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Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs

https://doi.org/10.1073/pnas.2010470117
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Tree-Guided Graph Neural Networks with Multilevel Optimization for Protein–Protein Interaction Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01066openalex-snapshot
Modeling the Sensitivity of Large-Scale Virtual Screening to Scoring Function Accuracy, Artifacts, and Library Composition
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00602openalex-snapshot
Mutexa: A Computational Ecosystem for Intelligent Protein Engineering
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c01661openalex-snapshot
Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c02026openalex-snapshot
BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00930openalex-snapshot
Charged Systems in Absolute Binding Free Energy Calculations: An Analytical Electrostatic Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c01030openalex-snapshot
Alchemical Free-Energy Framework for Multiresidue Reoptimization of Antimicrobial Peptide-Membrane Affinity
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c01475openalex-snapshot
Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c00796openalex-snapshot
Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c00627openalex-snapshot
PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c00869openalex-snapshot
Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c03043openalex-snapshot
Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c10718openalex-snapshot
Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c02123openalex-snapshot
Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04370openalex-snapshot
Standard Binding Free-Energy Calculations: How Far Are We from Automation?
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6c02208openalex-snapshot
Predicting Nirmatrelvir Resistance in SARS-CoV-2 M pro Mutants with an Integrated Computational Framework
inferred← citeshttps://doi.org/10.1021/acs.jpclett.2c01193openalex-snapshot
Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV-2
inferred← citeshttps://doi.org/10.1021/acs.jpclett.4c02656openalex-snapshot
RED-E-Function-Based Equilibrium Parameter Finder: Finding the Best Restraint Parameters in Absolute Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jpclett.5c00525openalex-snapshot
Zooming across the Alchemical Space
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00637openalex-snapshot
COVID-19: The Effect of Host Genetic Variations on Host–Virus Interactions
inferred← citeshttps://doi.org/10.1021/acscentsci.1c00910openalex-snapshot
Evaluation of SARS-CoV-2 Main Protease Inhibitors Using a Novel Cell-Based Assay
inferred← citeshttps://doi.org/10.1021/acsomega.2c05376openalex-snapshot
Predicting In Vitro and In Vivo Anti-SARS-CoV-2 Activities of Antivirals by Intracellular Bioavailability and Biochemical Activity
inferred← citeshttps://doi.org/10.1021/acsomega.3c06968openalex-snapshot
Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data
inferred← citeshttps://doi.org/10.1021/acsptsci.0c00074openalex-snapshot
Potential Therapeutic Agents and Associated Bioassay Data for COVID-19 and Related Human Coronavirus Infections
inferred← citeshttps://doi.org/10.1021/acsptsci.0c00215openalex-snapshot
A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics
inferred← citeshttps://doi.org/10.1038/s41534-023-00696-7openalex-snapshot
Towards practical and massively parallel quantum computing emulation for quantum chemistry
inferred← citeshttps://doi.org/10.1038/s41579-024-01036-yopenalex-snapshot
COVID-19 drug discovery and treatment options
inferred← citeshttps://doi.org/10.1038/s41598-020-77602-0openalex-snapshot
In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis
inferred← citeshttps://doi.org/10.1038/s41598-021-93500-5openalex-snapshot
Informing selection of drugs for COVID-19 treatment through adverse events analysis
inferred← citeshttps://doi.org/10.1038/s41598-025-88388-4openalex-snapshot
Identification of potential SARS-CoV-2 inhibitors among well-tolerated drugs using drug repurposing and in vitro approaches
inferred← citeshttps://doi.org/10.1038/s42255-021-00479-4openalex-snapshot
Pharmacological inhibition of fatty acid synthesis blocks SARS-CoV-2 replication
inferred← citeshttps://doi.org/10.1039/d0ra09858bopenalex-snapshot
Binding of inhibitors to the monomeric and dimeric SARS-CoV-2 Mpro
inferred← citeshttps://doi.org/10.1039/d1ra02529eopenalex-snapshot
Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1039/d1ra03852dopenalex-snapshot
Potential inhibitors for SARS-CoV-2 Mpro from marine compounds
inferred← citeshttps://doi.org/10.1039/d1ra06534copenalex-snapshot
Searching and designing potential inhibitors for SARS-CoV-2 Mpro from natural sources using atomistic and deep-learning calculations
inferred← citeshttps://doi.org/10.1039/d1ra07584eopenalex-snapshot
The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies
inferred← citeshttps://doi.org/10.1039/d1ra08752eopenalex-snapshot
Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M pro
inferred← citeshttps://doi.org/10.1039/d1sc05892dopenalex-snapshot
Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation
inferred← citeshttps://doi.org/10.1039/d2cp03681aopenalex-snapshot
Optimization of potential non-covalent inhibitors for the SARS-CoV-2 main protease inspected by a descriptor of the subpocket occupancy
inferred← citeshttps://doi.org/10.1039/d2cp04476eopenalex-snapshot
Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches
inferred← citeshttps://doi.org/10.1039/d2sc05837eopenalex-snapshot
Peptide valence-induced breaks in plasmonic coupling
inferred← citeshttps://doi.org/10.1039/d4ra00692eopenalex-snapshot
Alchemical approach performance in calculating the ligand-binding free energy
inferred← citeshttps://doi.org/10.1039/d5cp00380fopenalex-snapshot
Molecular dynamics-driven drug discovery
inferred← citeshttps://doi.org/10.1055/s-0040-1714273openalex-snapshot
Pharmacotherapy for Prevention and Management of Thrombosis in COVID-19
inferred← citeshttps://doi.org/10.1073/pnas.2024420118openalex-snapshot
Dipyridamole, chloroquine, montelukast sodium, candesartan, oxytetracycline, and atazanavir are not SARS-CoV-2 main protease inhibitors
inferred← citeshttps://doi.org/10.1073/pnas.2024937118openalex-snapshot
Reply to Ma and Wang: Reliability of various in vitro activity assays on SARS-CoV-2 main protease inhibitors
inferred← citeshttps://doi.org/10.1073/pnas.2106095118openalex-snapshot
Inhibitor potency and assay conditions: A case study on SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1073/pnas.2108209118openalex-snapshot
Reply to Behnam and Klein: Potential role of the His-tag in C-terminal His-tagged SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1080/03639045.2021.1934857openalex-snapshot
Reckoning γ-Glutamyl-S-allylcysteine as a potential main protease (mpro) inhibitor of novel SARS-CoV-2 virus identified using docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/07391102.2021.1967786openalex-snapshot
Venetoclax: a promising repurposed drug against SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1080/07391102.2021.1972041openalex-snapshot
Discovery of novel inhibitors of SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1080/07391102.2022.2036640openalex-snapshot
Accelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBD
inferred← citeshttps://doi.org/10.1080/07391102.2022.2054470openalex-snapshot
Computational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1080/07391102.2022.2112618openalex-snapshot
Interaction of panduratin A and derivatives with the SARS-CoV-2 main protease (m pro ): a molecular docking study
inferred← citeshttps://doi.org/10.1080/10406638.2022.2036777openalex-snapshot
Synthetic Aromatic Organic Compounds Bearing 4, 4-Dimethyl-3-Thiosemicarbazide Moiety: Theoretical and Experimental Approach
inferred← citeshttps://doi.org/10.1080/1062936x.2024.2375513openalex-snapshot
A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods
inferred← citeshttps://doi.org/10.1080/14786419.2023.2241973openalex-snapshot
Invalidation of geraniin as a potential inhibitor against SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1080/17460441.2025.2468289openalex-snapshot
High performance-oriented computer aided drug design approaches in the exascale era
inferred← citeshttps://doi.org/10.1093/bib/bbaa422openalex-snapshot
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19
inferred← citeshttps://doi.org/10.1093/bib/bbab491openalex-snapshot
BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution
inferred← citeshttps://doi.org/10.1093/bib/bbac604openalex-snapshot
Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human–virus protein–protein interactions
inferred← citeshttps://doi.org/10.1093/nsr/nwab105openalex-snapshot
Perspective of drug design with high-performance computing
inferred← citeshttps://doi.org/10.1098/rsos.211480openalex-snapshot
Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations
inferred← citeshttps://doi.org/10.1098/rsos.252347openalex-snapshot
Computational identification of potential inhibitors for chikungunya virus nsP2pro
inferred← citeshttps://doi.org/10.1101/2020.05.26.114033openalex-snapshot
Enantiomers of Chloroquine and Hydroxychloroquine Exhibit Different Activities Against SARS-CoV-2 in vitro , Evidencing S -Hydroxychloroquine as a Potentially Superior Drug for COVID-19
inferred← citeshttps://doi.org/10.1101/2021.06.08.447613openalex-snapshot
Cellular Activities of SARS-CoV-2 Main Protease Inhibitors Reveal Their Unique Characteristics
inferred← citeshttps://doi.org/10.1101/2021.12.18.473330openalex-snapshot
The N -Terminal Carbamate is Key to High Cellular and Antiviral Potency for Boceprevir-Based SARS-CoV-2 Main Protease Inhibitors
inferred← citeshttps://doi.org/10.1101/2022.11.05.515305openalex-snapshot
Novel inhibitors against COVID-19 main protease suppressed viral infection
inferred← citeshttps://doi.org/10.1109/access.2020.3009328openalex-snapshot
Artificial Intelligence (AI) and Big Data for Coronavirus (COVID-19) Pandemic: A Survey on the State-of-the-Arts
inferred← citeshttps://doi.org/10.1109/sc41404.2022.00019openalex-snapshot
Large-Scale Simulation of Quantum Computational Chemistry on a New Sunway Supercomputer
inferred← citeshttps://doi.org/10.1111/jcpt.13251openalex-snapshot
Neutrophil elastase inhibitor (sivelestat) may be a promising therapeutic option for management of acute lung injury/acute respiratory distress syndrome or disseminated intravascular coagulation in COVID‐19
inferred← citeshttps://doi.org/10.1128/mbio.00784-22openalex-snapshot
Gain-of-Signal Assays for Probing Inhibition of SARS-CoV-2 M pro /3CL pro in Living Cells
inferred← citeshttps://doi.org/10.1140/epjp/s13360-021-01657-9openalex-snapshot
Role of plasmonics in detection of deadliest viruses: a review
inferred← citeshttps://doi.org/10.1155/2022/2044282openalex-snapshot
Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies
inferred← citeshttps://doi.org/10.1177/10943420221117797openalex-snapshot
Free energy perturbation–based large-scale virtual screening for effective drug discovery against COVID-19
inferred← citeshttps://doi.org/10.1177/1358863x20932640openalex-snapshot
COVID–19-associated coagulopathy: An exploration of mechanisms
inferred← citeshttps://doi.org/10.1177/1934578x21991723openalex-snapshot
Rutin: A Potential Antiviral for Repurposing as a SARS-CoV-2 Main Protease (M pro ) Inhibitor
inferred← citeshttps://doi.org/10.1186/s13321-025-01022-3openalex-snapshot
Moldrug algorithm for an automated ligand binding site exploration by 3D aware molecular enumerations
inferred← citeshttps://doi.org/10.1186/s13578-021-00720-3openalex-snapshot
Development of a simple and miniaturized sandwich-like fluorescence polarization assay for rapid screening of SARS-CoV-2 main protease inhibitors
inferred← citeshttps://doi.org/10.1186/s43088-023-00406-4openalex-snapshot
Identification of possible SARS-CoV-2 main protease inhibitors: in silico molecular docking and dynamic simulation studies
inferred← citeshttps://doi.org/10.13040/ijpsr.0975-8232.12(5).2950-56openalex-snapshot
inferred← citeshttps://doi.org/10.1371/journal.pone.0272941openalex-snapshot
Nicotine has no significant cytoprotective activity against SARS-CoV-2 infection
inferred← citeshttps://doi.org/10.1371/journal.pone.0277328openalex-snapshot
Repositioning of anti-dengue compounds against SARS-CoV-2 as viral polyprotein processing inhibitor
inferred← citeshttps://doi.org/10.17576/jsm-2023-5212-04openalex-snapshot
Characterisation of Recombinant 3CL Protease from SARS-CoV-2 Produced in E. coli BL21 (DE3) for Screening Anti-Covid Drug Candidates using Rhodamine 110-Synthetic Peptide Conjugate as A Substrate
inferred← citeshttps://doi.org/10.17576/jsm-2024-5305openalex-snapshot
inferred← citeshttps://doi.org/10.17576/jsm-2024-5305-01openalex-snapshot
Unlocking Therapeutic Potential: Identifying Small Molecule Inhibitors for Sars-Cov-2 Variants' Main Protease (MPRO) Through Molecular Docking Analysis
inferred← citeshttps://doi.org/10.17749/2070-4909/farmakoekonomika.2022.135openalex-snapshot
Dietary factors influencing the COVID-19 epidemic process
inferred← citeshttps://doi.org/10.18502/ijaai.v20i4.6948openalex-snapshot
Montelukast and Coronavirus Disease 2019: A Scoping Review
inferred← citeshttps://doi.org/10.20944/preprints202308.1518.v1openalex-snapshot
A Molecular Modeling and Molecular Dynamics Simulations Investigation of the Potential Therapeutic Applications of Main Protease Inhibitors for SARS-CoV-2
inferred← citeshttps://doi.org/10.21055/preprints-3111986openalex-snapshot
The development and outcomes of the COVID-19 disease correlate with the type of nutrition
inferred← citeshttps://doi.org/10.21203/rs.3.rs-27313/v1openalex-snapshot
Exploring structurally diverse plant secondary metabolites as a potential source of drug targeting different molecular mechanisms of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pathogenesis: An in silico approach
inferred← citeshttps://doi.org/10.2142/biophysico.bppb-v18.022openalex-snapshot
Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.2144/fsoa-2023-0112openalex-snapshot
SARS-CoV-2-induced phosphorylation and its pharmacotherapy backed by artificial intelligence and machine learning
inferred← citeshttps://doi.org/10.2147/aabc.s393084openalex-snapshot
In silico Screening of Potential SARS-CoV-2 Main Protease Inhibitors from Thymus schimperi
inferred← citeshttps://doi.org/10.2147/dddt.s320320openalex-snapshot
COVID-19: Vaccine Delivery System, Drug Repurposing and Application of Molecular Modeling Approach
inferred← citeshttps://doi.org/10.21577/0103-5053.20210061openalex-snapshot
DFT, Molecular Docking, and ADME/Tox Screening Investigations of Market‑Available Drugs against SARS‑CoV‑2
inferred← citeshttps://doi.org/10.2174/0115701638253929230922115127openalex-snapshot
Drug Repositioning: A Monetary Stratagem to Discover a New Application of Drugs
inferred← citeshttps://doi.org/10.2174/0929867330666230321103731openalex-snapshot
Exploring Scoring Function Space: Developing Computational Models for Drug Discovery
inferred← citeshttps://doi.org/10.2174/1874467214666210906125959openalex-snapshot
Structural Understanding of SARS-CoV-2 Drug Targets, Active Site Contour Map Analysis and COVID-19 Therapeutics
inferred← citeshttps://doi.org/10.2174/2212697x08666211210103711openalex-snapshot
Hydroxychloroquine (HCQ) Exhibits Better Binding to the Main Protease (Mpro) Compared to Spike Protein (S protein) of SARS-CoV-2: An In-silico Analysis
inferred← citeshttps://doi.org/10.2196/19515openalex-snapshot
Using Information Technology to Manage the COVID-19 Pandemic: Development of a Technical Framework Based on Practical Experience in China
inferred← citeshttps://doi.org/10.26434/chemrxiv.13096157openalex-snapshot
A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery
inferred← citeshttps://doi.org/10.26434/chemrxiv.13292768openalex-snapshot
Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2’s Spike Protein
inferred← citeshttps://doi.org/10.26434/chemrxiv.13292768.v1openalex-snapshot
Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2’s Spike Protein
inferred← citeshttps://doi.org/10.26434/chemrxiv.13292768.v2openalex-snapshot
Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2’s Spike Protein
inferred← citeshttps://doi.org/10.26434/chemrxiv.13318523openalex-snapshot
A Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV2 Mpro
inferred← citeshttps://doi.org/10.26434/chemrxiv.13318523.v1openalex-snapshot
A Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV2 Mpro
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