4.7 Article

SARS-COV-2 Mpro conformational changes induced by covalently bound ligands

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging

Wioletta Rut et al.

Summary: A team of researchers synthesized a new type of antiviral agent, demonstrating through experiments its high efficacy in inhibiting SARS-CoV-2 with a low effective concentration, providing new insights for antiviral treatment. By observing the active SARS-CoV-2 M-pro in the cells of patients infected with COVID-19, important clues were provided for the design of antiviral drugs and diagnostic tests.

NATURE CHEMICAL BIOLOGY (2021)

Article Chemistry, Multidisciplinary

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Chun-Hui Zhang et al.

Summary: Starting from known drugs, the study redesigned perampanel into potent noncovalent inhibitors of SARS-CoV-2 main protease with ca. 20 nM IC50 values. Free-energy perturbation calculations and high-resolution X-ray crystal structures guided the design efforts and rapid development of effective analogues. Cell-based antiviral assays confirmed the potential of the compounds for COVID-19 treatment, highlighting the power of computational chemistry in drug discovery.

ACS CENTRAL SCIENCE (2021)

Article Biochemistry & Molecular Biology

Identification of mutation resistance coldspots for targeting the SARS-CoV2 main protease

Navaneethakrishnan Krishnamoorthy et al.

Summary: A study identified 24 mutational coldspots in the SARS-CoV2 main protease (M-pro), with three coldspot residues assisting in forming the active site and seven contributing to dimer formation necessary for M-pro activity. The surface of the dimer interface is more resistant to mutations compared to the active site, and most coldspots are found in conserved clusters across coronaviruses. Identification of these coldspots provides a new perspective for targeting SARS-CoV2 M-pro while avoiding mutation-based drug resistance.

IUBMB LIFE (2021)

Article Multidisciplinary Sciences

The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors

Lucia Silvestrini et al.

Summary: The study investigated the structural features and thermodynamics of the SARS-CoV-2 M-pro protein using Small Angle X-ray Scattering (SAXS), providing key information for therapeutic intervention. It was found that small molecule inhibitors can affect dimerization and enzymatic activity of M-pro to varying extents, potentially serving as leads for antiviral drug development.

SCIENTIFIC REPORTS (2021)

Article Chemistry, Multidisciplinary

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Anna Pavlova et al.

Summary: The main protease of SARS-CoV-2 is a promising target for antiviral therapeutics, crucial in the viral life cycle. The stability of its structure is highly sensitive to the protonation states of key residues, impacting drug design efforts.

CHEMICAL SCIENCE (2021)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Biochemistry & Molecular Biology

Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

Maria Bzowka et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Multidisciplinary Sciences

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Zhenming Jin et al.

NATURE (2020)

Review Pharmacology & Pharmacy

Safety perspectives on presently considered drugs for the treatment of COVID-19

Sophie L. Penman et al.

BRITISH JOURNAL OF PHARMACOLOGY (2020)

Article Chemistry, Medicinal

SARS-CoV-2 Main Protease: A Molecular Dynamics Study

Dimas Suarez et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Multidisciplinary Sciences

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation

Teruhisa S. Komatsu et al.

SCIENTIFIC REPORTS (2020)

Article Biochemical Research Methods

Prediction of potential inhibitors of the dimeric SARS-CoV2 main proteinase through the MM/GBSA approach

Martiniano Bello

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2020)

Article Chemistry, Physical

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

Katarina Roos et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Biochemistry & Molecular Biology

Inhibition of Porcine Aminopeptidase M (pAMP) by the Pentapeptide Microginins

Glaucio Monteiro Ferreira et al.

MOLECULES (2019)

Article Chemistry, Physical

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Edward Harder et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Biochemistry & Molecular Biology

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

G. Madhavi Sastry et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)

Article Chemistry, Multidisciplinary

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

Robert Abel et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

Review Multidisciplinary Sciences

Dynamic personalities of proteins

Katherine Henzler-Wildman et al.

NATURE (2007)

Article Multidisciplinary Sciences

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

Tom Young et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biochemistry & Molecular Biology

Only one protomer is active in the dimer of SARS 3C-like proteinase

Hao Chen et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2006)

Review Biochemistry & Molecular Biology

Water structure and interactions with protein surfaces

TM Raschke

CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)

Article Chemistry, Organic

Molecular simplification in bioactive molecules:: Formal synthesis of (+)-muconin

FRP Crisóstomo et al.

JOURNAL OF ORGANIC CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Design of wide-spectrum inhibitors targeting coronavirus main proteases

HT Yang et al.

PLOS BIOLOGY (2005)

Article Biochemistry & Molecular Biology

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

M Landau et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

A hierarchical approach to all-atom protein loop prediction

MP Jacobson et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Quaternary structure of the severe acute respiratory syndrome (SARS) coronavirus main protease

CY Chou et al.

BIOCHEMISTRY (2004)