, OCH3, NO2 e X = SO2, SO, S, foram modelados tendo como ponto de partida a estrutura cristalográfica do composto da mesma família com Y = Br e X= SO. As estruturas tridimensionais das enzimas COX-1 e COX-2 foram obtidas no PDB. Os resultados dos cálculos de docking molecular foram avaliados considerando-se o padrão de orientações/conformações, as interações intermoleculares, as interações π e os escores. OS resultados desses experimentos permitiram propor um mecanismo de ação, bem como um modo de ligação preferencial para explicar a atuação desses compostos como possíveis inibidores da COX-2, condição necessária para atuar como anti-inflamatório. Em particular, o composto com Y = OCH3 e X = SO2 (5-OCH3) é o que apresentou o melhor potencial para atuar como anti-inflamatório, sendo seletivo à COX-2. Isto porque o substituinte OCH3 ocupou o subsítio S1 dessa enzima, mantendo a interação com a His90 e o grupo SO2, apresentou interação com a Tyr355, aminoácido importante para o metabolismo do substrato da COX-2, o ácido araquidônico. As outras interações feitas pelo composto, como as interações π, são importantes para fixação do ligante ao sítio ativo, embora não estejam diretamente ligadas com a sua seletividade. Os experimentos in vitro e in vivo permitiram confirmar os resultados dos experimentos in silico, uma vez que o ensaio imunoenzimático mostrou que este composto apresenta maior inibição da COX-2 em relação à COX-1. Ainda, a atividade do composto 5-OCH3 foi avaliada em modelo de edema de pata induzido por carragenina e zymosan, como agentes irritantes, resultando em uma diminuição significativa da espessura das patas após duas horas e diminuição da temperatura após uma hora da aplicação do agente anti-inflamatório. Uma vez que os melhores resultados foram obtidos para o modelo do edema de pata com a carragenina isto sugere o composto atua melhor no caso da inflamação aguda.
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Canto, Vanessa Petry do. "Estudo computacional das monoaminoxidases A e B com substratos e inibidores." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2014. http://hdl.handle.net/10183/97873.
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A monoaminoxidase (MAO) é uma enzima importante, que pode atuar como alvo terapêutico. Inibidores da MAO-A apresentam atividade no tratamento de distúrbios de humor, enquanto os inibidores seletivos da MAO-B tem uso, especialmente, no tratamento da Doença de Parkinson. O conhecimento das interações ENZIMA-INIBIDOR é importante no planejamento de fármacos. Nesse contexto, foram realizados estudos das enzimas MAO-A e MAO-B com diferentes ligantes, através da combinação das metodologias de docking, Dinâmica Molecular e Ensemble Docking. Foram escolhidos os ligantes derivados da 1,4-naftoquinona (1,4-NQ), lapachol, menadiona, norlapachol, A2, B2 e C2, os inibidores comerciais clorgilina (MAO-A) e selegilina (MAO-B) e os substratos naturais serotonina (MAO-A) e dopamina (MAO-B). Os resultados do docking mostraram interação de todos os ligantes com algum dos resíduos da "gaiola aromática" (FAD, Tyr407/Tyr444 para MAO-A, Tyr398/Tyr435 para MAO-B), uma importante região catalítica da MAO. Além disso, a seletividade observada experimentalmente da menadiona com a MAO-B também foi observada no docking. Através da DM, foi possível observar algumas diferenças conformacionais entre as estruturas da MAO-A e MAO-B, que podem explicar a seletividade entre as duas isoformas, como por exemplo, distâncias entre resíduos do sítio ativo e ligações de hidrogênio. A partir do Ensemble Docking, foi verificado que a conformação do receptor influencia significativamente o escore das interações ENZIMA+LIGANTE para ligantes volumosos.Monoamine oxidase (MAO) is an important enzyme that acts as therapeutic target. MAO-A inhibitors show pharmacological activity in the treatment of mood disorders, whereas MAO-B inhibitors are used especially in treatment of Parkinson's Disease. Knowledge of enzyme-inhibitor interactions is important in drug design. Therefore, studies of MAO-A and MAO-B enzymes with different ligands were performed by combining docking, Molecular Dynamics and Ensemble Docking methodologies. Ligands derived from 1,4-naphthoquinone, lapachol, menadione, nor-lapachol, A2, B2, C2, commercial inhibitors clorgyline (MAO-A) and selegiline (MAO-B) and the natural substrates serotonin (MAO-A) and dopamine (MAO-B) were chosen. The docking results shows interactions of all ligands with some residue of the "aromatic cage” (FAD cofactor, Tyr407/Tyr444 for MAO-A and Tyr398/Tyr435 for MAO-B), an important catalytic region of MAO. Furthermore, the experimentally observed selectivity of menadione with MAO-B was also observed by Docking. In Molecular Dynamics results, conformational differences were observed between MAO-A and MAO-B structures, which could explain the selectivity observed between isoforms, e.g. distances between residues of the active site and hydrogen bonds. Ensemble Docking results shows that the conformation of the receptor significantly influence the score of ENZYME+LIGAND interactions for bulky ligands.
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Shimo, Helder Ken. "Auto-organização da população em sistemas imunológicos artificiais aplicada ao docking de proteínas." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-30082012-161501/.
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Vários problemas do mundo real podem ser analisados como problemas de otimização. Na bioinformática, em especial, como exemplos podem ser citados o alinhamento múltiplo de sequências, a filogenia, a predição de estruturas de proteínas e RNA, entre outros. As Meta-heurísticas Populacionais (MhP) são técnicas baseadas em interações de conjuntos de soluções candidatas, como elementos de uma população, utilizadas na otimização de funções. Seu uso é especialmente interessante na otimização de problemas onde há conhecimento parcial ou nenhum do espaço de busca. O objetivo deste trabalho é investigar o uso de auto-organização da população de um sistema imunológico artificial (AIS) a fim de aplicá-lo no problema de docking, que pode ser visto como um problema de otimização multimodal complexo. O AIS é um tipo de MhP inspirado na microevolução do sistema imunológico adaptativo de organismos complexos. Neste, as soluções candidatas representam células do sistema imunológico que busca se adaptar para a eliminação de um patógeno. O desenvolvimento do algoritmo foi baseado no opt-aiNet, que utiliza dos princípios das teorias de seleção clonal e maturação de afinidade para realizar a otimização de funções. Adicionalmente, o opt-aiNet, inspirado na teoria de redes imunológicas, realiza uma etapa de supressão, que busca eliminar soluções semelhantes, aumentando assim a diversidade populacional. Esta etapa é computacionalmente custosa, dado que é feito o cálculo da distância entre todos os possíveis pares de células (soluções) afim de eliminar aquelas próximas de acordo com um dado critério. A proposta deste trabalho é o desenvolvimento de um algoritmo de supressão auto-organizável, inspirado no fenômeno da criticalidade auto-organizada, buscando diminuir a influência da seleção de parâmetros e a complexidade da etapa de supressão. O algoritmo proposto foi testado em um conjunto de funções contínuas conhecidas e comumente utilizadas pela comunidade de computação evolutiva. Os resultados obtidos foram comparados com aqueles de uma implementação do opt-aiNet. Em adição, foi proposta a utilização de operadores de mutação com distribuição q-gaussiana nos AISs desenvolvidos. O algoritmo foi também aplicado no problema de docking rígido baseado em complementaridade de superfícies e minimização de colisões, especificamente no docking de proteínas. Os resultados foram comparados com aqueles de um algoritmo genético, resultando em um melhor desempenho obtido pelo algoritmo proposto.Many real world problems can be described as optimization problems. In bioinformatics in special, there is multiple sequence alignment, filogeny and RNA and Protein structure prediction, among others. Population based metaheuristics are techniques based in the interaction of a set of candidate solutions as elements of a population. Its use is specially interesting in optimization problems where there is little or no knowledge of the search space. The objective of this work is to study the use of self-organization of population in an artificial imune system for use in the docking problem, considered a complex multimodal optimization problem. The artificial imunme system is a type of population based methaheuristics inspired in the microevolution of the adaptive immune system of complex organisms. Candidate solutions represent cells of the immune system adapting its antibodies to eliminate a pathogen. The development of the algorithm was based in the opt-aiNet, based in the principles of clonal selection and affinity maturation for function optimization. Additionally, the opt-aiNet, inspired in theories of immune network, makes a suppression stage to eliminate similiar solutions and control diversity. This stage is computationally expensive as it calculates the distance between every possible pair of cells (solutions) eliminating those closer than a threshold. This work proposes a self-organized suppression algorithm inspired in the self-organized criticality, looking to minimize the influence of parameter selection and complexity of the suppression stage in opt-aiNet. The proposed algorithm was tested in a set of well-known functions in the evolutionary computation community. The results were compared to those of an implementation of the opt-aiNet. In addition, we proposed a mutation operator with q-Gaussian distribution for the artificial immune systems. The algorithm was then applied in the rigid protein docking problem based in surface complementarity and colision avoidance. The results were compared with a genetic algorithm and achieved a better performance.
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Leis, Simon [Verfasser], Martin [Akademischer Betreuer] Zacharias, and Iris [Akademischer Betreuer] Antes. "Impact of Protein conformational Changes on Molecular Docking - Design of a Docking Approach including Receptor Flexibility / Simon Leis. Gutachter: Iris Antes. Betreuer: Martin Zacharias." München : Universitätsbibliothek der TU München, 2012. http://d-nb.info/1030099464/34.
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RABELLO, Marcelo Montenegro. "Desenvolvimento e automação de metolodogias in silico para o estudo de complexos de inclusão utilizados na inova o terapêutica." Universidade Federal de Pernambuco, 2016. https://repositorio.ufpe.br/handle/123456789/17588.
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Este trabalho apresenta uma metodologia in silico para o estudo de complexos de inclus o utilizados na inova o terap utica. Um complexo de inclus o formado por um host (hospedeiro), e por um guest (h spede). Neste trabalho, o host estudado a ciclodextrina (e seus derivados) e o guest, um ligante (f rmaco, em potencial), formando o complexo host:guest. O objetivo desse projeto desenvolver uma plataforma (CycloMolder) capaz de realizar estudos in silico dos complexos de inclus o de forma autom tica e precisa, fazendo uso de uma interface gr fica de usu rio. Esse objetivo foi tra ado para facilitar os estudos de modelagem molecular para este tipo de sistema qu mico, com interesse farmac utico. A plataforma composta por dois m dulos: CycloGen e CycloDock. O primeiro m dulo (CycloGen) constr i modelos com mais de uma estrutura para representar um derivado de ciclodextrina. O segundo m dulo (CycloDock) realiza o c lculo de docking molecular entre as mol culas host e guest, utilizando o programa Autodock Vina e apresenta os resultados obtidos, incluindo gr ficos que mostram a distribui o energ tica e as intera es intermoleculares do complexo. O programa CycloMolder foi testado atrav s de estudos de casos inspirados em problemas farmac uticos reais. Os testes realizados destacaram a import ncia da gera o de mais de uma configura o para representar significativamente um derivado de ciclodextrina, e tamb m mostrou o potencial anal tico do programa, proporcionado pela automa o do estudo de modelagem, execu o dos c lculos e an lise dos resultados. De forma geral, o programa CycloMolder atinge seus objetivos, automatizando e simplificando os estudos in silico dos complexos de inclus o, contribuindo desta forma para a inova o terap utica.
This work presents an in silico methodology for study of inclusion complexes used in therapeutic innovation. An inclusion complex is formed by a host and a guest. In this work, the host is the cyclodextrin and their derivatives and the guest is a potential drug, forming a host:guest complex. The goal of this work is to development a platform (CycloMolder) able to perform in silico studies of inclusion complexes in an automated and precise fashion, making use of a graphical user interface. The platform (CycloMolder) consists of two modules: CycloGen and CycloDock. The first module (CycloGen) builds models with more than one chemical structure to represent a cyclodextrin derivative. The second module (CycloDock) performs the molecular docking calculations between the host and guest molecules, using the AutoDock Vina program, and displays the results, including graphs showing the energy distribution and intermolecular interactions present in the host:guest complexes. The CycloMolder program was tested through case studies inspired by real pharmaceutical problems. The tests highlighted the importance of generating more than one chemical structure to better represent a ciclodextrin derivative, also showed the analytical potential of the program, provided by the automation of the modeling study, execution of calculations and analysis of results. Overall, the CycloMolder program achieves its goals by automating and simplifying the in silico studies of inclusion complexes, thus contributing to the therapeutic innovation.
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Tunca, Guzin. "A virtual screening procedure combining pharmacophore filtering and molecular docking with the LIE method." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/284031.
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Actualment, el cribratge virtual juga un paper central en el món del descobriment de fàrmacs. L’anàlisi in silico permet el cribatge de milions de molècules petites i la tria de les més prometedores per a les proves experimentals. Per trobar candidats que puguin esdevenir fàrmacs, és crucial reunir una sèrie d’eines computacionals individuals i complementàries. En aquesta tesi, es descriu un procediment automatitzat de cribatge virtual que combina el modelat de farmacòfors i el seu ús en cerques, mètodes d’alt rendiment d’acoblament molecular, puntuació de consens i estimació d'energia lliure d'unió mitjançant el mètode d’energia d'interacció lineal (LIE) a partir de simulacions de dinàmica molecular.
Un dels objectius d'aquesta tesi ha estat el de construir una metodologia flexible i versàtil de cribratge virtual, que permeti la integració de diferents eines en les diferents etapes de l’estudi. El procediment, que es va iniciar com la combinació d'un senzill filtre per tamany, la simulació de l’acoblament molecular i una puntuació de consens, ha derivat en un procediment computacional elaborat i automatitzat amb l'addició de cerques basades en farmacòfor i l'estimació de l'energia lliure d'unió mitjançant el mètode LIE. Aquest mètode integrat té l’objectiu de compensar les debilitats individuals de les diferents tècniques usades i permet avaluar i comparar el rendiment i la l’exactitud d'aquestes tècniques. Una altra fita important ha estat l'aplicació del procediment computacional a proteïnes diana concretes per tal d’avaluar-ne la capacitat de trobar molècules que puguin ser candidats a fàrmacs. Tests experimentals realitzats per a la β-Glucosidasa àcida i la hidrolasa de Bleomicina humanes indiquen que diverses molècules petites seleccionades pel procediment computacional tenen activitat inhibitòria micromolar. El mètode LIE emprat en aquest treball es va aplicar sobre més de deu mil complexos proteïna-lligand per a tres proteïnes diana diferents, el que és, al nostre entendre, la primera aplicació del mètode LIE a aquesta escala.Virtual screening plays a central role in the world of drug discovery today. In silico testing allows to screen millions of small molecules and to choose only the most promising ones for experimental testing. To find potential drug candidates, it is crucial to bring together individual and complementary computational tools. In this thesis, I describe an automated virtual screening procedure that combines pharmacophore modeling and searches, high-throughput molecular docking, consensus scoring and binding free energy estimation with the linear interaction energy (LIE) method through molecular dynamics simulations. One goal of this thesis was to build an evolving and versatile virtual screening methodology, which enables integration of different tools at different steps. The procedure that started as a combination of a simple size filter, molecular docking and consensus scoring, advanced into an elaborate and automated computational workflow with the addition of pharmacophore searches and binding free energy estimation with LIE. This integrated method intends to compensate for weaknesses of individual structure-based techniques and allows the evaluation and comparison of the performance and accuracy of these techniques. Another important goal was to apply the computational workflow to target proteins and find hits that could be drug candidates. Experimental testing performed for human acid β-Glucosidase and bleomycin hydrolase indicate that several small molecules selected by the computational workflow display micromolar inhibitory activity. The standard LIE method used in this work was applied to more than ten thousand ligand-protein complexes for three different targets, which is, to our knowledge, the first time application of LIE at such large scale.
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Leves, Natalia. "Nanopartículas de grafite para carreamento de antiinflamatórios não esteroidais por estudos de docking molecular." Universidade Federal de São Carlos, 2013. https://repositorio.ufscar.br/handle/ufscar/7035.
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Previous issue date: 2013-08-13The non steroidal anti-inflammatory drugs have been known for over 100 years and has been widely used by mankind. However cause adverse effects, since gastrointestinal complications to cardiac diseases many of these symptoms related to its nonspecific action in biological systems. Thus, the proposal of a drug delivery system for loading these drugs to the site of inflammation, could reduce these unwanted effects in the body due to the limitation of more targeted effects beyond its site of action.In this study, the graphene and graphite plates were used as carriers, since studies demonstrate the usefulness of other conformational structures of carbon as drug carriers for the treatment of cancer, for example. Two models were studied for the plates by softwares of molecular docking: template sandwich, which comprises two carbon plates, with ligant between them, and the model surfing with one carbon plate comprising the ligant. The compounds were obtained from data banks, such as CSD, PDB and SD, the plates were obtained by molecular modeling. The analysis of intermolecular interactions, essential knowledge for understanding the structures obtained was done using molecular imaging with high resolution. The experimental results showed that the in silico model sandwich was the most favorable for this system, providing stability and protection for the ligand that this does not become detached from the plates during the path taken in the body to the desired location.
Os anti-inflamatórios não esteroidais são conhecidos há mais de 100 anos e vem sendo amplamente utilizados pela humanidade. No entanto, causam efeitos adversos, desde problemas gastrointestinais até complicações cardíacas, muitos desses sintomas relacionados com sua ação inespecífica nos sistemas biológicos. Dessa forma, a proposta de um sistema de drug delivery para o carreamento desses fármacos até o local da inflamação, poderia reduzir esses efeitos indesejados no organismo devido a limitação de alvos mais específicos além do seu local de ação. No presente estudo, foram utilizadas placas de grafeno e grafite como carreadores, uma vez que estudos demonstram a utilidade de outras estruturas conformacionais do carbono como carreadores de fármaco para o tratamento de câncer, por exemplo. Foram estudados dois modelos para as placas por meio de software de docking molecular: modelo sandwich, o qual engloba duas placas de carbono, com os ligantes entre elas, e o modelo surf, com uma placa de carbono comportando o ligante. Os compostos estudados foram obtidos dos bancos de dados como CSD, SD e PDB e as placas foram obtidas por modelagem molecular. A análise das interações intermoleculares, conhecimento essencial para o entendimento das estruturas obtidas, foi feita utilizando visualização molecular de alta resolução. Os resultados dos experimentos in silico mostraram que o modelo sandwich foi o mais favorável para esse sistema, posto que confere estabilidade e proteção ao ligante para que este não se desprenda das placas durante o caminho percorrido pelo organismo até o local desejado.
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Fernandes, Vinícius Alves. "Ação do colesterol sobre a arquitetura da cromatina : docking molecular do colesterol ao nucleossomo." reponame:Repositório Institucional da UnB, 2010. http://repositorio.unb.br/handle/10482/21454.
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Dissertação (mestrado)—Universidade de Brasília, Faculdade de Ciências da Saúde, Programa de Pós-Graduação em Ciências Farmacêuticas, 2016.Submitted by Camila Duarte (camiladias@bce.unb.br) on 2016-09-12T19:56:50Z No. of bitstreams: 1 2016_ViníciusAlvesFernandes.pdf: 4594049 bytes, checksum: 48f78b5328fa30fbeae24f268a04373c (MD5)
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A cromatina é essencial para manutenção da fisiologia celular por desempenhar papel-chave na regulação da transcrição, reparo e replicação do DNA. Para tanto, esta deve ser altamente dinâmica, permitindo alterações entre estados compactados e relaxados. O primeiro nível de compactação da cromatina é o nucleossomo, formado pelo DNA e um octâmero de histonas. Moléculas que se ligam ao nucleossomo tem potencial para modular a cromatina. Diversas evidências apontam para o colesterol, lipídio importante para o funcionamento basal das células, como uma molécula ligante de cromatina. Recentemente, foi demonstrado que o colesterol pode modular a estrutura das fibras de cromatina reconstituídas in vitro. Juntos, estes dados sugerem que o colesterol possui um efeito modulador da arquitetura da cromatina por se ligar diretamente ao nucleossomo. Entretanto, os detalhes moleculares da ação do colesterol sobre a estrutura da cromatina ainda não foram esclarecidos. O objetivo deste estudo foi investigar, in silico, a ligação do colesterol ao nucleossomo e observar seu impacto ao nível atômico. Logo, metodologias capazes de tratar interações moleculares com resolução atomística são fundamentais, como a dinâmica molecular (DM) e docking molecular. Aqui identificamos vários sítios de ligação do colesterol distribuídos pelo nucleossomo. Após 200 ns de DM, seis moléculas de colesterol amostradas permaneceram ligadas ao nucleossomo. Para cada sítio investigado, a energia livre de ligação, estimada pelo método LIE (Linear Interactions Energy), indica o favorecimento do complexo entre o colesterol e o nucleossomo. Foi observado um impacto nas flutuações atômicas de vários aminoácidos formadores dos sítios de ligação. Dentre estes, alguns são conhecidamente importantes para modulação da estrutura da cromatina. Além disso, houve redução significativa do número de moléculas de água nas interfaces de interação colesterol-nucleossomo, especialmente em regiões hidrofóbicas essenciais para a manutenção estrutural do nucleossomo. Esses resultados sugerem que o colesterol pode afetar a arquitetura da cromatina através da interação direta com o nucleossomo nos múltiplos sítios de ligação. _______________________________________________________________________________________________ ABSTRACT
Chromatin is essential for maintenance of cell physiology playing a key role in transcription regulation, DNA repair and replication. Therefore, it must be highly dynamic, allowing changes between compacted and relaxed states. The first level of chromatin compaction is the nucleosome, formed by DNA and histone octamer. Molecules that bind to the nucleosome have the potential to modulate chromatin. Several evidences indicate that cholesterol, important lipid for cell function, may bind to chromatin. Recently, it was demonstrated that in vitro cholesterol may modulate the structure of reconstituted chromatin fibers. Together, these data suggest that cholesterol may modulate chromatin architecture by direct binding to the nucleosome. However, the molecular details of cholesterol’s action on chromatin structure remain unclear. The aim of this study was an in silico investigation of the cholesterol binding to the nucleosome and its impact at the atomic level. Therefore, methodologies capable of handling molecular interactions with atomistic resolution are critical, such as molecular dynamics (MD) and molecular docking. Here, we identified several cholesterol binding sites distributed over the nucleosome. After 200 ns of MD, six sampled cholesterol molecules remained bound to the nucleosome. For every site, the estimated absolute free energies obtained by the LIE method, favour cholesterol binding thus explaining the stability of the molecular complex. Cholesterol impacts the atomic fluctuations of several amino acids forming the binding sites. Among these, some are well-known to modulate the chromatin structure. Furthermore, a significant reduction in the number of water molecules in cholesterol-nucleosome interfaces was observed, especially at key hydrophobic regions for nucleosome structural maintenance. These results suggest that cholesterol may affect the chromatin's architecture via direct interaction with the nucleosome through multiple binding sites.
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Sasi, Abd-Alkarim Nour-Addin. "Cardiovascular effects, molecular docking and chemo informatics analysis of compounds isolated from leonotis leonurus." Thesis, University of the Western Cape, 2015. http://hdl.handle.net/11394/5342.
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>Magister Scientiae - MScLeonotis leonurus (L. Leonurus) has relatively abundant diterpenes and has been used as a traditional herbal medicine for treating several ailments including influenza, muscular cramps, skin related diseases, menstrual, antilipidemic, hyperglycaemia and hypertension. In this study, diterpenoid compounds such as; Dubiin, SaponifiedDubiin, Hispanol, Marrubiin and DC9 were isolated from L. Leonurus plant. The cardiovascular effects of these isolated compounds were investigated in order to determine the response of anaesthetised normotensive Wistar rats (in-vivo) to the compounds. Also, the druglikeness of the isolated diterpenoid compounds and their binding interaction with β1 adrenoceptor (PDB: 2Y04), angiotensin II receptor (Ang II) (PDB: 3R8A), Angiotensin converting enzyme (ACE) (PDB: 4XX3), and renin receptor (PDB: 2X8Z) by using molecular docking methods and Chemoinformatics analysis was performed (in-silico). Important molecular descriptors and molecular docking were used in our Chemoinformatics (in-silico) analysis to study the druglikeness and the binding affinity for of each molecule (Dubiin, SaponifiedDubiin, Hispanol, Marrubiin and DC9). The molecular descriptors and the binding energy were calculated by using the molecular operating environment software (MOE 2013). The lowest energy and highest cluster conformations of the molecules were further analysed. All the five (5) diterpenoids were predicted to have good oral bioavailability after oral administration and passed the BloodBrain Barrier (BBB) rules. Also, the compounds were predicted to have high probability of being good Druglike candidates, except for DC9, which is predicted to have lower possibilities of being Druglike candidate than the other diterpenoids. Furthermore, these compounds (Dubiin, SaponifiedDubiin, Hispanol, Marrubiin and DC9) were shown to interact with β1 adrenoceptors in-silico, an interaction that was confirmed in-vivo by increases in Blood pressure (SP, DP and MAP) and Heart rate (HR). In anaesthetized normotensive male Wistar rats (in-vivo), Dubiin (0.5 40mg/kg; IV), SaponifiedDubiin (0.5 60mg/kg; IV) Hispanol (0.5 40mg/kg; IV), DC9 (0.5 40mg/kg; IV) and Marrubiin (0.5 40mg/kg; IV) produced dose dependent increase in Systolic pressure (SP), Diastolic pressure (DP), and Mean arterial pressure (MAP) at all doses. Also, the compounds produced dose dependent increase in Heart rate (HR). From the in-vivo and in-silico studies it can be concluded that all the five (5) isolated diterpenoid compounds showed cardiovascular effects on Blood pressure (BP) and Heart rate (HR) by acting as β1 adrenoceptor agonists. Also, these diterpenoids compounds could be responsible for the cardiovascular effect observed in the methanol extracts from previous studies. These cardioactive compounds are prototype or ''lead compounds'' for designing and developing new nontoxic and effective drugs for cardiovascular disease (CVD) treatment.
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Grasel, Fábio dos Santos. "Investigação da interação de ligantes fluorescentes derivados de benzazóis com B-DNA por docking e dinâmica molecular." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2013. http://hdl.handle.net/10183/88548.
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Neste trabalho foi realizado o estudo por docagem e simulação de dinâmica molecular de doze derivados benzazólicos fluorescentes por ESIPT, interagindo com o dodecâmero de Dickerson-Drew na forma B-DNA. Estes doze ligantes foram divididos em dois grupos (A e B), sendo o primeiro grupo composto por derivados do 2-(2’-hidroxifenil)-benzoxazol e o segundo grupo composto por três derivados do 2-(4’-amino-2’-hidroxifenil)-benzazóis, alternando entre N, S e O no anel azólico, mais três bases de Tröger derivadas dos mesmos. Na análise da docagem molecular do grupo A, os derivados com grupamento –NH2 no anel fenólico apresentaram energias de interação mais favoráveis com o DNA, verificando um favorecimento ainda maior, para os ligantes que continham –NO2 como substituinte no anel benzoxazólico. Na análise da docagem molecular para grupo B, as bases de Tröger (4ac) apresentaram interações significativamente mais favoráveis, quando comparados com seus respectivos precursores (3ac). Na análise da DM, tanto o grupo A, quanto o B, apresentaram a formação de complexos estáveis. O grupo A apresentou uma indução a alterações estruturais mínimas no DNA, sendo as maiores alterações a abertura do Rise quando os ligantes estavam intercalados, acompanhado pelo desenrolamento do parâmetro Twist. Nas interações de sulco menor, o ligante 2a foi o que formou o complexo mais estável com o DNA. Na análise da DM do grupo B, as bases de Tröger apresentaram uma preferência maior por interações do tipo intercalação que seus precursores, sendo os primeiros, os quais induziram o oligonucleotídeo a maiores alterações estruturais. Durante todas as simulações os ligantes mantiveram-se com uma forte interação com o oligonucleotídeo, sem causar a desnaturação do mesmo. Devido às interações estáveis, e também as propriedades fotofísicas peculiares dos ligantes estudados, esta classe de moléculas pode atuar como possíveis sondas biológicas.In this work we carried out a study by docking and molecular dynamics simulations of twelve ESIPT-fluorescent benzazoles, interacting with the Dickerson-Drew dodecamer in the canonical B-DNA form. These twelve ligands were divided into two groups (A and B), with the first group consisting of derivatives of 2-(2’-hydroxphenyl)-benzoxazole and the second group consisting of three derivatives of 2-(4’-amino-2’-hydroxyphenyl)-benzazoles, alternating between N, S and O in the azole ring and three Tröger bases derived from them. In the analysis of the molecular docking of group A, the derivatives with group –NH2 in the phenolic ring presented more favorable interaction energies with the DNA, and the score was even more favorable for the ligands which contained –NO2 as substituent in the benzoxazolic ring. In the analysis of the molecular docking for group B, the Tröger bases (4ac) presented significantly more favorable interactions, when compared with their respective precursors (3ac). In the analysis of the DM, both groups A and B formed stable complexes. Group A induced only slight structural distortions in the DNA, being the largest modifications the increase of the Rise parameter when the ligands were intercalated, accompanied by the unwinding of Twist parameter. Regarding minor groove interactions, the ligand 2a formed the most stable complex with the DNA. In the analysis of the DM both groups A and B, the Tröger bases presented a greater preference for intercalation interactions than their precursors and the Tröger bases induced the largest structural changes to the oligonucleotide. During all the simulations the ligands maintained a strong interaction with the oligonucleotide, without causing the denaturation of the same. Due to the stable interactions, and also the peculiar photophysical properties of the ligands studied, this class of molecules can act as possible biological probes.
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Buldrini, Oviedo María Teresa. "Identificación de Potenciales Residuos Determinantes de Mayor Afinidad a Celulosa en una Endoglucanasa Mediante Estudios de Docking Molecular." Tesis, Universidad de Chile, 2012. http://repositorio.uchile.cl/handle/2250/104415.
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El bioetanol es un combustible complementario a las gasolinas, producido mediante fermentación de azúcares simples derivados de sacarosa, almidón o celulosa. Debido a su gran abundancia el material celulósico es particularmente atractivo como fuente de combustible. La hidrólisis de la celulosa puede realizase utilizando métodos químicos (ácidos o bases) o enzimáticos. La hidrólisis enzimática genera productos más puros y consume menos energía; sin embargo, debido a su bajo rendimiento se requiere usar grandes cantidades de enzima, lo cual eleva considerablemente los costos de producción.
Las endoglucanasas son glicosil hidrolasas que rompen enlaces β-1,4 en polímeros de glucosa. Actúan sobre enlaces internos de la celulosa amorfa generando su despolimerización. La estructura de las celulasas incluye un módulo catalítico, unido a un dominio que actúa como centro de anclaje a la celulosa, por lo que se le ha denominado Modulo de Unión a Carbohidrato (CBM por su sigla en Inglés). Estudios previos han demostrado que una alta afinidad a celulosa se correlaciona con un aumento en la hidrólisis de ésta. En el presente trabajo se proponen mutaciones en el CBM de la endo β-1,4 glucanasa de Trametes versicolor (TvEG), que aumenten la adsorción de la enzima sobre celulosa, buscando de este modo aumentar la hidrólisis de ésta.
Se generó un modelo tridimensional del CBM de la endoglucanasa de T. versicolor mediante modelación comparativa. La estructura obtenida está formada por tres hojas beta antiparalelas unidas entre sí mediante dos puentes disulfuro. El modelo generado se utilizó para llevar a cabo estudios de Docking Molecular, para identificar regiones de interacción celulosa–CBM.
Usando los resultados de la simulación computacional de la interacción CBM-celulosa, se identificaron dos zonas de unión. La primera concuerda con la reportada previamente para CBM’s de la familia I, mientras que no existen reportes en la literatura sobre interacción de la celulosa con la segunda zona identificada. A continuación se simuló mediante Docking Molecular, la interacción de celulosa con variantes de CBM que contenían diferentes aminoácidos en las posiciones clave de la segunda zona de interacción; los valores de energía libre de unión entregados por la simulación permitieron sugerir tres variantes de secuencia de CBM. Las variantes seleccionadas fueron: variante 1 (G7Y, F10W), variante 2 (G7Y, F10W, G12Q) y variante 3 (G7Y, G9Q, F10W, G12Q), donde G es glicina, Y tirosina, F fenilalanina, W triptófano y Q glutamina.
Se generó un sistema de expresión recombinante de TvEG mediante clonamiento del gen silvestre de la enzima en el vector pET22b(+) y transformación en E. coli BL21(DE3); la proteína se acumuló intracelularmente en forma activa. Las mutaciones planteadas fueron construidas exitosamente mediante mutagénesis sitio dirigida, utilizando la metodología de mutación por extensión de superposición. De esta forma, se deja planteado un sistema de expresión recombinante de las variantes construidas, de modo de en el futuro cuantificar experimentalmente la adsorción de los CBM mutados y validar los resultados del análisis realizado in sílico.
Se concluye que la estrategia utilizada permitió simular apropiadamente la interacción CBM-celulosa. Los resultados permitieron proponer en base a los estudios de DM, una estrategia de doble anclaje del CBM a celulosa, que si bien es cierto debe ser comprobado experimentalmente, resulta ser novedoso. Además, permitió proponer variantes del CBM de TvEG que potencialmente se adsorberán con mayor afinidad sobre celulosa. Si bien estas mutaciones deben ser validadas experimentalmente, fueron planteadas a partir de un diseño racional lo que aumentaría la probabilidad que éstas presenten mayor afinidad a celulosa.
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Jiao, Wanting. "The Use of Molecular Modelling to Study Enzymic Action." Thesis, University of Canterbury. Department of Chemistry, 2011. http://hdl.handle.net/10092/6257.
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Molecular modelling has become widely used in chemistry and biology. The aim of this project is to use a range of molecular modelling techniques to study enzymic actions. This thesis consists of two parts.
Part A of this thesis describes computational studies conducted for the calpain-calpastatin system. Calpain is a cysteine protease. Over-expression of calpain is associated with many diseases. Calpastatin is the naturally occurring specific regulator of calpain activity. In this part of the thesis, the dynamic conformational preferences of region B of the inhibitory domain in calpastatin were examined in detail by using molecular dynamics simulations and stochastic dynamic simulations with Monte Carlo sampling.
Part B of the thesis explores the structure and function of the enzyme 3-dexoy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtuDAH7PS). MtuDAH7PS catalyses the first reaction of the shikimate pathway and is a target for the development of anti-tuberculosis drugs. MtuDAH7PS is found to be synergistically inhibited by combinations of aromatic amino acids (Trp+Phe or Trp+Tyr), but not by any single aromatic amino acids. In this part of the thesis, this unique
mechanism of allosteric regulation in MtuDAH7PS was investigated by using a range molecular modelling techniques. Firstly protein crystal structure refinements were conducted and those crystal structures of MtuDAH7PS in
complex with various ligand molecules are described in Chapter 4. Secondly, the reaction mechanism and roles of active site residues were investigated in Chapter 5, through docking calculations (both rigid docking and induced fit docking) of a series of designed active site inhibitors. Finally, Chapter 6 discusses the molecular basis of the communication mechanism of allosteric
regulation in MtuDAH7PS.
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Silva, Viviane Aparecida. "Estudo, por modelagem molecular, da inibição da enzima acetohidroxiácido sintase utilizando diferentes derivados pirimidinilsalicilatos." Universidade Federal de Uberlândia, 2017. http://dx.doi.org/10.14393/ufu.di.2018.94.
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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorHerbicides inhibitors of the enzyme acetohydroxyacid synthase (AHAS) present high efficiency in the inhibitory activity with low doses of application and low toxicity for man and the environment. However, several weeds are getting resistence to some classes of herbicides, mainly in the case of AHAS group. Therefore, a proper computational planning of new bioactive compounds is crucial area to model new herbicides. In this study, the enzyme-herbicide interactions were analyzed from the analogous derivated of the pyrimidinylsalicylates group (PSA) which are AHAS inhibitors using quantum- mechanical and molecular docking calculations. The molecular properties obtained after running computer calculation shown that the volume and molecular area can make influence on the inhibition capacity of the ligand, neverthenless, the substituent group has more influence on this parameter. Electronical properties from the HOMO orbitals can certanly make influence on the biological activity due its electron donor capability. The binding free energies of the ligand on the enzyme after docking calculation ranged from - 1.88 to 4.50 kcal mol- 1 , whereas, H, CH3, COCH3 , OH, NO2 and NH2 had the best scored binding energies as substituent groups. Those favorable binding free energies can be justified by the intermolecular interactions between PSAs ligands and AHAS active site residues. In terms of effiency, hydrogen bonds formation can be explained by carboxylate group from the ligands and ARG-377 group from AHAS.
Os herbicidas inibidores da enzima acetohidroxiácido sintase (AHAS) apresentam alta eficiência na atividade inibitória com baixas doses de aplicação com baixa toxicidade para o homem e o meio ambiente. No entanto, várias ervas daninhas estão obtendo resistência a algumas classes de herbicidas, principalmente no caso do grupo AHAS. Portanto, um planejamento computacional adequado de novos compostos bioativos é área crucial para modelar novos herbicidas. Neste estudo, as interações enzima-herbicida foram analisadas a partir do derivado análogo do grupo pirimidinilsalicilato (PSA) que são inibidores de AHAS usando cálculos mecânicoquânticos e de docking molecular. As propriedades moleculares obtidas mostraram que o volume e a área molecular podem influenciar a capacidade de inibição do ligante, mesmo que o grupo substituinte tenha mais influência sobre este parâmetro. As propriedades eletrônicas dos orbitais HOMO podem certamente influenciar a atividade biológica devido à sua capacidade de doação de elétrons. As energias livres de ligação do ligante na enzima após o cálculo de docking variaram de -1,88 a - 4,50 kcal mol- 1 , enquanto que H, CH3, COCH3, OH, NO2 e NH2 apresentaram as melhores energias de ligação pontuadas como grupos substituintes. Estas energias livres de ligação favoráveis podem ser justificadas pelas interações intermoleculares entre ligantes de PSAs e resíduos de sítio ativo de AHAS. Em termos de eficiência, a formação de ligações de hidrogênio pode ser explicada pelo grupo carboxilato partir dos ligantes e do grupo ARG-377 de AHAS.
Dissertação (Mestrado)