Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Feb 14;62(3):618-626.
doi: 10.1021/acs.jcim.1c01223. Epub 2022 Feb 2.

Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease

Debarati DasGupta  1 , Wallace K B Chan  2 , Heather A Carlson  1
Affiliations

Computational Identification of Possible Allosteric Sites and Modulators of the SARS-CoV-2 Main Protease

Debarati DasGupta et al. J Chem Inf Model. .

Abstract

In this study, we target the main protease (Mpro) of the SARS-CoV-2 virus as it is a crucial enzyme for viral replication. Herein, we report three plausible allosteric sites on Mpro that can expand structure-based drug discovery efforts for new Mpro inhibitors. To find these sites, we used mixed-solvent molecular dynamics (MixMD) simulations, an efficient computational protocol that finds binding hotspots through mapping the surface of unbound proteins with 5% cosolvents in water. We have used normal mode analysis to support our claim of allosteric control for these sites. Further, we have performed virtual screening against the sites with 361 hits from Mpro screenings available through the National Center for Advancing Translational Sciences (NCATS). We have identified the NCATS inhibitors that bind to the remote sites better than the active site of Mpro, and we propose these molecules may be allosteric regulators of the system. After identifying our sites, new X-ray crystal structures were released that show fragment molecules in the sites we found, supporting the notion that these sites are accurate and druggable.

PubMed Disclaimer

Conflict of interest statement

The authors declare no financial competing interest.

Figures

Figure 1.
Figure 1.
The Mpro dimer structure is shown in surface topology, with sites mapped via MixMD (Z=30) using neutral probes (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink). The active site and allosteric sites probed in this work are outlined in red.
Figure 2.
Figure 2.
The catalytic site of Mpro mapped using neutral probes (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink) as seen in these 6 crystal structures; the solvent densities are represented in isomesh contours and CoM mapping is depicted for all probe types. The occupancies are proportional to residence times of these probe molecules in their binding sites PDB IDs (A) 6Y2G, (B) 7CUU, (C) 7AKU, (D) 7CUT, (E) 7N8C, and (F) 7NT1.
Figure 3.
Figure 3.
Docked poses of the top-15 candidates for allosteric sites 1(A) and 2(B) and the top-13 candidates for site 3(C).
Figure 4.
Figure 4.
Allosteric Site 1 mapped by our neutral probes visualized as CoM grids (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink); ligand AT7519 in crystal structure 7AGA is overlaid to show agreement.
Figure 5.
Figure 5.
Allosteric Site 1 mapped by neutral probes visualized as CoM grids (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink); ligand Z24758179 in crystal structure 5REF is overlaid to show agreement.
Figure 6.
Figure 6.
Allosteric Site 2 mapped by neutral probes visualized as CoM grids (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink); ligand pelitinib in crystal structure 7AXM is overlaid to show agreement. The ligand’s cyano side chain is <3Å from allosteric Site 2; the chloro flurophenyl substituent in pelitinib points directly towards allosteric site 1 in the cavity.
Figure 7.
Figure 7.
Allosteric Site 2 mapped by neutral probes visualized as CoM grids (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink); ligand Ifenprodil in crystal structure 7AQI is overlaid to show agreement.
Figure 8.
Figure 8.
Allosteric Site 3 mapped by neutral probes visualized as CoM grids (ACN-orange, IPA-blue, PYR-purple, IMI-black, MAC-yellow, and EOH-warmpink); ligand AR-42 in crystal structure 7AXO is overlaid to show agreement.
Figure 9.
Figure 9.
Ligands bound to PDB IDs 7AGA (right side) and 7ABU (left side) show space for linking chemistry (region in red dashed lines), where the two compounds could be optimized and linked through a calculated hotspot.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Zhang YZ; Holmes EC, A Genomic Perspective on the Origin and Emergence of SARS-CoV-2. Cell 2020, 181, 223–227. - PMC - PubMed
    1. Jin Z; Du X; Xu Y; Deng Y; Liu M; Zhao Y; Zhang B; Li X; Zhang L; Peng C; Duan Y; Yu J; Wang L; Yang K; Liu F; Jiang R; Yang X; You T; Liu X; Yang X; Bai F; Liu H; Liu X; Guddat LW; Xu W; Xiao G; Qin C; Shi Z; Jiang H; Rao Z; Yang H, Structure of M(pro) from SARS-CoV-2 and discovery of its inhibitors. Nature 2020, 582, 289–293. - PubMed
    1. Zhang L; Lin D; Sun X; Curth U; Drosten C; Sauerhering L; Becker S; Rox K; Hilgenfeld R, Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science 2020, 368, 409–412. - PMC - PubMed
    1. Ghanakota P; Carlson HA, Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J Phys Chem B 2016, 120, 8685–95. - PMC - PubMed
    1. Ghanakota P; DasGupta D; Carlson HA, Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. J Chem Inf Model 2019, 59, 2035–2045. - PMC - PubMed

Publication types