A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication

Shin-Ichiro Hattori; Nobuyo Higashi-Kuwata; Hironori Hayashi; Srinivasa Rao Allu; Jakka Raghavaiah; Haydar Bulut; Debananda Das; Brandon J Anson; Emma K Lendy; Yuki Takamatsu; Nobutoki Takamune; Naoki Kishimoto; Kazutaka Murayama; Kazuya Hasegawa; Mi Li; David A Davis; Eiichi N Kodama; Robert Yarchoan; Alexander Wlodawer; Shogo Misumi; Andrew D Mesecar; Arun K Ghosh; Hiroaki Mitsuya

doi:10.1038/s41467-021-20900-6

A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication

Nat Commun. 2021 Jan 28;12(1):668. doi: 10.1038/s41467-021-20900-6.

Authors

Shin-Ichiro Hattori¹, Nobuyo Higashi-Kuwata¹, Hironori Hayashi^{2

3}, Srinivasa Rao Allu⁴, Jakka Raghavaiah⁴, Haydar Bulut⁵, Debananda Das⁵, Brandon J Anson⁶, Emma K Lendy⁶, Yuki Takamatsu¹, Nobutoki Takamune⁷, Naoki Kishimoto⁸, Kazutaka Murayama⁹, Kazuya Hasegawa¹⁰, Mi Li^{11

12}, David A Davis¹³, Eiichi N Kodama^{3

14}, Robert Yarchoan¹³, Alexander Wlodawer¹¹, Shogo Misumi⁸, Andrew D Mesecar⁶, Arun K Ghosh⁴, Hiroaki Mitsuya^{15

16

17}

Affiliations

¹ Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
² Department of Intelligent Network for Infection Control, Tohoku University Hospital, Miyagi, Japan.
³ Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan.
⁴ Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
⁵ Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
⁶ Department of Biochemistry and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
⁷ Kumamoto Innovative Development Organization, Kumamoto University, Kumamoto, Japan.
⁸ Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
⁹ Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan.
¹⁰ Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.
¹¹ Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD, USA.
¹² Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
¹³ Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁴ Department of Infectious Diseases, Graduate School of Medicine and Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
¹⁵ Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, Japan. hmitsuya@hosp.ncgm.go.jp.
¹⁶ Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. hmitsuya@hosp.ncgm.go.jp.
¹⁷ Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan. hmitsuya@hosp.ncgm.go.jp.

Abstract

Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (M^pro). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC₅₀ values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with M^pro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead M^pro inhibitor for the development of therapeutics for SARS-CoV-2 infection.

Publication types

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

MeSH terms

Adenosine Monophosphate / analogs & derivatives
Adenosine Monophosphate / pharmacology
Alanine / analogs & derivatives
Alanine / pharmacology
Animals
Antiviral Agents / pharmacology
COVID-19 Drug Treatment*
Cell Line
Chlorocebus aethiops
Coronavirus Protease Inhibitors / pharmacology*
Humans
Indoles / pharmacology
Pyridines / pharmacology
SARS-CoV-2 / drug effects*
Vero Cells
Viral Proteases / drug effects*
Viral Proteases / metabolism

Substances

5-chloropyridin-3-yl indoline-4-carboxylate
Antiviral Agents
Coronavirus Protease Inhibitors
Indoles
Pyridines
remdesivir
Adenosine Monophosphate
indoline
Viral Proteases
Alanine

Abstract

Publication types

MeSH terms

Substances

Grants and funding