Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings

Bioorg Med Chem. 2014 Jan 1;22(1):167-77. doi: 10.1016/j.bmc.2013.11.041. Epub 2013 Dec 1.


We have used a combination of virtual screening (VS) and high-throughput screening (HTS) techniques to identify novel, non-peptidic small molecule inhibitors against human SARS-CoV 3CLpro. A structure-based VS approach integrating docking and pharmacophore based methods was employed to computationally screen 621,000 compounds from the ZINC library. The screening protocol was validated using known 3CLpro inhibitors and was optimized for speed, improved selectivity, and for accommodating receptor flexibility. Subsequently, a fluorescence-based enzymatic HTS assay was developed and optimized to experimentally screen approximately 41,000 compounds from four structurally diverse libraries chosen mainly based on the VS results. False positives from initial HTS hits were eliminated by a secondary orthogonal binding analysis using surface plasmon resonance (SPR). The campaign identified a reversible small molecule inhibitor exhibiting mixed-type inhibition with a K(i) value of 11.1 μM. Together, these results validate our protocols as suitable approaches to screen virtual and chemical libraries, and the newly identified compound reported in our study represents a promising structural scaffold to pursue for further SARS-CoV 3CLpro inhibitor development.

Keywords: 3 Chymotrypsin-like cysteine protease; 3CL(pro); CSM; Docking; FRET; HTS; High-throughput screening; K(D); K(i); MD; MLPCN; Molecular Libraries Probe Production Centers Network; Pharmacophore modeling; RMSD; ROC; SARS 3CL(pro); SARS-CoV; SPR; Severe Acute Respiratory Syndrome coronavirus; Surface plasmon resonance; VS; Virtual screening; computational solvent mapping; equilibrium dissociation constant; fluorescence resonance energy transfer; high-throughput screening; inhibition constant; molecular dynamics; receiver operating characteristic; root mean square deviation; surface plasmon resonance; virtual screening.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • High-Throughput Screening Assays
  • Humans
  • Models, Molecular
  • Molecular Structure
  • SARS Virus / enzymology*
  • SARS Virus / metabolism
  • Tissue Engineering
  • Tissue Scaffolds