Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

Daniel W. Kneller; Hui Li; Stephanie Galanie; Gwyndalyn Phillips; Audrey Labbé; Kevin L. Weiss; Qiu Zhang; Mark A. Arnould; Austin Clyde; Heng Ma; Arvind Ramanathan; Colleen B. Jonsson; Martha S. Head; Leighton Coates; John M. Louis; Peter V. Bonnesen; Andrey Kovalevsky

doi:10.1021/acs.jmedchem.1c01475

Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

Daniel W. Kneller, Hui Li, Stephanie Galanie, Gwyndalyn Phillips, Audrey Labbé, Kevin L. Weiss, Qiu Zhang, Mark A. Arnould, Austin Clyde, Heng Ma, Arvind Ramanathan, Colleen B. Jonsson, Martha S. Head, Leighton Coates, John M. Louis, Peter V. Bonnesen, Andrey Kovalevsky

Research output: Contribution to journal › Article › peer-review

38 Scopus citations

Abstract

Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

Original language	English
Pages (from-to)	17366-17383
Number of pages	18
Journal	Journal of Medicinal Chemistry
Volume	64
Issue number	23
DOIs	https://doi.org/10.1021/acs.jmedchem.1c01475
State	Published - Dec 9 2021

Funding

This research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory (NVBL), a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act. This research used resources at the Center for Nanophase Materials Sciences, the Spallation Neutron Source, and the HighFlux Isotope Reactor, which are DOE Office of Science User Facilities operated by the Oak Ridge National Laboratory. The Office of Biological and Environmental Research supported research at ORNL’s Center for Structural Molecular Biology (CSMB), a DOE Office of Science User Facility. This research used resources of the Spallation Neutron Source Second Target Station Project at the Oak Ridge National Laboratory (ORNL). ORNL is managed by UT-Battelle LLC for DOE’s Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The authors thank Dr. Hugh M. O’Neill from ORNL for assistance during expression of the partially deuterated protein. L.C. acknowledges support from the NIH (R01-GM071939). They also thank Annie Aniana from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) for excellent technical assistance. This work was also supported by the Intramural Research Program of NIDDK, NIH.

Funders	Funder number
National Virtual Biotechnology Laboratory
ORNL’s Center for Structural Molecular Biology
National Institutes of Health
U.S. Department of Energy
National Institute of General Medical Sciences	R01GM071939
National Institute of Diabetes and Digestive and Kidney Diseases
Office of Science
Biological and Environmental Research
Canadian Society for Molecular Biosciences

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1021/acs.jmedchem.1c01475

Cite this

Kneller, D. W., Li, H., Galanie, S., Phillips, G., Labbé, A., Weiss, K. L., Zhang, Q., Arnould, M. A., Clyde, A., Ma, H., Ramanathan, A., Jonsson, C. B., Head, M. S., Coates, L., Louis, J. M., Bonnesen, P. V., & Kovalevsky, A. (2021). Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. Journal of Medicinal Chemistry, 64(23), 17366-17383. https://doi.org/10.1021/acs.jmedchem.1c01475

@article{11c3129e3ee247ecb23609c7305a430a,

title = "Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease",

abstract = "Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.",

author = "Kneller, {Daniel W.} and Hui Li and Stephanie Galanie and Gwyndalyn Phillips and Audrey Labb{\'e} and Weiss, {Kevin L.} and Qiu Zhang and Arnould, {Mark A.} and Austin Clyde and Heng Ma and Arvind Ramanathan and Jonsson, {Colleen B.} and Head, {Martha S.} and Leighton Coates and Louis, {John M.} and Bonnesen, {Peter V.} and Andrey Kovalevsky",

note = "Publisher Copyright: {\textcopyright} ",

year = "2021",

month = dec,

day = "9",

doi = "10.1021/acs.jmedchem.1c01475",

language = "English",

volume = "64",

pages = "17366--17383",

journal = "Journal of Medicinal Chemistry",

issn = "0022-2623",

publisher = "American Chemical Society",

number = "23",

}

Kneller, DW, Li, H, Galanie, S, Phillips, G, Labbé, A, Weiss, KL , Zhang, Q, Arnould, MA, Clyde, A, Ma, H, Ramanathan, A, Jonsson, CB, Head, MS, Coates, L, Louis, JM, Bonnesen, PV & Kovalevsky, A 2021, 'Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease', Journal of Medicinal Chemistry, vol. 64, no. 23, pp. 17366-17383. https://doi.org/10.1021/acs.jmedchem.1c01475

TY - JOUR

T1 - Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

AU - Kneller, Daniel W.

AU - Li, Hui

AU - Galanie, Stephanie

AU - Phillips, Gwyndalyn

AU - Labbé, Audrey

AU - Weiss, Kevin L.

AU - Zhang, Qiu

AU - Arnould, Mark A.

AU - Clyde, Austin

AU - Ma, Heng

AU - Ramanathan, Arvind

AU - Jonsson, Colleen B.

AU - Head, Martha S.

AU - Coates, Leighton

AU - Louis, John M.

AU - Bonnesen, Peter V.

AU - Kovalevsky, Andrey

PY - 2021/12/9

Y1 - 2021/12/9

N2 - Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

AB - Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

UR - http://www.scopus.com/inward/record.url?scp=85118863575&partnerID=8YFLogxK

U2 - 10.1021/acs.jmedchem.1c01475

DO - 10.1021/acs.jmedchem.1c01475

M3 - Article

C2 - 34705466

AN - SCOPUS:85118863575

SN - 0022-2623

VL - 64

SP - 17366

EP - 17383

JO - Journal of Medicinal Chemistry

JF - Journal of Medicinal Chemistry

IS - 23

ER -

Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease

Abstract

Funding

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this