Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease
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Summary
This study provides a proof of concept for the integration of MM/GBSA energy analysis and drug resistance information at the stage of virtual screening and sheds light on future HIV drug design and the use of virtual screenings to combat drug resistance.
- Type
- article
- Published
- 2015-06-16
- Cited by
- 20
- References
- 76
- OpenAlex
- https://openalex.org/W305648487
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:7815201
Keywords
Virtual screening, Protease, Drug resistance, HIV-1 protease, Drug
References
- Human immunodeficiency virus reverse transcriptase and protease sequence database
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- P1 and P1' para-fluoro phenyl groups show enhanced binding and favorable predicted pharmacological properties: structure-based virtual screening of extended lopinavir analogs against multi-drug resistant HIV-1 protease
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- Comparison of simple potential functions for simulating liquid water
- Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.
- Folded Monomer of HIV-1 Protease*
- Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
- Ligand Pose and Orientational Sampling in Molecular Docking
- Semiempirical molecular orbital calculations with linear system size scaling
- The particle concept: placing discrete water molecules during protein‐ligand docking predictions
- Solution Structure of the Mature HIV-1 Protease Monomer
- Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
- Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures
- Automatic atom type and bond type perception in molecular mechanical calculations.
- Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.
Cited by
- Reaching beyond HIV/HCV: nelfinavir as a potential starting point for broad-spectrum protease inhibitors against dengue and chikungunya virus
- Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models
- Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends.
- Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study
- The in silico identification of human bile salt export pump (ABCB11) inhibitors associated with cholestatic drug-induced liver injury.
- Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2.
- The molecular mechanism of two coreceptor binding site antibodies X5 and 17b neutralizing HIV‐1: Insights from molecular dynamics simulation
- Insight into tetrodotoxin blockade and resistance mechanisms of Nav1.2 sodium channel by theoretical approaches
- Exploring the binding mechanisms of PDE5 with chromeno[2,3-c]pyrrol-9(2H)-one by theoretical approaches
- Classification of HIV-1 Protease Inhibitors by Machine Learning Methods
- Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry
- End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
- A computational approach yields selective inhibitors of human excitatory amino acid transporter 2 (EAAT2)
- The design of compounds with desirable properties – The anti‐HIV case study
- Inhibitory selectivity to the AKR1B10 and aldose reductase (AR): insight from molecular dynamics simulations and free energy calculations
- Pharmacophore-Assisted Covalent Docking Identifies a Potential Covalent Inhibitor for Drug-Resistant Genotype 3 Variants of Hepatitis C Viral NS3/4A Serine Protease
- Computational study on the mechanism of small molecules inhibiting NLRP3 with ensemble docking and molecular dynamic simulations
- Pharmacophore-Assisted Covalent Docking Identifies a Potential Covalent Inhibitor for Drug-Resistant Genotype 3 Variants of Hepatitis C Viral NS3/4A Serine Protease
- Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery
- HIV / HCV : nel fi navir as a potential starting point for broad-spectrum protease inhibitors against dengue and chikungunya virus †
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