Docking Paradigm in Drug Design

Curr Top Med Chem. 2021;21(6):507-546. doi: 10.2174/1568026620666201207095626.

Abstract

Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.

Keywords: CADD; COVID-19; Docking; Global optimization; Inhibitors; Mpro; Quantum docking; SARS-CoV-2.

Publication types

  • Review

MeSH terms

  • Amino Acid Sequence
  • Antiviral Agents / chemistry*
  • Antiviral Agents / classification
  • Antiviral Agents / pharmacology
  • COVID-19 Drug Treatment
  • Catalytic Domain
  • Coronavirus 3C Proteases / antagonists & inhibitors*
  • Coronavirus 3C Proteases / chemistry
  • Coronavirus 3C Proteases / genetics
  • Coronavirus 3C Proteases / metabolism
  • Drug Design
  • Drug Repositioning / methods
  • Gene Expression
  • Humans
  • Molecular Docking Simulation / methods*
  • Prescription Drugs / chemistry*
  • Prescription Drugs / classification
  • Prescription Drugs / pharmacology
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / classification
  • Protease Inhibitors / pharmacology
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • SARS-CoV-2 / chemistry*
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / enzymology
  • Structure-Activity Relationship

Substances

  • Antiviral Agents
  • Prescription Drugs
  • Protease Inhibitors
  • 3C-like proteinase, SARS-CoV-2
  • Coronavirus 3C Proteases