Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

Nicole L. Inniss; Ján Kozic; Fengling Li; Monica Rosas-Lemus; George Minasov; Jiří Rybáček; Yingjie Zhu; Radek Pohl; Ludmilla Shuvalova; Lubomír Rulíšek; Joseph S Brunzelle; Lucie Bednárová; Milan Štefek; Ján Michael Kormaník; Erik Andris; Jaroslav Šebestík; Alice Shi Ming Li; Peter J. Brown; Uli Schmitz; Kumar Saikatendu; Edcon Chang; Radim Nencka; Masoud Vedadi; Karla J.F. Satchell

doi:10.1021/acsinfecdis.3c00203

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

Nicole L. Inniss, Ján Kozic, Fengling Li, Monica Rosas-Lemus, George Minasov, Jiří Rybáček, Yingjie Zhu, Radek Pohl, Ludmilla Shuvalova, Lubomír Rulíšek, Joseph S Brunzelle, Lucie Bednárová, Milan Štefek, Ján Michael Kormaník, Erik Andris, Jaroslav Šebestík, Alice Shi Ming Li, Peter J. Brown, Uli Schmitz, Kumar SaikatenduEdcon Chang^*, Radim Nencka^*, Masoud Vedadi^*, Karla J.F. Satchell^*

^*Corresponding author for this work

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

7 Scopus citations

Abstract

A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

Original language	English (US)
Pages (from-to)	1918-1931
Number of pages	14
Journal	ACS Infectious Diseases
Volume	9
Issue number	10
DOIs	https://doi.org/10.1021/acsinfecdis.3c00203
State	Published - Oct 13 2023

Keywords

antiviral
coronavirus
covalent inhibitors
nsp16 methyltransferase
structural biology

ASJC Scopus subject areas

Infectious Diseases

UN SDGs

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

Access to Document

10.1021/acsinfecdis.3c00203

Cite this

Inniss, N. L., Kozic, J., Li, F., Rosas-Lemus, M., Minasov, G., Rybáček, J., Zhu, Y., Pohl, R., Shuvalova, L., Rulíšek, L., Brunzelle, J. S., Bednárová, L., Štefek, M., Kormaník, J. M., Andris, E., Šebestík, J., Li, A. S. M., Brown, P. J., Schmitz, U., ... Satchell, K. J. F. (2023). Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infectious Diseases, 9(10), 1918-1931. https://doi.org/10.1021/acsinfecdis.3c00203

@article{a9f30e5d84004e8c8d356b4d0a38e5ca,

title = "Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors",

abstract = "A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.",

keywords = "antiviral, coronavirus, covalent inhibitors, nsp16 methyltransferase, structural biology",

author = "Inniss, {Nicole L.} and J{\'a}n Kozic and Fengling Li and Monica Rosas-Lemus and George Minasov and Ji{\v r}{\'i} Ryb{\'a}{\v c}ek and Yingjie Zhu and Radek Pohl and Ludmilla Shuvalova and Lubom{\'i}r Rul{\'i}{\v s}ek and Brunzelle, {Joseph S} and Lucie Bedn{\'a}rov{\'a} and Milan {\v S}tefek and Korman{\'i}k, {J{\'a}n Michael} and Erik Andris and Jaroslav {\v S}ebest{\'i}k and Li, {Alice Shi Ming} and Brown, {Peter J.} and Uli Schmitz and Kumar Saikatendu and Edcon Chang and Radim Nencka and Masoud Vedadi and Satchell, {Karla J.F.}",

note = "Publisher Copyright: {\textcopyright} 2023 American Chemical Society.",

year = "2023",

month = oct,

day = "13",

doi = "10.1021/acsinfecdis.3c00203",

language = "English (US)",

volume = "9",

pages = "1918--1931",

journal = "ACS Infectious Diseases",

issn = "2373-8227",

publisher = "American Chemical Society",

number = "10",

}

Inniss, NL, Kozic, J, Li, F, Rosas-Lemus, M, Minasov, G, Rybáček, J, Zhu, Y, Pohl, R, Shuvalova, L, Rulíšek, L, Brunzelle, JS, Bednárová, L, Štefek, M, Kormaník, JM, Andris, E, Šebestík, J, Li, ASM, Brown, PJ, Schmitz, U, Saikatendu, K, Chang, E, Nencka, R, Vedadi, M & Satchell, KJF 2023, 'Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors', ACS Infectious Diseases, vol. 9, no. 10, pp. 1918-1931. https://doi.org/10.1021/acsinfecdis.3c00203

TY - JOUR

T1 - Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

AU - Inniss, Nicole L.

AU - Kozic, Ján

AU - Li, Fengling

AU - Rosas-Lemus, Monica

AU - Minasov, George

AU - Rybáček, Jiří

AU - Zhu, Yingjie

AU - Pohl, Radek

AU - Shuvalova, Ludmilla

AU - Rulíšek, Lubomír

AU - Brunzelle, Joseph S

AU - Bednárová, Lucie

AU - Štefek, Milan

AU - Kormaník, Ján Michael

AU - Andris, Erik

AU - Šebestík, Jaroslav

AU - Li, Alice Shi Ming

AU - Brown, Peter J.

AU - Schmitz, Uli

AU - Saikatendu, Kumar

AU - Chang, Edcon

AU - Nencka, Radim

AU - Vedadi, Masoud

AU - Satchell, Karla J.F.

PY - 2023/10/13

Y1 - 2023/10/13

N2 - A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

AB - A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

KW - antiviral

KW - coronavirus

KW - covalent inhibitors

KW - nsp16 methyltransferase

KW - structural biology

UR - http://www.scopus.com/inward/record.url?scp=85174689302&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85174689302&partnerID=8YFLogxK

U2 - 10.1021/acsinfecdis.3c00203

DO - 10.1021/acsinfecdis.3c00203

M3 - Article

C2 - 37728236

AN - SCOPUS:85174689302

SN - 2373-8227

VL - 9

SP - 1918

EP - 1931

JO - ACS Infectious Diseases

JF - ACS Infectious Diseases

IS - 10

ER -

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16

Cite this

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Datasets

Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16

Cite this