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Dissertations / Theses on the topic 'Drugs Molecular dynamics'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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1

Athri, Prashanth. "Application of Computer-Aided Drug Discovery Methodologies Towards the Rational Design of Drugs Against Infectious Diseases." Digital Archive @ GSU, 2008. http://digitalarchive.gsu.edu/chemistry_diss/20.

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Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug development to provide a rational basis of drug synthesis, rather than a trial and error approach. Molecular dynamics (MD) studies focus on investigating the details of drug-target interactions to elucidate various biophysical characteristics of interest. Infectious diseases like Trypanosoma brucei rhodesiense (TBR) and P. falciparum (malaria) are responsible for m

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2

Dezi, Cristina. "Modeling of 5-HT2A and 5-HT2C receptors and of theirs complexes with actual and potential antypsichotic drugs." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7127.

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La presente tesis "Modelling of 5-HT2A and 5-HT2C receptors and of their complexes with actual and potential antipsychotic drugs" tiene como objetivo de profundizar los conocimientos actuales sobre el mecanismo de acción de los fármacos antipsicóticos. En este proyecto de larga duración, se han construidos modelos computacionales de los receptores 5-HT2A y 5-HT2C, utilizando un nuevo protocolo de modelización basado sobre los datos experimentales de otras proteínas GPCR de la misma familia. Las estructuras 3D se han validado e utilizado en estudios de acoplamiento ligando-receptor, simulacione

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3

Dias, Igor Wanderley Reis. "POLI-"-CAPROLACTONA COMO CARREADOR DE FÁRMACOS VIA MODELAGEM MOLECULAR." Universidade Franciscana, 2011. http://tede.universidadefranciscana.edu.br:8080/handle/UFN-BDTD/193.

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Made available in DSpace on 2018-06-27T18:56:22Z (GMT). No. of bitstreams: 3 Igor Wanderley Reis Dias.pdf: 6016779 bytes, checksum: 86bcdcfbfacb63d4d4a518ace6997161 (MD5) Igor Wanderley Reis Dias.pdf.txt: 208576 bytes, checksum: cd35138cd2ea03d785b3e9c7e488c5c9 (MD5) Igor Wanderley Reis Dias.pdf.jpg: 3431 bytes, checksum: 2d647e86ee0171ea4dfc34ba86f497fd (MD5) Previous issue date: 2011-08-10<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>One of the widely used biodegradable polymers to control drug release in specific sites of action is the poly-ε-caprolactone (PCL).

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4

Cameron, Linda. "Elucidation of the sequence selective binding mode of the DNA minor groove binder adozelesin, by high-field ¹H NMR and restrained molecular dynamics." Thesis, University of Bath, 1999. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311174.

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5

Shamsudin, Khan Yasmin. "Non-Steroidal Anti-Inflammatory Drugs in Cyclooxygenases 1 and 2 : Binding modes and mechanisms from computational methods and free energy calculations." Doctoral thesis, Uppsala universitet, Beräkningsbiologi och bioinformatik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-328478.

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Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used classes of drugs. They target the cyclooxygenases (COX) 1 and 2 to reduce the physiological responses of pain, fever, and inflammation. Due to their role in inducing angiogenesis, COX proteins have also been identified as targets in cancer therapies. In this thesis, I describe computational protocols of molecular docking, molecular dynamics simulations and free energy calculations. These methods were used in this thesis to determine structure-activity relationships of a diverse set of NSAIDs in binding to their ta

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6

Onywera, David Harris. "Influence of non-synonymous sequence mutations on the architecture of HIV-1 clade C protease receptor site : docking and molecular dynamics studies." Thesis, Rhodes University, 2014. http://hdl.handle.net/10962/d1013133.

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Despite the current interventions to avert contagions and AIDS-related deaths, sub-Saharan Africa is still the region most severely affected by the HIV/AIDS pandemic, where clade C is the dominant circulating HIV-1 strain. The pol-encoded HIV-1 protease enzyme has been extensively exploited as a drug target. Protease inhibitors have been engineered within the framework of clade B, the commonest in America, Europe and Australia. Recent studies have attested the existence of sequence and catalytic disparities between clades B and C proteases that could upset drug susceptibilities. Emergence of d

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7

Sadiq, S. K. S'ad. "Molecular dynamics simulation studies of drug resistance in HIV-1 protease." Thesis, University College London (University of London), 2008. http://discovery.ucl.ac.uk/1445831/.

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Overcoming the emergence of drug resistance in HIV is a major challenge to the scientific community. We use the established computational method of classical molecular dynamics to investigate the molecular basis of resistance in HIV-1 protease to the inhibitor saquinavir, using the wildtype and the G48V, L90M and G48V7L90M mutant HIV-1 proteases throughout this thesis. Firstly we reveal insights into a G48V mutation-assisted lateral drug escape mechanism from the protease active site. Such a mechanism allows drug escape without the full opening of the flaps of the protease. Furthermore, the me

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8

Wahab, Habibah Bin. "Effect of a penetration enhancer on lipid membranes : a molecular dynamics study." Thesis, King's College London (University of London), 1999. https://kclpure.kcl.ac.uk/portal/en/theses/effect-of-a-penetration-enhancer-on-lipid-membranes--a-molecular-dynamics-study(15d6388d-136f-4763-90d1-71ff975b6869).html.

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9

Elsheshiny, Asmaa Abdelghafar Ahmed. "Molecular dynamics simulations for the future : applications in nanotechnology and drug design." Thesis, University of Leeds, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.659032.

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Molecular dynamics simulations can provide atomistic details of the dynamics of proteins over timescales in the range of pico to micro seconds, and is therefore complementary to experimental structural techniques such as X-ray crystallography, which only provides static information, and Nuclear Magnetic resonance (NMR), which does not provide fully atomistic detail. In this work atomistic molecular dynamics simulation has been used to investigate the electromechanical properties of three structurally distinct proteins, and has revealed that the conformational changes that occur are strongly de

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10

Wright, D. W. "Molecular dynamics simulation of drug resistance in HIV-1 protease and reverse transcriptase." Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1331997/.

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The emergence of drug resistant strains of HIV represents a major challenge in the treatment of patients who contract the virus. We investigate the use of classical molecular dynamics to give quantitative and qualitative molecular insight into the causes of resistance in the two main drug targets in HIV, protease and reverse transcriptase. We initially establish a simulation and free energy analysis protocol for the study of resistance in protease. Focusing on the binding of the inhibitor lopinavir to a series of six mutants with increasing resistance we demonstrate that ensemble simulations e

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11

Wilbe, Karin. "Genetic dynamics of HIV-1: recombination, drug resistance and intrahost evolution /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-959-5/.

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12

Nagireddy, Bharat. "AN EFFECTIVE DRUG DELIVERY PROCESS USING A NOVEL CYLINDRICAL PARTICLE MODEL JUSTIFIED BY MOLECULAR DYNAMICS SIMULATION." University of Akron / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=akron1187105640.

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13

Martínez, Rosell Gerard 1990. "Applications of molecular dynamics in drug discovery and technology transfer via a web-based platform." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/665077.

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In this thesis we apply molecular dynamics (MD) simulations and other in silico techniques in drug discovery. Specifically, (a) we developed an algorithm to detect cryptic pockets based on MD simulations of the protein solvated in a mixture of water and benzene, (b) we performed the first 150-fragment screening against the chemokine CXCL12 using a MD-driven protocol and (c) we studied the conformational plasticity of the μ-opioid receptor (MOR) bound to two different drugs to study the molecular basis of selective modulation. Additionally, we created a web platform entitled PlayMolecule, wher

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14

Ferruz, Capapey Noelia 1988. "Understanding ligand-receptor recognition by means of high-throughput molecular dynamics : a perspective for drug discovery." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/363212.

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Understanding how receptor-ligand interactions occur is a first step towards designing new drugs. The complete reconstruction of the binding process in a drug-receptor system provides all the physical-chemistry variables for rational design of inhibitors of a chosen target, an important step in drug discovery. Although very powerful, direct experimental observation of full binding processes is very hard to perform. In this thesis, by using high-throughput molecular dynamics in the distributed computing project GPUGRID.net and analysing the resulting data by Markov state models (MSM), we succ

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Perez, Benito Laura. "Application of Molecular Dynamics methods to the study of biological systems." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/402258.

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La aplicación de métodos de dinámica molecular (MD) para el estudio de sistemas biológicos. Esta tesis se centra en la aplicación tanto de dinámica molecular clásica como perturbación de energía libre (FEP) para estudiar sistemas biológicos tales como los receptores acoplados a proteínas G y los inhibidores de BACE1. La tesis se divide en 5 secciones, en primer lugar, una introducción donde se explica la evolución de la metodología de MD, en segundo lugar, una sección sobre métodos utilizados en esta tesis, la tercera sección se centra en el uso de simulaciones de MD para estudiar dos asp

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Atzori, Alessio. "Conformational analysis of peptides and proteins for drug design using molecular simulations." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/conformational-analysis-of-peptides-and-proteins-for-drug-design-using-molecular-simulations(050ba296-a4c4-4a5b-87bf-66d90f7ddc5a).html.

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The intrinsic plasticity of biological systems provides opportunities for rational design of selective and potent ligands. Increasingly, computational methods are being applied to predict biomolecular flexibility. However, the motions involved in these processes can be large and occur on time scales generally difficult to achieve with standard simulation methods. In order to overcome the intrinsic limitations of classical molecular dynamics, this Ph.D. project focuses on the application of advanced sampling computational techniques to capture the plasticity of diverse biological systems. The f

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Sharp, Amanda Kristine. "Probing Orthologue and Isoform Specific Inhibition of Kinases using In Silico Strategies: Perspectives for Improved Drug Design." Thesis, Virginia Tech, 2020. http://hdl.handle.net/10919/98471.

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Kinases are involved in a multitude of signaling pathways, such as cellular growth, proliferation, and apoptosis, and have been discovered to be important in numerous diseases including cancer, Alzheimer's disease, cardiovascular health, rheumatoid arthritis, and fibrosis. Due to the involvement in a wide variety of disease types, kinases have been studied for exploitation and use as targets for therapeutics. There are many limitations with developing kinase target therapeutics due to the high similarity of kinase active site composition, making the utilization of new techniques to determine k

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Selvam, Balaji. "The role of a dynamic conformational ensemble in molecular recognition, activation and drug design." Thesis, Queen's University Belfast, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.603067.

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The bioaminergic receptors belong to the G protein-coupled receptors and represent the important drug targets for cardiovascular and neurodegenerative disorders. In this work, molecular dynamics simulations of the bioaminergic receptors in the free form and ligand bound forms have been conducted in the realistic environment in order to address the pharmacological issues such as ligand sub-type selectivity, functional selectivity and selective polypharmacology. Our results provide novel computational protocols that can be used for structure-based drug design of the bioaminergic receptors and ar

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Sourmaidou, Damiani. "Computational nanoscience and molecular modelling of shock wave interactions with biological membranes." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/7283.

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Lateral diffusion of membrane components (lipids and proteins) is an important membrane property to measure since the essential process of absorption of anti-cancer and other drugs -some of which are not soluble in lipids and therefore would not be able to penetrate the cell membrane through passive diffusion- lies on it. In particular, the procedure of diffusion into the cell cytoplasm is reliant on free volumes in the membrane (passive diffusion) as well as carrier proteins (facilitated diffusion). By enhancing the mobility of lipids and/or proteins, the possibility of the carrier protein to

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20

Majewski, Maciej. "Implications of Structural Stability for Drug Design." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/671195.

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The relevance of structural stability in drug design has been shown by the use of DUck in virtual screening campaign, as reported previously. The method provides a fast and easy way to assess hydrogen bond-based structural stability of a complex. However, the cause and consequences of structural stability in molecular recognition remain unknown. DUck still has some limitations and requires previous knowledge about the system to be applied successfully. GENERAL OBJECTIVE: The general objective of this work is to deepen the knowledge of the role and origin of structural stability in mole

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Li, Xiuli. "Block Copolymer Solutions: Transport and Dynamics, Targeted Cargo Delivery, and Molecular Partitioning and Exchange." Diss., Virginia Tech, 2020. http://hdl.handle.net/10919/104197.

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Block copolymers have been extensively applied in diverse fields including packaging, electrolytes, delivery devices, and biosensors. Multiple investigations have been carried out on polymeric materials for cargo delivery purpose to understand how they behave over time. Block copolymer micelles (BCMs) have demonstrated superiority to deliver cargo, especially in drug delivery due to their encapsulation of hydrophobic agents. This dissertation will mainly study BCMs for potential applications in cargo delivery. Methods to study BCMs, including NMR spectroscopy, relaxometry and diffusometry, ca

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22

John, Mongan. "Implicit solvent method development and application fast molecular surfaces, constant pH and accelerated dynamics, and rational drug design /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3201196.

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Thesis (Ph. D.)--University of California, San Diego, 2006.<br>Title from first page of PDF file (viewed March 1, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references ( p. 146-163).

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23

Siegel, Sasha Victoria. "Mitochondrial Heteroplasmy Contributes to the Dynamic Atovaquone Resistance Response in Plasmodium falciparum." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6586.

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Of the considerable challenges researchers face in the control and elimination of malaria, the development of antimalarial drug resistance in parasite populations remains a significant hurdle to progress worldwide. Atovaquone is used in combination with proguanil (Malarone) as an antimalarial treatment in uncomplicated malaria, but is rendered ineffective by the rapid development of atovaquone resistance during treatment. Previous studies have established that de novo mutant parasites confer resistance to atovaquone with a substitution in amino acid 268 in the cytochrome b gene encoded by the

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Polêto, Marcelo Depólo. "Parametrização de anéis aromáticos comumente usados no desenvolvimento de fármacos e química medicinal." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2016. http://hdl.handle.net/10183/150648.

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Métodos computacionais assumiram a partir de 1980, um papel de destaque no planejamento de novos fármacos, oferecendo abordagens racionais para reduzir o grau de incerteza na geração de novos compostos bioativos. Dentre estes métodos, destacam-se aqueles dependentes de campos de força, como o atracamento e a dinâmica molecular. Infelizmente, estes métodos exigem estratégias de parametrização capazes de lidar com a diversidade química associada ao planejamento de fármacos. Os esforços atuais neste sentido são focados em fase gasosa, como no caso do GAFF e MMFF94, Assim, o presente trabalho busc

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Ibrahim, Mahmoud Arafat Abd el-hamid. "Developments and applications in computer-aided drug discovery." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/developments-and-applications-in-computeraided-drug-discovery(eb57dde8-6190-4ea6-8fa8-219693788daf).html.

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Noncovalent interactions are of great importance in studies on crystal design and drug discovery. One such noncovalent interaction, halogen bonding, is present between a covalently bound halogen atom and a Lewis base. A halogen bond is a directional interaction caused by the anisotropic distribution of charge on a halogen atom X covalently bound to A, which in turn forms a positive region called σ-hole on the A–X axis. Utilization of halogen bonds in lead optimization have been rarely considered in drug discovery until recently and yet more than 50% of the drug candidates are halogenated. To d

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Ramamoorthy, Divya. "Design of Novel Inhibitors for Infectious Diseases using Structure-based Drug Design: Virtual Screening, Homology Modeling and Molecular Dynamics." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4393.

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The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and

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27

Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.

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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-an

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28

Isaacs, Darren Mathew. "Molecular dynamic simulation studies of the South African HIV-1 Integrase subtype C protein to understand the structural impact of naturally occurring polymorphisms." University of Western Cape, 2021. http://hdl.handle.net/11394/8365.

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>Magister Scientiae - MSc<br>The viral Integrase (IN) protein is an essential enzyme of all known retroviruses, including HIV-1. It is responsible for the insertion of viral DNA into the human genome. It is known that HIV-1 is highly diverse with a high mutation rate as evidenced by the presence of a large number of subtypes and even strains that have become resistant to antiretroviral drugs. It remains inconclusive what effect this diversity in the form of naturally occurring polymorphisms/variants exert on IN in terms of its function, structure and susceptibility to IN inhibitory antiretrovi

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Chihota, Violet. "The molecular epidemiology of mycobacterium tuberculosis : role in understanding disease dynamics in high prevalence settings in Southern Africa region." Thesis, Stellenbosch : University of Stellenbosch, 2011. http://hdl.handle.net/10019.1/6902.

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Thesis (PhD)--University of Stellenbosch, 2011.<br>ENGLISH ABSTRACT: The tuberculosis (TB) incidence has increased in Southern Africa and the situation is worsened by the emergence of drug-resistant Mycobacterium tuberculosis strains. Molecular biological techniques have been used to understand the disease dynamics of TB. In a series of studies we describe the use of these techniques to understand the disease dynamics of TB in Southern Africa. Using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) to characterize M. tuberculosis strains from TB patients in Zimbabw

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Sartori, Geraldo Rodrigues. "Planejamento de inibidores baseado em fragmentos moleculares para a enzima gliceraldeído-3-fosfato desidrogenase de Trypanosoma cruzi." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/75/75133/tde-24072012-142746/.

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A Doença de Chagas, endêmica na América Latina, é causada pelo parasito tripanossomatídeo Trypanosoma cruzi e atualmente já se espalha para o restante do mundo devido à migração humana. Os dois medicamentos disponíveis para o tratamento dessa doença, o Nifurtimox, (banido do Brasil), e o Benzonidazol, são eficazes somente na etapa aguda da doença e possuem efeitos colaterais severos. Recentemente, três novas substâncias para o tratamento chegaram à fase clínica de testes contra essa doença, mas ainda é necessária a pesquisa de novas moléculas contra esse parasito. A enzima Gliceraldeído-3-fosf

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Ozen, Aysegul. "Structure and Dynamics of Viral Substrate Recognition and Drug Resistance: A Dissertation." eScholarship@UMMS, 2005. http://escholarship.umassmed.edu/gsbs_diss/677.

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Drug resistance is a major problem in quickly evolving diseases, including the human immunodeficiency (HIV) and hepatitis C viral (HCV) infections. The viral proteases (HIV protease and HCV NS3/4A protease) are primary drug targets. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition; the drug resistant protease variants are no longer effectively inhibited by the competitive drug molecules but can process the natural substrates with enough efficiency for viral survival. Therefore, the inhibitors that better mimic the natural substrate bindin

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Ozen, Aysegul. "Structure and Dynamics of Viral Substrate Recognition and Drug Resistance: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/677.

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Drug resistance is a major problem in quickly evolving diseases, including the human immunodeficiency (HIV) and hepatitis C viral (HCV) infections. The viral proteases (HIV protease and HCV NS3/4A protease) are primary drug targets. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition; the drug resistant protease variants are no longer effectively inhibited by the competitive drug molecules but can process the natural substrates with enough efficiency for viral survival. Therefore, the inhibitors that better mimic the natural substrate bindin

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Schneider, Melanie. "Integrative chemoinformatics to guide drug design : application to re-design a clinical protein kinase inhibitor." Thesis, Montpellier, 2019. http://www.theses.fr/2019MONTT057.

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Malgré des années de recherche et de développement intensifs, le cancer reste l’une des principales causes de décès dans le monde. La chimiothérapie est le traitement le plus couramment utilisé contre le cancer, car la chirurgie et la radiothérapie ne sont souvent pas efficaces pour traiter le cancer à tous les endroits où il se propage. Cependant, la pharmacorésistance des cellules cancéreuses aux agents chimiothérapeutiques et / ou la réduction de l’efficacité d’un médicament est la principale cause d’échec de la chimiothérapie. Les médicaments sont développés pour se lier efficacement à une

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Aldhumani, Ali Hamed. "Pharmacophore Model Development: Targeting Noncoding RNA for Antibacterial/Antiviral Drug Discovery." Ohio University / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1610705872573225.

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Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.

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Braka, Abdennour. "Prédiction de la cinétique des inhibiteurs de protéines kinases et de leur affinité par docking flexible." Thesis, Orléans, 2018. http://www.theses.fr/2018ORLE2016.

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Dans le cadre d’un projet de drug design, l’amélioration de la prédiction de l’affinité représente toujours un défi malgré les nombreux efforts déployés dans ce sens. De plus, les constantes cinétiques d’association et de dissociation sont d'un intérêt majeur pour la découverte de nouveaux médicaments, notamment au stade précoce de l'optimisation des molécules afin de mieux évaluer leurs tolérances et efficacités. De par la récente émergence des études de constantes cinétiques, il existe peu de méthodes de prédiction de ces dernières et aucune approche efficace n'a encore été développée pour e

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Gude, Manjiri. "Effect of lipid-based formulation on the solubilization patterns if poorly water-soluble drugs." Thesis, Uppsala universitet, Institutionen för farmaci, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-445332.

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Poorly water-soluble drugs (PWSDs), to date, require advanced formulation techniques to improve solubility and achieve the required plasma concentration to show a therapeutic effect when orally administered. Lipid-based formulations (LBFs) are an enabling strategy that is being used to improve the oral delivery of PWSDs. The aim of this study was to investigate the effect of lipid-based formulation, Type IIIA-LC, on the solubilization patterns of PWSDs, namely, carvedilol and felodipine. Solubility studies, for both drugs, were performed with LBF dispersed in -1) dog intestinal fluid (DIF), an

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Pietersen, Gerbrecht Elizabeth. "Molecular epidemiology, susceptibility profiles, outcomes and transmission dynamics in patients with extensively drug-resistant tuberculosis (XDR-TB) in two provinces of South Africa." Doctoral thesis, University of Cape Town, 2017. http://hdl.handle.net/11427/24499.

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Background: Recent gains in TB control in South Africa are being reversed by drug-resistant tuberculosis (MDR-TB and XDR-TB), which has a high mortality, is a threat to health care workers, and is prohibitively costly to treat. MDR-TB has been supplanted by XDR-TB, resistance beyond XDR-TB, and programmatically incurable TB. Short-term treatment-related outcomes of XDR-TB patients are known to be poor. However, there are no prospective data to inform longterm treatment-related outcomes, design of effective XDR-TB treatment regimens, and public health interventions required to interrupt transmi

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Gonçalves, Ricardo Lemes. "Mecanismos da interação entre monômeros da NS1 dos vírus Zika e Dengue como alvo do design racional de fármaco." Universidade Federal de Goiás, 2017. http://repositorio.bc.ufg.br/tede/handle/tede/8019.

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Submitted by Franciele Moreira (francielemoreyra@gmail.com) on 2017-12-06T14:22:57Z No. of bitstreams: 2 Dissertação - Ricardo Lemes Gonçalves - 2017.pdf: 6297486 bytes, checksum: 3393a7cb0ffe26eafd0acd04f1198ab0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)<br>Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-07T10:18:10Z (GMT) No. of bitstreams: 2 Dissertação - Ricardo Lemes Gonçalves - 2017.pdf: 6297486 bytes, checksum: 3393a7cb0ffe26eafd0acd04f1198ab0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5

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Berry, Michael. "Massively-Parallel Computational Identification of Novel Broad Spectrum Antivirals to Combat Coronavirus Infection." University of the Western Cape, 2015. http://hdl.handle.net/11394/8321.

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Philosophiae Doctor - PhD<br>Given the significant disease burden caused by human coronaviruses, the discovery of an effective antiviral strategy is paramount, however there is still no effective therapy to combat infection. This thesis details the in silica exploration of ligand libraries to identify candidate lead compounds that, based on multiple criteria, have a high probability of inhibiting the 3 chymotrypsin-like protease (3CUro) of human coronaviruses. Atomistic models of the 3CUro were obtained from the Protein Data Bank or theoretical models were successfully generated by homology m

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Ferreira, Glaucio Monteiro. "Busca por inibidores seletivos de Sirtuína 2 de T. cruzi empregando técnicas de planejamento de fármacos baseadona estrutura do receptor." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/9/9141/tde-08032019-174942/.

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A doença de Chagas, causada pelo parasita Trypanosoma cruzi, acomete entre 6 a 8 milhões de pessoas em todo o mundo. Conhecida como tripanossomíase americana, por ter sido considerada endêmica apenas na América Latina, esta doença, se espalhou para outros continentes devido aos movimentos migratórios se tornando um problema de sáude mundial. Estima-se que 56.000 novos casos e cerca de 12.000 mortes por complicações relacionadas à doença de Chagas anualmente. A quimioterapia disponível para o tratamento é composta apenas por dois fármacos, nifurtimox e benznidazol, no entanto são pouco eficazes

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Prachanronarong, Kristina L. "Understanding Drug Resistance and Antibody Neutralization Escape in Antivirals: A Dissertation." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/840.

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Antiviral drug resistance is a major problem in the treatment of viral infections, including influenza and hepatitis C virus (HCV). Influenza neuraminidase (NA) is a viral sialidase on the surface of the influenza virion and a primary antiviral target in influenza. Two subtypes of NA predominate in humans, N1 and N2, but different patterns of drug resistance have emerged in each subtype. To provide a framework for understanding the structural basis of subtype specific drug resistance mutations in NA, we used molecular dynamics simulations to define dynamic substrate envelopes for NA to determi

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Pollum, Marvin. "Applying Fundamental Photochemistry to Drive Drug Development: The Photo-Dynamics and Reactions of Sulfur-Substituted Nucleic Acids." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1481287737895585.

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Alonso, Hernan, and hernan alonso@anu edu au. "Computer Modelling and Simulations of Enzymes and their Mechanisms." The Australian National University. The John Curtin School of Medical Research, 2006. http://thesis.anu.edu.au./public/adt-ANU20061212.161155.

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Although the tremendous catalytic power of enzymes is widely recognized, their exact mechanisms of action are still a source of debate. In order to elucidate the origin of their power, it is necessary to look at individual residues and atoms, and establish their contribution to ligand binding, activation, and reaction. Given the present limitations of experimental techniques, only computational tools allow for such detailed analysis. During my PhD studies I have applied a variety of computational methods, reviewed in Chapter 2, to the study of two enzymes: DfrB dihydrofolate reductase (DHFR) a

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Cao, Yichen. "APPLICATION OF LINEAR FREE ENERGY RELATIONSHIPS IN THE PREDICTION OF TRIGLYCERIDE/WATER PARTITION COEFFICIENTS AND LIPID BILAYER PERMEABILITY COEFFICIENTS OF SMALL ORGANIC MOLECULES AND PEPTIDES." UKnowledge, 2008. http://uknowledge.uky.edu/gradschool_diss/655.

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Computational methods such as linear free energy relationships (LFERs) offer a useful high-throughput solution to quickly evaluate drug developability, e.g. membrane permeability, organic solvent/water partition coefficients, and solubility. LFERs typically assume the contribution of structural components/functional groups to the overall properties of a given molecule to be constant and independent. This dissertation describes a series of studies in which linear free energy relationships were developed to predict solvation of small organic molecules in lipid formulations, specifically, triglyc

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Ragland, Debra A. "The Structural Basis for the Interdependence of Drug Resistance in the HIV-1 Protease." eScholarship@UMMS, 2012. http://escholarship.umassmed.edu/gsbs_diss/879.

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The human immunodeficiency virus type 1 (HIV-1) protease (PR) is a critical drug target as it is responsible for virion maturation. Mutations within the active site (1°) of the PR directly interfere with inhibitor binding while mutations distal to the active site (2°) to restore enzymatic fitness. Increasing mutation number is not directly proportional to the severity of resistance, suggesting that resistance is not simply additive but that it is interdependent. The interdependency of both primary and secondary mutations to drive protease inhibitor (PI) resistance is grossly understudied. To s

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Ragland, Debra A. "The Structural Basis for the Interdependence of Drug Resistance in the HIV-1 Protease." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/879.

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The human immunodeficiency virus type 1 (HIV-1) protease (PR) is a critical drug target as it is responsible for virion maturation. Mutations within the active site (1°) of the PR directly interfere with inhibitor binding while mutations distal to the active site (2°) to restore enzymatic fitness. Increasing mutation number is not directly proportional to the severity of resistance, suggesting that resistance is not simply additive but that it is interdependent. The interdependency of both primary and secondary mutations to drive protease inhibitor (PI) resistance is grossly understudied. To s

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Shinada, Nicolas. "Détection, caractérisation et comparaison des interactions protéine - ligand." Thesis, Sorbonne Paris Cité, 2019. http://www.theses.fr/2019USPCC090.

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Appréhender le mécanisme fin de la liaison d’un ligand sur sa protéine est un enjeu majeur de l’industrie pharmaceutique. L’objectif principale de cette thèse est d’améliorer la compréhension de ce mécanisme par l’étude des interactions moléculaires. A cette fin, une méthode de détection de contacts à grande échelle fut mise en place. Les premiers chapitres illustrent les différents types d’interaction recensés dans la littérature ainsi que les outils qui ont été développés au cours de cette thèse pour en permettre l’analyse. A l’aide des contacts générés par notre méthode, une analyse exhaust

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Gomes, Fabiano do Esp?rito Santo. "Obten??o de sistemas microemulsionados e estudo de simula??o por din?mica molecular de sistemas micelares objetivando a veicula??o de produtos naturais bioativos." Universidade Federal do Rio Grande do Norte, 2010. http://repositorio.ufrn.br:8080/jspui/handle/123456789/17718.

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Made available in DSpace on 2014-12-17T15:42:08Z (GMT). No. of bitstreams: 1 FabianoESG_TESE.pdf: 2562039 bytes, checksum: f41fc74bb604ad5b4eb0383a80628c68 (MD5) Previous issue date: 2010-03-30<br>Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico<br>Among the new drugs launched into the market since 1980, up to 30% of them belong to the class of natural products or they have semisynthetic origin. Between 40-70% of the new chemical entities (or lead compounds) possess poor water solubility, which may impair their commercial use. An alternative for administration of poorly water-so

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Pham, Khoa Ngoc. "Conformational Dynamics and Stability Associated with Magnesium or Calcium Binding to DREAM in the Regulation of Interactions between DREAM and DNA or Presenilins." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/2589.

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Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca2+ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca2+ and/or Mg2+ association at the EF-hands in DREAM. Therefore, understanding the conforma

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