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Relevant bibliographies by topics / Ligand-protein binding, molecular dynamics, molecular docking, structure-based / Journal articles

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Journal articles on the topic 'Ligand-protein binding, molecular dynamics, molecular docking, structure-based'

Author: Grafiati

Published: 9 March 2023

Last updated: 10 March 2023

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1

Naqvi, Ahmad Abu Turab, Taj Mohammad, Gulam Mustafa Hasan, and Md Imtaiyaz Hassan. "Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships." Current Topics in Medicinal Chemistry 18, no. 20 (2018): 1755–68. http://dx.doi.org/10.2174/1568026618666181025114157.

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Protein-ligand interaction is an imperative subject in structure-based drug design and protein function prediction process. Molecular docking is a computational method which predicts the binding of a ligand molecule to the particular receptor. It predicts the binding pose, strength and binding affinity of the molecules using various scoring functions. Molecular docking and molecular dynamics simulations are widely used in combination to predict the binding modes, binding affinities and stability of different protein-ligand systems. With advancements in algorithms and computational power, molec

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Rayevsky, O. V., O. M. Demchyk, P. A. Karpov та ін. "Structure-based virtual screening for new lead compounds targeted Plasmodium α-tubulin". Faktori eksperimental'noi evolucii organizmiv 28 (31 серпня 2021): 135–39. http://dx.doi.org/10.7124/feeo.v28.1389.

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Aim. Search for new dinitroaniline and phosphorothioamide compounds, capable of selective binding with Plasmodium α-tubulin, affecting its mitotic apparatus. Methods. Structural biology methods of computational prediction of protein-ligand interaction: molecular docking, molecular dynamics and pharmacophore analysis. Selection of compounds based on pharmacophore characteristics and virtual screening results. Results. The protocol and required structural conditions for target (α-tubulin of P. falciparum) preparation and correct modeling of the ligand-protein interaction (docking and virtual scr

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Karpov, P. A., S. I. Spivak, O. V. Rayevsky, O. Yu Nyporko, S. P. Ozheredov та Ya B. Blume. "Assessment of structural peculiarities of glaziovianin A interaction with human α-, β and γ-tubulins". Faktori eksperimental'noi evolucii organizmiv 22 (9 вересня 2018): 340–44. http://dx.doi.org/10.7124/feeo.v22.972.

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Aim. To determine the features of the ligand-protein interaction of glaziovianin A and human α-, β- and γ-tubulin. Methods. Protein and ligand spatial structure modelling (I-Tasser, Grid), molecular docking (CCDC Gold), molecular dynamics simulation (GROMACS). Results. Using the method of molecular docking in CCDC Gold ligand-protein complexes of glaziovianin A and human α-, β- and γ-tubulin were reconstructed. Studied ligand interactions in GTP/GDP-exchange and colchicine binding sites of different tubulin isotypes. The built ligand-protein complexes were studied using molecular dynamics simu

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Ozheredov, S. P., O. M. Demchuk, P. A. Karpov, S. I. Spivak та Ya B. Blume. "Identification of plant α-tubulin amino acids playing a key role in specific binding of nitroaniline compounds". Faktori eksperimental'noi evolucii organizmiv 24 (30 серпня 2019): 333–37. http://dx.doi.org/10.7124/feeo.v24.1125.

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Aim. Computational prediction of amino acid residues critical for specific binding of nitro- and dinitroaniline compounds in plant α-tubulin. Methods. Protein structure modeling (I-Tasser, Grid-computing) and ligand library preparation, molecular docking (CCDC Gold), molecular dynamics (MD, Gromacs computing in Grid). Evaluation of the amino acid ensemble associated with ligand binding based on results of MD energy perturbations of protein-ligand complex. Results. The structural model of plant α-tubulin from Avena sativa was build. Also, the virtual library of 25 nitroaniline compounds was pre

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Panchangam, Sameera Sastry. "BabyBoom: 3-Dimensional Structure-Based Ligand and Protein Interaction Prediction by Molecular Docking." Biomolecules 12, no. 11 (2022): 1633. http://dx.doi.org/10.3390/biom12111633.

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Baby Boom (BBM) is a key transcription factor that triggers embryogenesis, enhances transformation and regeneration efficiencies, and regulates developmental pathways in plants. Triggering or activating BBM in non-model crops could overcome the bottlenecks in plant breeding. Understanding BBM’s structure is critical for functional characterization and determination of interacting partners and/or ligands. The current in silico study aimed to study BBM’s sequence and conservation across all plant proteomes, predict protein-protein and protein-ligand interactions, and perform molecular docking an

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Menin, Silvia, Matteo Pavan, Veronica Salmaso, Mattia Sturlese, and Stefano Moro. "Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement." International Journal of Molecular Sciences 24, no. 4 (2023): 3596. http://dx.doi.org/10.3390/ijms24043596.

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Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In th

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Bera, Indrani, and Pavan V. Payghan. "Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery." Current Pharmaceutical Design 25, no. 31 (2019): 3339–49. http://dx.doi.org/10.2174/1381612825666190903153043.

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Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). M

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Hidayatullah, Arief, Wira Eka Putra, Sustiprijatno Sustiprijatno, Diana Widiastuti, Wa Ode Salma, and Muhammad Fikri Heikal. "Molecular Docking and Molecular Dynamics Simulation-Based Identification of Natural Inhibitors against Druggable Human Papilloma Virus Type 16 Target." Trends in Sciences 20, no. 4 (2023): 4891. http://dx.doi.org/10.48048/tis.2023.4891.

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The E5 protein is the smallest known oncoprotein linked to HPV 16 cancer development. In this study, we determined the potential of asarinin and thiazolo as an inhibitor of the E5 protein through molecular dynamics. The results showed that the binding site is unstable because of its hydrophobic nature and small size, causing considerable changes in the binding site for each of the 3 drugs examined. Except for asarinin, which still interacts with the first hydrophobic domain, they preserved their capacity to prevent endosomal acidification, hyper amplification of the EGFR pathway and contact wi

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Mishra and Dey. "Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood." Biomolecules 9, no. 11 (2019): 740. http://dx.doi.org/10.3390/biom9110740.

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Natural products from plants, such as chemopreventive agents, attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure-based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide-based therapeutics have been developed to combat

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Nagamalla, Lavanya, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, et al. "Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations." Crystals 12, no. 8 (2022): 1158. http://dx.doi.org/10.3390/cryst12081158.

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AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding fr

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Viegas, Aldino, João Sardinha, Filipe Freire, et al. "Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11)." Biochemical Journal 451, no. 2 (2013): 289–300. http://dx.doi.org/10.1042/bj20120627.

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Non-catalytic cellulosomal CBMs (carbohydrate-binding modules) are responsible for increasing the catalytic efficiency of cellulosic enzymes by selectively putting the substrate (a wide range of poly- and oligo-saccharides) and enzyme into close contact. In the present study we carried out an atomistic rationalization of the molecular determinants of ligand specificity for a family 11 CBM from thermophilic Clostridium thermocellum [CtCBM11 (C. thermocellum CBM11)], based on a NMR and molecular modelling approach. We have determined the NMR solution structure of CtCBM11 at 25°C and 50°C and der

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Yin, Jian, Junkun Lei, Jialin Yu, et al. "Assessment of AI-Based Protein Structure Prediction for the NLRP3 Target." Molecules 27, no. 18 (2022): 5797. http://dx.doi.org/10.3390/molecules27185797.

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The recent successes of AlphaFold and RoseTTAFold have demonstrated the value of AI methods in highly accurate protein structure prediction. Despite these advances, the role of these methods in the context of small-molecule drug discovery still needs to be thoroughly explored. In this study, we evaluated whether the AI-based models can reliably reproduce the three-dimensional structures of protein–ligand complexes. The structure we chose was NLRP3, a challenging protein target in terms of obtaining a three-dimensional model both experimentally and computationally. The conformation of the bindi

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Highland, Hyacinth, Monica Thakur, Pujan Pandya, Archana Mankad, and Linz-Buoy George. "Molecular Dynamics of A Biglycan-Rosmarinic Acid Complex with Focal Adhesion Kinase for Possible Arrest of Metastasis in Non-Small Cell Lung Cancer (NSCLC): An In- Silico Study." Journal of Drug Delivery and Therapeutics 9, no. 4-A (2019): 159–66. http://dx.doi.org/10.22270/jddt.v9i4-a.3382.

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Background: Non-small cell lung cancer (NSCLC) is the major cause of mortality all over the world. Significant increase of biglycan is seen in the lung cancer cells when compared with the normal cells. It promotes tumor invasion and metastasis by activating Focal Adhesion Kinase (FAK) signaling pathway. The increased FAK activity may contribute to the metastatic potential of malignant tumors. This study was carried out to establish binding interactions of some selected phytocomponents against biglycan for the possible arrest of metastasis. Methods: Protein-ligand interaction studies were

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De Paris, Renata, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto de Souza, and Rodrigo C. Barros. "Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments." Computational Intelligence and Neuroscience 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/916240.

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Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we d

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PRECUPAS, Aurica, and Sorana IONESCU. "Exploring the interaction of 5,6- benzocoumarin-3-carboxylic acid with bovine serum albumin at the molecular level: A biophysical investigation using molecular dynamics." Revue Roumaine de Chimie 66, no. 1 (2021): 49–58. http://dx.doi.org/10.33224/rrch.2021.66.1.05.

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In this work, molecular dynamics (MD) is used to monitor the conformational space spanned by a ligand when in the binding pocket of a protein. 5,6-benzocoumarin-3-carboxylic acid was chosen as it is a relatively rigid molecule, with only one rotational degree of freedom, useful in its simplicity, whereas bovine serum albumin was used as a model protein. The initial geometry of the protein-ligand complex was obtained by molecular docking. The MD simulation was carried out for 90 ns and the dynamic evolution of the system was explored based on the usual parameters: root mean square deviation (RM

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Demchuk, O. M., P. A. Karpov, A. V. Rayevsky та ін. "Alanine scanning of dinitroaniline/phosphorothioamidate site of α-tubulin in plasmodium species distributed in India". Faktori eksperimental'noi evolucii organizmiv 26 (1 вересня 2020): 293–97. http://dx.doi.org/10.7124/feeo.v26.1282.

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Aim. Identification of amino acid residues participating in specific binding of dinitroaniline and phosphorothioamidate compounds with α-tubulin in Plasmodium falciparum. Methods. Protein structure modelling, protein structure optimization using molecular dynamics method, ligand-protein docking, alanine scanning mutagenesis. Results. Molecular docking of canonical compounds and alanine scanning mutagenesis, indicate two key (Arg2, Val250) and one minor (Glu3) residues involved in binding of both - dinitroaniline and phosphorothioamidate compounds. At the same time, it was revealed two minor re

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Abdullah, Asif, Partha Biswas, Md Sahabuddin, et al. "Molecular Dynamics Simulation and Pharmacoinformatic Integrated Analysis of Bioactive Phytochemicals from Azadirachta indica (Neem) to Treat Diabetes Mellitus." Journal of Chemistry 2023 (March 3, 2023): 1–19. http://dx.doi.org/10.1155/2023/4170703.

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Diabetes mellitus is a chronic hormonal and metabolic disorder in which our body cannot generate necessary insulin or does not act in response to it, accordingly, ensuing in discordantly high blood sugar (glucose) levels. Diabetes mellitus can lead to systemic dysfunction in the multiorgan system, including cardiac dysfunction, severe kidney disease, lowered quality of life, and increased mortality risk from diabetic complications. To uncover possible therapeutic targets to treat diabetes mellitus, the in silico drug design technique is widely used, which connects the ligand molecules with tar

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Ayyamperumal, Selvaraj. "Molecular docking analysis of α-Topoisomerase II with δ-Carboline derivatives as potential anticancer agents". Bioinformation 17, № 1 (2021): 249–65. http://dx.doi.org/10.6026/97320630017249.

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The enzyme, α-topoisomerase II (α-Topo II), is known to regulate efficiently the topology of DNA. It is highly expressed in rapidly proliferating cells and plays an important role in replication, transcription and chromosome organisation. This has prompted several investigators to pursue α-Topo II inhibitors as anticancer agents. δ-Carboline, a natural product, and its synthetic derivatives are known to exert potent anticancer activity by selectively targeting α-Topo II. Therefore, it is of interest to design carboline derivatives fused with pyrrolidine-2,5-dione in this context. δ-Carbolines

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Ifaya, Mus, Ida Musfiroh, Sahidin та ін. "MOLECULAR DOCKING AND DYNAMICS SIMULATIONS OF FENOLIC CONTENTS ON HENNA PLANT (Lawsonia inermis L.) AS ANTIDIBETIC THROUGH INHIBITION OF DIGESTIVE ENZYME α-AMYLASE". RASAYAN Journal of Chemistry 15, № 02 (2022): 861–69. http://dx.doi.org/10.31788/rjc.2022.1526654.

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Diabetes mellitus is a disease caused by high blood glucose levels, and one way to overcome it is by inhibiting the digestive enzyme, α-amylase. The henna plant (Lawsonia inermis L.) has been shown to show potential as an antidiabetic through inhibition of the enzyme digestive, but its molecular mechanism has not been revealed. Therefore, the aim of this study was to reveal the α-amylase enzyme inhibitory activity of phenolic compounds in the henna plant by molecular docking and molecular dynamics. The protein used was a high-resolution α-amylase crystallographic protein with the code PDB: 1XD

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Vavra, Ondrej, Jiri Filipovic, Jan Plhak, et al. "CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels." Bioinformatics 35, no. 23 (2019): 4986–93. http://dx.doi.org/10.1093/bioinformatics/btz386.

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Abstract Motivation Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins’ external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement dockin

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Mishra, SHASHANK, and C. S. SHARMA. "MOLECULAR DOCKING, BINDING ENERGY AND MOLECULAR DYNAMICS SIMULATION STUDIES OF PIPERAZIN-1-YLPYRIDAZINE DERIVATIVES AS DCTPASE INHIBITORS." International Journal of Pharmaceutical Sciences and Drug Research 14, no. 02 (2020): 171–80. http://dx.doi.org/10.25004/ijpsdr.2022.140203.

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Cancer is a most serious health problem globally due to increased mortality. Deoxycytidine triphosphate pyrophosphatase (dCTPase) enzyme involved in cancer progression and cancer cell stemness and found over-expressed in breast cancer. This overexpression makes it of attractive target to discover new class of anticancer therapy. In the present work, we have selected piperazin-1-ylpyridazine derivatives as dCTPase inhibitors and performed molecular docking and dynamics simulations analysis to evaluate the binding pattern of selected compounds with target protein. Compound P21 has highest bindin

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Khare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, et al. "Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease." Brain Sciences 12, no. 6 (2022): 770. http://dx.doi.org/10.3390/brainsci12060770.

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Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structur

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Hung, Tzu-Chieh, Tung-Ti Chang, Ming-Jen Fan, Cheng-Chun Lee, and Calvin Yu-Chian Chen. "In SilicoInsight into Potent of Anthocyanin Regulation of FKBP52 to Prevent Alzheimer’s Disease." Evidence-Based Complementary and Alternative Medicine 2014 (2014): 1–20. http://dx.doi.org/10.1155/2014/450592.

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Alzheimer’s disease (AD) is caused by the hyperphosphorylation of Tau protein aggregation. FKBP52 (FK506 binding protein 52) has been found to inhibit Tau protein aggregation. This study found six different kinds of anthocyanins that have high binding potential. After analyzing the docking positions, hydrophobic interactions, and hydrogen bond interactions, several amino acids were identified that play important roles in protein and ligand interaction. The proteins’ variation is described using eigenvectors and the distance between the amino acids during a molecular dynamics simulation (MD). T

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Wang, Yuwei, Rui Han, Huimin Zhang, et al. "Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists." BioMed Research International 2017 (2017): 1–18. http://dx.doi.org/10.1155/2017/3572394.

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The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestostero

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Motsilanyane, Andrew Rabontsi, Zimbili Mkhize, and Sphelele Sosibo. "Computational Studies for Selected Medicinal Plants against Dolutegravir using Ligand Based Pharmacophore, Molecular Docking, ADMET Predictionsand Molecular Dynamics Simulation." Pakistan Journal of Medical and Health Sciences 16, no. 1 (2022): 927–36. http://dx.doi.org/10.53350/pjmhs22161927.

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Human immunodeficiency virus type 1 (HIV-1) is the causative agent for acquired immunodeficiency syndrome (AIDS). In 2020, South Africa recorded an estimated 8,2 million people living with HIV. This extensive figure is a red flag to the country, as it causes serious economic burden to its health care system. In the quest for finding a suitable inhibitor for HIV-1 protease, computer aided drug design (CADD) approachstands out to be one of the leading fields of study in pursuit of a new drug for HIV. The Lipinski rule of five was applied in screening the ninety-two plant extracts from Ocium sant

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Nichols, Sara E., Robert V. Swift, and Rommie E. Amaro. "Rational Prediction with Molecular Dynamics for Hit Identification." Current Topics in Medicinal Chemistry 12, no. 18 (2013): 2002–12. http://dx.doi.org/10.2174/1568026611212180007.

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Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, w

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Subasi, Erk, and Cagatay Basdogan. "A New Haptic Interaction and Visualization Approach for Rigid Molecular Docking in Virtual Environments." Presence: Teleoperators and Virtual Environments 17, no. 1 (2008): 73–90. http://dx.doi.org/10.1162/pres.17.1.73.

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Many biological activities take place through the physicochemical interaction of two molecules. This interaction occurs when one of the molecules finds a suitable location on the surface of the other for binding. This process is known as molecular docking, and it has applications to drug design. If we can determine which drug molecule binds to a particular protein, and how the protein interacts with the bonded molecule, we can possibly enhance or inhibit its activities. This information, in turn, can be used to develop new drugs that are more effective against diseases. In this paper, we propo

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Baroroh, Umi, Nur Asni Setiani, Irma Mardiah, Dewi Astriany, and Muhammad Yusuf. "Computational Design of Nanobody Binding to Cortisol to Improve Their Binding Affinity Using Molecular Docking and Molecular Dynamics Simulations." Indonesian Journal of Chemistry 22, no. 2 (2022): 515. http://dx.doi.org/10.22146/ijc.71480.

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Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity. A single and double substitution at positions 53 and 101 have been introduced to the nanobody structure through molecular modeling. The affinity toward cortisol was evaluated using molecular docking to get the binding pose. The highest binding energy pose was used as the initial coordinate to analyze further using 100 ns molecular dynamics si

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Khalil, Ahmed, Amany S. El-Khouly, Eslam B. Elkaeed, and Ibrahim H. Eissa. "The Inhibitory Potential of 2′-dihalo Ribonucleotides against HCV: Molecular Docking, Molecular Simulations, MM-BPSA, and DFT Studies." Molecules 27, no. 14 (2022): 4530. http://dx.doi.org/10.3390/molecules27144530.

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Sofosbuvir is the first approved direct-acting antiviral (DAA) agent that inhibits the HCV NS5B polymerase, resulting in chain termination. The molecular models of the 2′-dihalo ribonucleotides used were based on experimental biological studies of HCV polymerase inhibitors. They were modeled within HCV GT1a and GT1b to understand the structure–activity relationship (SAR) and the binding interaction of the halogen atoms at the active site of NS5B polymerase using different computational approaches. The outputs of the molecular docking studies indicated the correct binding mode of the tested com

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Antes, Iris, Antoine Marion, Chen Zheng, and Okke Melse. "Accurate Prediction of Protein-Ligand Binding by Combined Molecular Dynamics-Based Docking and QM/MM Methods." Biophysical Journal 114, no. 3 (2018): 42a. http://dx.doi.org/10.1016/j.bpj.2017.11.282.

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K. R. Jayanthi, K. R. Jayanthi, K. Hemapriya K. Hemapriya, and Subban Ravi. "Synthesis, Cytotoxicity, Molecular Docking, Molecular Simulation and ADME Properties of Cinnamoylated Chloroquine Hybrid Analogues as Corona Virus Protease Inhibitors." Oriental Journal Of Chemistry 38, no. 1 (2022): 163–71. http://dx.doi.org/10.13005/ojc/380120.

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In an attempt to challenge COVID-19, molecular docking of cinnamoylated chloroquine compounds 1 – 15 against main protease (Mpro) enzyme of SARS-CoV-2 was undertaken. To study the stability of the complex formed between the drug and the receptor, suitable docking possesses were selected and put into molecular dynamics studies. Further ADME properties were determined using SWISS ADME software. In the docking studies compounds 5, 9, 14 and 15 exhibited encouragable binding with the Mpro crystal structure with docking scores of -8.1, -7.9, -7.8 and -7.9 Kcal/mole respectively. It was observed tha

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De Vita, Simona, Maria Giovanna Chini, Giuseppe Bifulco, and Gianluigi Lauro. "Insights into the Ligand Binding to Bromodomain-Containing Protein 9 (BRD9): A Guide to the Selection of Potential Binders by Computational Methods." Molecules 26, no. 23 (2021): 7192. http://dx.doi.org/10.3390/molecules26237192.

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The estimation of the binding of a set of molecules against BRD9 protein was carried out through an in silico molecular dynamics-driven exhaustive analysis to guide the identification of potential novel ligands. Starting from eight crystal structures of this protein co-complexed with known binders and one apo form, we conducted an exhaustive molecular docking/molecular dynamics (MD) investigation. To balance accuracy and an affordable calculation time, the systems were simulated for 100 ns in explicit solvent. Moreover, one complex was simulated for 1 µs to assess the influence of simulation t

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Kar, Rajiv K., Md Yousuf Ansari, Priyanka Suryadevara, et al. "Computational Elucidation of Structural Basis for Ligand Binding withLeishmania donovaniAdenosine Kinase." BioMed Research International 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/609289.

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Enzyme adenosine kinase is responsible for phosphorylation of adenosine to AMP and is crucial for parasites which are purine auxotrophs. The present study describes development of robust homology model ofLeishmania donovaniadenosine kinase to forecast interaction phenomenon with inhibitory molecules using structure-based drug designing strategy. Docking calculation using reported organic small molecules and natural products revealed key active site residues such as Arg131 and Asp16 for ligand binding, which is consistent with previous studies. Molecular dynamics simulation of ligand protein co

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Arcon, Juan Pablo, Carlos P. Modenutti, Demian Avendaño, et al. "AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions." Bioinformatics 35, no. 19 (2019): 3836–38. http://dx.doi.org/10.1093/bioinformatics/btz152.

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Abstract Summary The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein–ligand interactions, such as known ligand pharmacophore or interaction sites derived from cosolvent molecular dynamics. AutoDock Bias is a straightforward and easy to use script-based method that allows the introduction of different types of user-defined biases for fine-tuning AutoDock4 docking calculations. Availability and implementation AutoDock Bias is distributed with MGLTools (since version 1.5.7), and

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Ye, Jiahao, Lin Li, and Zhixi Hu. "Exploring the Molecular Mechanism of Action of Yinchen Wuling Powder for the Treatment of Hyperlipidemia, Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation." BioMed Research International 2021 (October 28, 2021): 1–14. http://dx.doi.org/10.1155/2021/9965906.

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Background. Yinchen Wuling powder is often used to treat clinical hyperlipidemia, although its mechanism of action remains unclear. In this study, we aimed to investigate the active ingredients found in Yinchen Wuling powder and find its mechanism of action when treating hyperlipidemia, using a combination of network pharmacology, molecular docking, and molecular dynamics simulation approaches. Methods. The TCMSP database was used to obtain the principle active ingredients found in Yinchen Wuling powder and the NCBI and DisGeNet databases were used to obtain the main target genes involved in h

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Halim, Sobia Ahsan, Almas Gul Sikandari, Ajmal Khan та ін. "Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation". Biomolecules 11, № 2 (2021): 329. http://dx.doi.org/10.3390/biom11020329.

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Tumor necrosis factor-α (TNF-α) is a drug target in rheumatoid arthritis and several other auto-immune disorders. TNF-α binds with TNF receptors (TNFR), located on the surface of several immunological cells to exert its effect. Hence, the use of inhibitors that can hinder the complex formation of TNF-α/TNFR can be of medicinal significance. In this study, multiple chem-informatics approaches, including descriptor-based screening, 2D-similarity searching, and pharmacophore modelling were applied to screen new TNF-α inhibitors. Subsequently, multiple-docking protocols were used, and four-fold po

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Elengoe, Asita, Mohammed Abu Naser, and Salehhuddin Hamdan. "A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif." International Journal of Genomics 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/391293.

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Currently, protein interaction ofHomo sapiensnucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simu

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Wang, Wei, Minghui Wan, Dongjiang Liao, et al. "Identification of Potent Chloride Intracellular Channel Protein 1 Inhibitors from Traditional Chinese Medicine through Structure-Based Virtual Screening and Molecular Dynamics Analysis." BioMed Research International 2017 (2017): 1–10. http://dx.doi.org/10.1155/2017/4751780.

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Chloride intracellular channel 1 (CLIC1) is involved in the development of most aggressive human tumors, including gastric, colon, lung, liver, and glioblastoma cancers. It has become an attractive new therapeutic target for several types of cancer. In this work, we aim to identify natural products as potent CLIC1 inhibitors from Traditional Chinese Medicine (TCM) database using structure-based virtual screening and molecular dynamics (MD) simulation. First, structure-based docking was employed to screen the refined TCM database and the top 500 TCM compounds were obtained and reranked by X-Sco

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Becerra, Edgardo, Giovanny Aguilera-Durán, Laura Berumen, Antonio Romo-Mancillas, and Guadalupe García-Alcocer. "Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics." Molecules 26, no. 4 (2021): 1051. http://dx.doi.org/10.3390/molecules26041051.

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Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coar

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Akçeşme, Faruk Berat, Nail Beşli, Jorge Peña-García, and Horacio Pérez-Sánchez. "Assessment of Interaction of Human OCT 1-3 Proteins and Metformin Using Silico Analyses." Acta Chimica Slovenica 67, no. 4 (2020): 1202–15. http://dx.doi.org/10.17344/acsi.2020.6108.

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Metformin, a drug frequently used by diabetic patients as the first-line treatment worldwide, is positively charged and is transported into the cell through human organic cation transporter (hOCT 1-3) proteins. We aimed to mimic the cellular uptake of metformin by hOCT1-3 with various bioinformatics methods and tools. 3D structure of OCT1-3 proteins was predicted by considering the structures and function of these proteins. We predicted functional regions (active and ligand binding sites) of OCT1-3 and performed comparative bioinformatics analysis. The predicted structure of hOCT1-3 was then a

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Fu, Yi, Juan Mei, and Ji Zhao. "Probing molecular docking problem by an improved quantum-behaved particle swarm optimization algorithm." Journal of Algorithms & Computational Technology 13 (January 2019): 174830261988112. http://dx.doi.org/10.1177/1748302619881121.

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The main objective of molecular docking is to find a model of interaction between a protein and ligand with a minimum binding energy. This process is driven by intricate algorithms and scoring functions. This paper mainly concentrates on the search algorithm used for solving the docking problem. Here, a new approach is proposed for the molecular docking problem that utilizes a hybrid algorithm that combines an improved quantum-behaved particle swarm optimization algorithm (QPSO) and the Solis and Wets algorithm. The improved QPSO algorithm that is based on individual particle evolutionary proc

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Kapla, Jon, Ismael Rodríguez-Espigares, Flavio Ballante, Jana Selent, and Jens Carlsson. "Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?" PLOS Computational Biology 17, no. 5 (2021): e1008936. http://dx.doi.org/10.1371/journal.pcbi.1008936.

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The determination of G protein-coupled receptor (GPCR) structures at atomic resolution has improved understanding of cellular signaling and will accelerate the development of new drug candidates. However, experimental structures still remain unavailable for a majority of the GPCR family. GPCR structures and their interactions with ligands can also be modelled computationally, but such predictions have limited accuracy. In this work, we explored if molecular dynamics (MD) simulations could be used to refine the accuracy of in silico models of receptor-ligand complexes that were submitted to a c

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Sarkar, Diptendu, and Sk Murtaj Ahamed. "Finding antagonist for the VP24 protein of the Ebola virus to treat infections using molecular docking and molecular dynamics studies." Science Archives 03, no. 04 (2022): 289–300. http://dx.doi.org/10.47587/sa.2022.3408.

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Among all known viruses, Ebola has the unfortunate distinction of having some of the highest case-fatality rates. It is critical that new antivirals be developed to fight Ebola virus infections. A simulated screening of nearly 20 compounds against the revised protein structure of Ebola as represented by the GP24 model resulted in the selection of one molecule (CID 3851453) that may one day be used as an antiviral drug for the Ebola virus. It was found that binding energy was -7.4 Kcal/mol. The physiological and bioactivity parameters were correctly predicted together with ADMET. The 50 ns mole

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Harathi, N., Madhusudana Pulaganti, C. M. Anuradha, and Suresh Kumar Chitta. "Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking." Advances in Bioinformatics 2016 (February 14, 2016): 1–13. http://dx.doi.org/10.1155/2016/9841250.

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The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics.

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Kishk, Safaa M., Rania M. Kishk, Asmaa S. A. Yassen, et al. "Molecular Insights into Human Transmembrane Protease Serine-2 (TMPS2) Inhibitors against SARS-CoV2: Homology Modelling, Molecular Dynamics, and Docking Studies." Molecules 25, no. 21 (2020): 5007. http://dx.doi.org/10.3390/molecules25215007.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), which caused novel corona virus disease-2019 (COVID-19) pandemic, necessitated a global demand for studies related to genes and enzymes of SARS-CoV2. SARS-CoV2 infection depends on the host cell Angiotensin-Converting Enzyme-2 (ACE2) and Transmembrane Serine Protease-2 (TMPRSS2), where the virus uses ACE2 for entry and TMPRSS2 for S protein priming. The TMPRSS2 gene encodes a Transmembrane Protease Serine-2 protein (TMPS2) that belongs to the serine protease family. There is no crystal structure available for TMPS2, therefore, a

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Salehi, Farnaz, Leila Emami, Zahra Rezaei, Soghra Khabnadideh, Behnaz Tajik, and Razieh Sabet. "Fluconazole-Like Compounds as Potential Antifungal Agents: QSAR, Molecular Docking, and Molecular Dynamics Simulation." Journal of Chemistry 2022 (March 31, 2022): 1–16. http://dx.doi.org/10.1155/2022/5031577.

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Today, fungal infection has become more common disease especially in some cases, such as AIDS, cancer, and organ transplant which the immune system is suppressed. On the other hand, due to the increasing resistance to current antifungal drugs, more and more options for design of novel more efficient compounds with higher resistance are needed. In this study, a series of a fluconazole analogues were subjected to quantitative structure-activity relationship analysis to find the structure requirements for modeling adequate candidate. The best multiple linear regression equation was achieved from

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Sundhani, Elza, Agung Endro Nugroho, Arief Nurrochmad, and Endang Lukitaningsih. "Molecular interactions of <i>Andrographis paniculata</i> Burm. f. Active Compound with Nuclear Receptor (CAR and PXR): An In Silico Assessment Approach." Indonesian Journal of Chemistry 22, no. 1 (2022): 126. http://dx.doi.org/10.22146/ijc.67981.

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The study aims to analyze the potential Herb-Drug Interactions (HDIs) of the chemical compound in Andrographis paniculate Burm. f. against Constitutive Androstane Receptor (CAR) and Pregnane X Receptor (PXR). The 1XVP and 1SKX obtained from the Protein Data Bank (PDB) were used as the targeted protein. The molecular docking analysis was done using the Molecular Operating Environment (MOE) and molecular dynamics simulation using Gromacs. The results of the docking analysis showed that 14-Deoxy-11,12-didehydroandrographolide had the strongest binding energy (1XVP-21.0998 Å) with the Arene-H bind

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Ali, Yasir, Hina Imtiaz, Muhammad Mutaal Tahir, et al. "Fragment-Based Approaches Identified Tecovirimat-Competitive Novel Drug Candidate for Targeting the F13 Protein of the Monkeypox Virus." Viruses 15, no. 2 (2023): 570. http://dx.doi.org/10.3390/v15020570.

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Monkeypox is a serious public health issue in tropical and subtropical areas. Antivirals that target monkeypox proteins might lead to more effective and efficient therapy. The F13 protein is essential for the growth and maturation of the monkeypox virus. F13 inhibition might be a viable therapeutic target for monkeypox. The in silico fragment-based drug discovery method for developing antivirals may provide novel therapeutic options. In this study, we generated 800 compounds based on tecovirimat, an FDA-approved drug that is efficacious at nanomolar quantities against monkeypox. These compound

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Huang, Hung-Jin, Cheng-Chun Lee, and Calvin Yu-Chian Chen. "Lead Discovery for Alzheimer’s Disease Related Target Protein RbAp48 from Traditional Chinese Medicine." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/764946.

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Deficiency or loss of function of Retinoblastoma-associated proteins (RbAp48) is related with Alzheimer’s disease (AD), and AD disease is associated with age-related memory loss. During normal function, RbAp48 forms a complex with the peptide FOG-1 (friend of GATA-1) and has a role in gene transcription, but an unstable complex may affect the function of RbAp48. This study utilizes the world’s largest traditional Chinese medicine (TCM) database and virtual screening to provide potential compounds for RbAp48 binding. A molecular dynamics (MD) simulation was employed to understand the variations

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Patra, Madhumita Dandopath. "Structural Studies on Different Ligand Binding Ability of Sialoadhesin Using Molecular Modeling Techniques." Asian Journal of Organic & Medicinal Chemistry 5, no. 4 (2020): 277–82. http://dx.doi.org/10.14233/ajomc.2020.ajomc-p279.

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Siglecs are the major homologous subfamily of I-type lectins with an ability to recognize sialylated glycans. Siglecs are attractive therapeutic targets because of their endocytic properties, ability to modulate receptor signaling and cell-type specific expression pattern. Sialoadhesin (Sn/ Siglec-1/ CD169), a member of the Siglec family expressed on subsets of resident and inflammatory macrophages and involves in modulation of inflammation and immunity. In this work, 3-D structure of human Siglec-1 (hSiglec-1) was predicted based on X-ray crystallo-graphically determined structure of mouse Si

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