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Effect of Flap Mutation I54L/M in Inhibition of Human Immunodeficiency Virus Type 1 Protease: Relationship to Drug Resistance

Rituraj Purohit
2010 Journal of computer science and systems biology  
The flap mutation I54M and I54L lowers the binding affinity of Darunavir by altering the position of binding site residues in 3D space.  ...  The HIV-1 protease enzyme is one of the prime and an utmost essentially important target towards the HIV therapy.  ...  Acknowledgment The authors thank the management of Vellore Institute of Technology University for providing the facilities to carry out this work.  ... 
doi:10.4172/jcsb.1000062 fatcat:tu7jwcnoerb6pkhmoxplu7yii4

Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function

Sergey Shityakov, Thomas Dandekar
2010 Bioinformation  
Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease.  ...  For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated  ...  Acknowledgments: The authors are grateful to the DFG (SFB630/C6, Da 208/11-1) and the IZKF (Interdisziplinäres Zentrum für Klinische Forschung der Universität Würzburg) for the support of this work.  ... 
doi:10.6026/97320630004295 pmid:20978602 pmcid:PMC2957763 fatcat:mvepovxe5ffi3opo4iwuiaepbe

HIV-PDI: A Protein Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 2. Examples of Use and Proof-of-Concept

GHEMTIO Leo, SOUCHET Michel, DJIKENG Appolinaire,, KEMINSE Lionel, KELBERT Patricia
2011 Journal of Health & Medical Informatics  
This work was supported in part by Region Lorraine within the framework of the PRST MISN (MBI operation).  ...  Acknowledgments The authors thank the Bill & Melinda Gates Foundation for financial support through the Grand Challenge Exploration grant N° 52034 (Round I).  ...  Another type of evidence that may be obtained from HIV-PDI concerning this patient is the shape of the binding site cavity in the mutated protease.  ... 
doi:10.4172/2157-7420.1000105 fatcat:f2zttzyqivetrfn4dyl66kcfxi

Future appeal of comparative studies on putative binding sites of HIV-1 virus-encoded proteolytic enzyme inhibitor of different Food and Drug Administration-approved compounds

Zainularifeen Abduljaleel, Mohammad Athar, Faisal Al-Allaf, Saied Al-Dehlawi, Sami Melebari, Waseem El-Huneidi
2020 HIV & AIDS Review. International Journal of HIV-Related Problems  
Results of this comparative binding mode analysis of seven FDA-approved drugs could be potential and useful for designing of a new effective inhibitor of HIV-1 protease.  ...  Results: The binding mode analysis showed that the active site was present at the interface of two chains A and B of the enzyme and the crucial amino acid remained responsible for the binding of inhibitors  ...  Acknowledgment The authors would like to thank the Makkah Regional Laboratories and the Umm Al-Qura University, Kingdom of Saudi Arabia for the continuous support of the research.  ... 
doi:10.5114/hivar.2020.96402 doaj:9ef9170fe08e4c808f320996efd3ebf7 fatcat:wpct7f3fy5hgnjv44edcorxmri

Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach

Majid Masso, Iosif I Vaisman
2003 Biochemical and Biophysical Research Communications - BBRC  
in HIV-1 protease.  ...  Profiles of residue scores derived from the four-body statistical potential are constructed for all 1881 mutants of the HIV-1 protease monomer and compared with the profile of the wild-type protein.  ...  Acknowledgments This work was supported in part by a pilot grant from the UNC Center for AIDS Research. We thank Zhibin Lu for his help with writing codes used in this study.  ... 
doi:10.1016/s0006-291x(03)00760-5 pmid:12745077 fatcat:ffqyrffkebhjlk6ivdn6cpv4yy

Small Molecules of Natural Origin as Potential Anti-HIV Agents: A Computational Approach

Luminita Crisan, Alina Bora
2021 Life  
Lys101, Tyr181, Tyr188, Trp229, and Tyr318 residues and free-binding energies have proved that ligands can stably bind to HIV-1 RT.  ...  These findings may open new avenues to guide the rational design of novel HIV-1 NNRTIs.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/life11070722 fatcat:5hrb5c4mnbd7tkmd32x4i37pma

Seeking novel leads through structure-based pharmacophore design

Luke S. Fisher, Osman F. Güner
2002 Journal of the Brazilian Chemical Society  
Este procedimento foi aplicado para inibidores da protease do vírus HIV-1.  ...  This procedure was applied to HIV-1 protease inhibitors. Several compounds retrieved by the top pharmacophore model were identified as moderately active (in µMolar range).  ...  Acknowledgments The authors would like to express gratitude to Omoshile Clement and Marvin Waldman for their critical review of this manuscript.  ... 
doi:10.1590/s0103-50532002000600008 fatcat:7wtk36eiofgvbnyvgf4m5mokbi

Multidimensional QSAR Modeling of Amprenavir Derivatives as HIV-Protease Inhibitors

Sonal Dubey, G. Gowtham
2011 Open Journal of Medicinal Chemistry  
A computational study has been performed on a series of 55 compounds having (S)-N-(3-(N-(cyclopen-tylmethyl) substituted-phenylsulfonamido)-2-hydroxypropyl) acetamide backbone as HIV-1 protease inhibitors  ...  The information obtained from these 3-D contour maps can be used for the design of amprenavir analogs possessing better protease inhibitory activity.  ...  Acknowledgements We wish to express our gratitude to Department of Science and Technology and All India Council for Technical Education, Govt. of India, New Delhi, India, for their financial assistance  ... 
doi:10.4236/ojmc.2011.11001 fatcat:5whl6xeas5htvfwvon4j3sybuu

HIV-PDI: A Protein-Drug Interaction Resource for Structural Analyses of HIV Drug Resistance: 1. Concepts and Associated Database

GHEMTIO Leo, SMAÏL-TABBONE Malika, DJIKENG Ap polinaire, DEVIGNES Mari e-Dominique, KEMINSE L ionel
2011 Journal of Health & Medical Informatics  
This work was also supported in part by Region Lorraine within the framework of the PRST MISN (MBI operation).  ...  Acknowledgments The authors thank the Bill & Melinda Gates Foundation for financial support through the Grand Challenge Exploration grant N° 52034 (Round I).  ...  the shape of its ligand binding site.  ... 
doi:10.4172/2157-7420.1000104 fatcat:odjpzcb6n5h6pp3dho5hyclrgy

An Allosteric Modulator of HIV-1 Protease Shows Equipotent Inhibition of Wild-Type and Drug-Resistant Proteases

Peter M.-U. Ung, James B. Dunbar, Jason E. Gestwicki, Heather A. Carlson
2014 Journal of Medicinal Chemistry  
NMR and MD simulations have demonstrated that the flaps of HIV-1 protease (HIV-1p) adopt a range of conformations that are coupled with its enzymatic activity.  ...  MD simulations of the ligand-protein complex show that NIT stably binds in the Eye site and restricts the flaps.  ...  To examine the change in the dynamic behaviors of HIV-1p due to the binding of NIT to the Eye site, essential dynamics analysis was applied to analyze the MD trajectories of NIT− protease complex and an  ... 
doi:10.1021/jm5008352 pmid:25062388 pmcid:PMC4136727 fatcat:vrsjclostjgevoub2ngm75uoke

In Silico Insights into the SARS CoV-2 Main Protease Suggest NADH Endogenous Defences in the Control of the Pandemic Coronavirus Infection

Annamaria Martorana, Carla Gentile, Antonino Lauria
2020 Viruses  
The proposed in silico findings identified new potential SARS CoV-2 main protease (MPRO) inhibitors that fit in the catalytic binding site of SARS CoV-2 MPRO.  ...  The clinical treatment of the severe acute respiratory syndrome (SARS) CoV-2 is currently based on the experimental administration of HIV antiviral drugs, such as lopinavir, ritonavir, and remdesivir (  ...  binding site of the protease.  ... 
doi:10.3390/v12080805 pmid:32722574 fatcat:pofbtyrh6vfvte44y5mawzquem

Mapping the 3D structures of small molecule binding sites

Joshua Meyers, Nathan Brown, Julian Blagg
2016 Journal of Cheminformatics  
Analysis of the 3D structures of protein-ligand binding sites can provide valuable insights for drug discovery.  ...  Clustering combined with intuitive visualization tools can be applied to map relationships between the 3D structures of protein binding sites.  ...  Yi Mok for his helpful guidance and comments on the manuscript. Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13321-016-0180-0 fatcat:73f2jlg3prgptgqhopojqveame

MoleGear: A Java-Based Platform for Evolutionary De Novo Molecular Design

Chu, He
2019 Molecules  
The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design.  ...  of binding free energy or a weighted-sum multi-objective fitness function.  ...  The authors acknowledge the Research Council of Norway for the funding in publishing this work through the CO2Hing project (#267615).  ... 
doi:10.3390/molecules24071444 fatcat:3a4tkj63nnh6jgql3jpauziqpy

Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations

Ekachai Jenwitheesuk, Ram Samudrala
2003 BMC Structural Biology  
Docking experiments were undertaken using the program AutoDock for twenty-five HIV-1 protease-inhibitor complexes determined by x-ray crystallography.  ...  This study describes the improvement of protein-ligand binding energy prediction by incorporating protein flexibility through the use of molecular dynamics (MD) simulations.  ...  We thank members of the Samudrala group for helpful comments.  ... 
pmid:12675950 pmcid:PMC154089 fatcat:ovvr34gsnvdt7eib6ckpjyzhza

Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection

Jian J. Tan, Xiao J. Cong, Li M. Hu, Cun X. Wang, Lee Jia, Xing-Jie Liang
2010 Drug Discovery Today  
This review presents details of the anti-HIV inhibitors discovered with computer-aided approaches and provides an overview of the recent five-year achievements in the treatment of HIV infection and the  ...  Most currently used anti-HIV drugs are reverse transcriptase inhibitors or protease inhibitors.  ...  Acknowledgements The authors thank Chinese Natural Science Foundation project  ... 
doi:10.1016/j.drudis.2010.01.004 pmid:20096804 pmcid:PMC2910421 fatcat:xnewf4jw2zfnhhlosgrazpz7di
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