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Large library docking for novel SARS‐CoV ‐2 main protease non‐covalent and covalent inhibitors

https://doi.org/10.1002/pro.4712
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Targeting the Main Protease of SARS‐CoV‐2: From the Establishment of High Throughput Screening to the Design of Tailored Inhibitors
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Discovery of Potent Pyrazoline‐Based Covalent SARS‐CoV‐2 Main Protease Inhibitors**
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A Quick Route to Multiple Highly Potent SARS‐CoV‐2 Main Protease Inhibitors**
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
inferredcites →https://doi.org/10.1002/pro.4712openalex-snapshot
Large library docking for novel SARS‐CoV ‐2 main protease non‐covalent and covalent inhibitors
inferredcites →https://doi.org/10.1007/s10822-013-9644-8openalex-snapshot
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
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Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease
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Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase
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Structure-based virtual screening against SARS-3CLpro to identify novel non-peptidic hits
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Synthesis and evaluation of isatin derivatives as effective SARS coronavirus 3CL protease inhibitors
inferredcites →https://doi.org/10.1016/j.bmcl.2008.08.082openalex-snapshot
Design, synthesis and antiviral efficacy of a series of potent chloropyridyl ester-derived SARS-CoV 3CLpro inhibitors
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Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding
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Structure-based discovery of conformationally selective inhibitors of the serotonin transporter
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High-Throughput Screening Identifies Inhibitors of the SARS Coronavirus Main Proteinase
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Stable Benzotriazole Esters as Mechanism-Based Inactivators of the Severe Acute Respiratory Syndrome 3CL Protease
inferredcites →https://doi.org/10.1016/j.chembiol.2021.05.018openalex-snapshot
An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor
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Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites
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Improved SARS-CoV-2 Mpro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies
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Discovery of SARS-CoV-2 main protease covalent inhibitors from a DNA-encoded library selection
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Discovery of boceprevir, a direct-acting NS3/4A protease inhibitor for treatment of chronic hepatitis C infections
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On the size of the active site in proteases. I. Papain
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Electrostatic Contributions to Heat Capacity Changes of DNA-Ligand Binding
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Potent and selective inhibitors of the proteasome: Dipeptidyl boronic acids
inferredcites →https://doi.org/10.1021/acs.biochem.2c00489openalex-snapshot
Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening
inferredcites →https://doi.org/10.1021/acs.jcim.0c00598openalex-snapshot
Property-Unmatched Decoys in Docking Benchmarks
inferredcites →https://doi.org/10.1021/acs.jcim.0c00675openalex-snapshot
ZINC20─A Free Ultralarge-Scale Chemical Database for Ligand Discovery
inferredcites →https://doi.org/10.1021/acs.jcim.1c00368openalex-snapshot
Ligand Strain Energy in Large Library Docking
inferredcites →https://doi.org/10.1021/acs.jcim.1c00851openalex-snapshot
High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor
inferredcites →https://doi.org/10.1021/acs.jcim.5b00559openalex-snapshot
ZINC 15 – Ligand Discovery for Everyone
inferredcites →https://doi.org/10.1021/acs.jmedchem.0c01019openalex-snapshot
Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4
inferredcites →https://doi.org/10.1021/acs.jmedchem.0c01063openalex-snapshot
Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19
inferredcites →https://doi.org/10.1021/acs.jmedchem.0c02253openalex-snapshot
A Crowding Barrier to Protein Inhibition in Colloidal Aggregates
inferredcites →https://doi.org/10.1021/acs.jmedchem.1c00598openalex-snapshot
Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro )
inferredcites →https://doi.org/10.1021/acs.jmedchem.1c01547openalex-snapshot
Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens
inferredcites →https://doi.org/10.1021/acs.jmedchem.1c02031openalex-snapshot
Structure-Based Design of a Chemical Probe Set for the 5-HT 5A Serotonin Receptor
inferredcites →https://doi.org/10.1021/acs.jmedchem.2c00117openalex-snapshot
Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19
inferredcites →https://doi.org/10.1021/acs.jmedchem.5b01461openalex-snapshot
An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy
inferredcites →https://doi.org/10.1021/acs.jmedchem.9b01828openalex-snapshot
α‑Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment
inferredcites →https://doi.org/10.1021/acscatal.0c00110openalex-snapshot
Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease
inferredcites →https://doi.org/10.1021/acscentsci.1c00039openalex-snapshot
Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV‑2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations
inferredcites →https://doi.org/10.1021/acscentsci.1c00529openalex-snapshot
In Vivo Measurement of Granzyme Proteolysis from Activated Immune Cells with PET
inferredcites →https://doi.org/10.1021/acscentsci.3c00538openalex-snapshot
Naturally Occurring Mutations of SARS-CoV-2 Main Protease Confer Drug Resistance to Nirmatrelvir
inferredcites →https://doi.org/10.1021/acsmedchemlett.1c00326openalex-snapshot
Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency
inferredcites →https://doi.org/10.1021/acsmedchemlett.2c00260openalex-snapshot
A Warhead Substitution Study on the Coronavirus Main Protease Inhibitor Nirmatrelvir
inferredcites →https://doi.org/10.1021/acsmedchemlett.6b00491openalex-snapshot
Discovery of GBT440, an Orally Bioavailable R-State Stabilizer of Sickle Cell Hemoglobin
inferredcites →https://doi.org/10.1021/bi0621415openalex-snapshot
Substrate Specificity Profiling and Identification of a New Class of Inhibitor for the Major Protease of the SARS Coronavirus,
inferredcites →https://doi.org/10.1021/ci100214aopenalex-snapshot
Rapid Context-Dependent Ligand Desolvation in Molecular Docking
inferredcites →https://doi.org/10.1021/ci400534hopenalex-snapshot
Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design
inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot
A new force field for molecular mechanical simulation of nucleic acids and proteins
inferredcites →https://doi.org/10.1021/jacs.1c08402openalex-snapshot
Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses
inferredcites →https://doi.org/10.1021/jacs.9b10377openalex-snapshot
Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
inferredcites →https://doi.org/10.1021/jm030266ropenalex-snapshot
A Specific Mechanism of Nonspecific Inhibition
inferredcites →https://doi.org/10.1021/jm0603926openalex-snapshot
Synthesis, Crystal Structure, Structure−Activity Relationships, and Antiviral Activity of a Potent SARS Coronavirus 3CL Protease Inhibitor
inferredcites →https://doi.org/10.1021/jm301580nopenalex-snapshot
Discovery, Synthesis, And Structure-Based Optimization of a Series of N-(tert-Butyl)-2-(N-arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease
inferredcites →https://doi.org/10.1021/jm701500eopenalex-snapshot
Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase
inferredcites →https://doi.org/10.1038/nature15699openalex-snapshot
Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65
inferredcites →https://doi.org/10.1038/nature19112openalex-snapshot
Structure-based discovery of opioid analgesics with reduced side effects
inferredcites →https://doi.org/10.1038/nature25758openalex-snapshot
Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone
inferredcites →https://doi.org/10.1038/nchembio.1666openalex-snapshot
Covalent docking of large libraries for the discovery of chemical probes
inferredcites →https://doi.org/10.1038/nchembio.662openalex-snapshot
Ligand discovery from a dopamine D3 receptor homology model and crystal structure
inferredcites →https://doi.org/10.1038/s41422-020-0356-zopenalex-snapshot
Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease
inferredcites →https://doi.org/10.1038/s41467-020-18709-wopenalex-snapshot
Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1038/s41467-022-31210-wopenalex-snapshot
Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance
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Crowdsourcing drug discovery for pandemics
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Advances in covalent drug discovery
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Ultra-large library docking for discovering new chemotypes
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The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity
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Virtual discovery of melatonin receptor ligands to modulate circadian rhythms
inferredcites →https://doi.org/10.1038/s41586-020-2223-yopenalex-snapshot
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
inferredcites →https://doi.org/10.1038/s41586-021-04175-xopenalex-snapshot
Structures of the σ2 receptor enable docking for bioactive ligand discovery
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Synthon-based ligand discovery in virtual libraries of over 11 billion compounds
inferredcites →https://doi.org/10.1038/s41586-022-05258-zopenalex-snapshot
Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity
inferredcites →https://doi.org/10.1038/s41589-020-00689-zopenalex-snapshot
SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging
inferredcites →https://doi.org/10.1038/s41596-021-00597-zopenalex-snapshot
A practical guide to large-scale docking
inferredcites →https://doi.org/10.1073/pnas.1120431109openalex-snapshot
Structure-based ligand discovery for the protein–protein interface of chemokine receptor CXCR4
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Structure-based discovery of selective positive allosteric modulators of antagonists for the M 2 muscarinic acetylcholine receptor
inferredcites →https://doi.org/10.1073/pnas.2212931120openalex-snapshot
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
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Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases
inferredcites →https://doi.org/10.1101/2020.10.29.339317openalex-snapshot
Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors
inferredcites →https://doi.org/10.1101/2022.06.07.495116openalex-snapshot
The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitor in vitro and confer resistance to nirmatrelvir
inferredcites →https://doi.org/10.1101/2022.06.23.497404openalex-snapshot
The Functional Landscape of SARS-CoV-2 3CL Protease
inferredcites →https://doi.org/10.1107/s0021889807021206openalex-snapshot
Phaser crystallographic software
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Scaling and assessment of data quality
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XDS
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Features and development of Coot
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REFMAC 5 for the refinement of macromolecular crystal structures
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Towards automated crystallographic structure refinement with phenix.refine
inferredcites →https://doi.org/10.1107/s0907444994003112openalex-snapshot
The CCP4 suite: programs for protein crystallography
inferredcites →https://doi.org/10.1126/sciadv.abf8711openalex-snapshot
Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking
inferredcites →https://doi.org/10.1126/sciadv.ade8778openalex-snapshot
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors
inferredcites →https://doi.org/10.1126/science.1085658openalex-snapshot
Coronavirus Main Proteinase (3CL pro ) Structure: Basis for Design of Anti-SARS Drugs
inferredcites →https://doi.org/10.1126/science.aan5468openalex-snapshot
D4dopamine receptor high-resolution structures enable the discovery of selective agonists
inferredcites →https://doi.org/10.1126/science.abb3405openalex-snapshot
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
inferredcites →https://doi.org/10.1126/science.abb4489openalex-snapshot
Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1126/science.abf1611openalex-snapshot
SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model
inferredcites →https://doi.org/10.1126/science.abl4784openalex-snapshot
An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19
inferredcites →https://doi.org/10.1126/science.abn7065openalex-snapshot
Structure-based discovery of nonopioid analgesics acting through the α 2A -adrenergic receptor
inferredcites →https://doi.org/10.1126/scitranslmed.abc5332openalex-snapshot
3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice
inferredcites →https://doi.org/10.1126/scitranslmed.abq7360openalex-snapshot
SARS-CoV-2 3CL pro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376
inferredcites →https://doi.org/10.1128/jvi.01348-12openalex-snapshot
Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses
inferredcites →https://doi.org/10.1128/jvi.02114-07openalex-snapshot
Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design
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Cinanserin Is an Inhibitor of the 3C-Like Proteinase of Severe Acute Respiratory Syndrome Coronavirus and Strongly Reduces Virus Replication In Vitro
inferredcites →https://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
inferredcites →https://doi.org/10.1128/mbio.02815-22openalex-snapshot
The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir
inferredcites →https://doi.org/10.1158/1538-7445.am2022-nd11openalex-snapshot
Abstract ND11: Discovery of GDC-6036, a clinical stage treatment for KRAS G12C-positive cancers
inferredcites →https://doi.org/10.1371/journal.pone.0075992openalex-snapshot
Ligand Pose and Orientational Sampling in Molecular Docking
inferredcites →https://doi.org/10.2174/187152606776056706openalex-snapshot
Discovery and Development of VX-950, a Novel, Covalent, and Reversible Inhibitor of Hepatitis C Virus NS3.4A Serine Protease
inferredcites →https://doi.org/10.3389/fchem.2022.852210openalex-snapshot
Crystallization of Feline Coronavirus Mpro With GC376 Reveals Mechanism of Inhibition
inferredcites →https://doi.org/10.3390/ijms222111779openalex-snapshot
Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L
inferredcites →https://doi.org/10.7554/elife.77433openalex-snapshot
Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Coronaviruses main proteases and their inhibitors
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Are protein–ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease?
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Hit identification in ultra large virtual screening: an integrative review and future challenges
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Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions
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Structure-based virtual screening of ultra-large chemical spaces: Advances and pitfalls
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Plant flavonoid inhibition of SARS-CoV-2 main protease and viral replication
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Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (Mpro) through pharmacophore modelling, covalent docking, and biological evaluation
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Early Kinetic Characterization of SARS-CoV-2 Main Protease Inhibitors: A Review and Guidance for Biochemical Assessments
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Structure-Based Identification of Organoruthenium Compounds as Nanomolar Antagonists of Cannabinoid Receptors
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Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking
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Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds
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SpaceHASTEN: A Structure-Based Virtual Screening Tool for Nonenumerated Virtual Chemical Libraries
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Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results
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Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase
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Large Library Docking and Biophysical Analysis of Small-Molecule TMPRSS2 Inhibitors
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Discovery of Coronavirus Main Protease Inhibitors with Enhanced Brain Exposure and Potent Oral Efficacy in SARS-CoV-2 and MERS Infection Models
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The Selectivity Implications of Docking Libraries with Greater and Lesser Similarities to Bio-like Molecules
inferred← citeshttps://doi.org/10.1021/acs.joc.4c00230openalex-snapshot
Electrochemical Formation of α-Ketoamides from Ketoximes through Non-Beckmann Mechanism Pathway
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Discovery of Covalent Ligands with AlphaFold3
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Structure-based rational design of covalent probes
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Rapid traversal of vast chemical space using machine learning-guided docking screens
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Surely you are joking, Mr Docking!
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On the origins of SARS-CoV-2 main protease inhibitors
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Noncovalent Inhibitors of SARS-CoV-2 Main Protease: A Rescaffolding Attempt
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Assessing probe reliability: Functional group–specific biases revealed by interactome-wide docking of general anesthetics
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From ML300 to Novel Non-covalent Inhibitors of SARS‑CoV‑2 Main Protease via Evolutionary De Novo Design, Virtual Screening, Molecular Dynamics, and Retrosynthetic Strategies
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Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds
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Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7 -methyltransferase
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Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M Pro inhibitors with potent in vivo efficacy
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Trillion Ligands per Day: Performance-Portable Virtual Screening via Compound Database Optimization and Multi-Target Docking
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Rapid Traversal of Ultralarge Chemical Space using Machine Learning Guided Docking Screens
inferred← citeshttps://doi.org/10.3390/bios13070682openalex-snapshot
A Prototype Assay Multiplexing SARS-CoV-2 3CL-Protease and Angiotensin-Converting Enzyme 2 for Saliva-Based Diagnostics in COVID-19
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A Comprehensive Survey of Prospective Structure-Based Virtual Screening for Early Drug Discovery in the Past Fifteen Years
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Phytochemicals in Drug Discovery—A Confluence of Tradition and Innovation
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DTBind: A Mechanism-Driven Deep Learning Framework for Accurate Prediction of Drug–Target Molecular Recognition
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