ArticleStructure (London, England : 1993)2009
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance.
Article in Structure (London, England : 1993), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- HIV Genome-Wide Protein Associations: a Review of 30 Years of Research.Microbiology and molecular biology reviews : MMBR · 2016Pooled it
- Unveiling the molecular activity of HIV towards the CD4: A study based on subtype C via docking and dynamics approach.Journal, genetic engineering & biotechnology · 2025Article
- FMO-guided design of darunavir analogs as HIV-1 protease inhibitors.Scientific reports · 2024Article
- Evolving Mutational Buildup in HIV-1 Protease Shifts Conformational Dynamics to Gain Drug Resistance.Journal of chemical information and modeling · 2023Article
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- Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates.Scientific reports · 2022Article
- Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.ACS catalysis · 2021Article
- Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2.International journal of molecular sciences · 2021Article
- On the cutting edge: protease-based methods for sensing and controlling cell biology.Nature methods · 2020Review
- Interdependence of Inhibitor Recognition in HIV-1 Protease.Journal of chemical theory and computation · 2017Article
- Hypothesis onPeerJ · 2016Article
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- In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2.Biochemistry · 2012Article
- Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity.PLoS computational biology · 2011Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Drug-resistant mutations (DRMs) in HIV-1 protease are a major challenge to antiretroviral therapy. Protease-substrate interactions that are determined to be critical for native selectivity could serve as robust targets for drug design that are immune to DRMs. In order to identify the structural mechanisms of selectivity, we developed a peptide-docking algorithm to predict the atomic structure of protease-substrate complexes and applied it to a large and diverse set of cleavable and noncleavable peptides. Cleavable peptides showed significantly lower energies of interaction than noncleavable peptides with six protease active-site residues playing the most significant role in discrimination. Surprisingly, all six residues correspond to sequence positions associated with drug resistance mutations, demonstrating that the very residues that are responsible for native substrate specificity in HIV-1 protease are altered during its evolution to drug resistance, suggesting that drug resistance and substrate selectivity may share common mechanisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.