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

被引：146

作者：

Hattori, Shin-ichiro ^{[1
]}

Higashi-Kuwata, Nobuyo ^{[1
]}

Hayashi, Hironori ^{[2
,3
]}

Allu, Srinivasa Rao ^{[4
,5
]}

Raghavaiah, Jakka ^{[4
,5
]}

Bulut, Haydar ^{[6
]}

Das, Debananda ^{[6
]}

Anson, Brandon J. ^{[7
,8
]}

Lendy, Emma K. ^{[7
,8
]}

Takamatsu, Yuki ^{[1
]}

Takamune, Nobutoki ^{[9
]}

Kishimoto, Naoki ^{[10
]}

Murayama, Kazutaka ^{[11
]}

Hasegawa, Kazuya ^{[12
]}

Li, Mi ^{[13
,14
]}

Davis, David A. ^{[15
]}

Kodama, Eiichi N. ^{[3
,16
,17
]}

Yarchoan, Robert ^{[15
]}

Wlodawer, Alexander ^{[13
]}

Misumi, Shogo ^{[10
]}

Mesecar, Andrew D. ^{[7
,8
]}

Ghosh, Arun K. ^{[4
,5
]}

Mitsuya, Hiroaki ^{[1
,6
,18
]}

机构：

[1] Natl Ctr Global Hlth & Med, Dept Refractory Viral Infect, Res Inst, Tokyo, Japan

[2] Tohoku Univ Hosp, Dept Intelligent Network Infect Control, Sendai, Miyagi, Japan

[3] Tohoku Univ, Int Res Inst Disaster Sci, Dept Infect Dis, Sendai, Miyagi, Japan

[4] Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA

[5] Purdue Univ, Dept Med Chem & Mol Pharmacol, W Lafayette, IN 47907 USA

[6] NCI, Expt Retrovirol Sect, HIV & AIDS Malignancy Branch, NIH, Bethesda, MD 20892 USA

[7] Purdue Univ, Dept Biochem, W Lafayette, IN 47907 USA

[8] Purdue Univ, Dept Biol Sci, W Lafayette, IN 47907 USA

[9] Kumamoto Univ, Kumamoto Innovat Dev Org, Kumamoto, Japan

[10] Kumamoto Univ, Fac Med & Pharmaceut Sci, Dept Environm & Mol Hlth Sci, Kumamoto, Japan

[11] Tohoku Univ, Grad Sch Biomed Engn, Sendai, Miyagi, Japan

[12] Japan Synchrotron Radiat Res Inst, Prot Crystal Anal Div, Sayo, Hyogo, Japan

[13] NCI, Prot Struct Sect, Ctr Struct Biol, Frederick, MD 21701 USA

[14] Frederick Natl Lab Canc Res, Leidos Biomed Res, Basic Sci Program, Frederick, MD USA

[15] NCI, Viral Oncol Sect, HIV & AIDS Malignancy Branch, NIH, Bethesda, MD 20892 USA

[16] Tohoku Univ, Grad Sch Med, Dept Infect Dis, Sendai, Miyagi, Japan

[17] Tohoku Univ, Tohoku Med Megabank Org, Sendai, Miyagi, Japan

[18] Kumamoto Univ Hosp, Dept Clin Sci, Kumamoto, Japan

来源：

NATURE COMMUNICATIONS | 2021年 / 12卷 / 01期

基金：

美国国家卫生研究院;

关键词：

RESPIRATORY SYNDROME CORONAVIRUS; SARS-COV; 3CLPRO; PAPAIN-LIKE PROTEASE; BIOLOGICAL EVALUATION; MECHANISM; DISCOVERY; DESIGN; SERIES;

D O I：

10.1038/s41467-021-20900-6

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 154 and 4.2 +/- 0.7 mu M 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.Here, using in vitro assays and structural analysis, the authors characterize the anti-SARS-CoV-2 properties of two small molcules, showing these to bind and target the virus main protease (M-pro), and to exhibit a synergistic antiviral effect when combined with remdesivir in vitro.

引用

页数：12

共 48 条

[1]

Anson B, 2020, RES SQUARE

[2] The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity [J].

Barretto, N ;

Jukneliene, D ;

Ratia, K ;

Chen, ZB ;

Mesecar, AD ;

Baker, SC .

JOURNAL OF VIROLOGY, 2005, 79 (24) :15189-15198

[3]

Beigel JH, 2020, NEW ENGL J MED, V383, P1813, DOI [10.1056/NEJMoa2007764, 10.1056/NEJMc2022236]

[4] Baseline predictors of CD4 T-lymphocyte recovery with combination antiretroviral therapy [J].

Bennett, KK ;

DeGruttola, VG ;

Marschner, IC ;

Havlir, DV ;

Richman, DD .

JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES, 2002, 31 (01) :20-26

[5] CRITERIA FOR ANALYZING INTERACTIONS BETWEEN BIOLOGICALLY-ACTIVE AGENTS [J].

BERENBAUM, MC .

ADVANCES IN CANCER RESEARCH, 1981, 35 :269-335

[6] SELECTIVE-INHIBITION OF HIV REPLICATION BY ADRIAMYCIN IN MACROPHAGES BUT NOT IN LYMPHOCYTES [J].

BERGAMINI, A ;

PERNO, CF ;

BALZARINI, J ;

CAPOZZI, M ;

MARINELLI, L ;

MILANESE, G ;

PESCE, CD ;

CALIO, R ;

ROCCHI, G .

AIDS RESEARCH AND HUMAN RETROVIRUSES, 1992, 8 (07) :1239-1247

[7] CALCULATION OF MICROBIAL ASSAYS [J].

BLISS, CI .

BACTERIOLOGICAL REVIEWS, 1956, 20 (04) :243-258

[8] Rapamycin synergizes with the epidermal growth factor receptor inhibitor erlotinib in non-small-cell lung, pancreatic, colon, and breast tumors [J].

Buck, Elizabeth ;

Eyzaguirre, Alexandra ;

Brown, Eric ;

Petti, Filippo ;

McCormack, Siobhan ;

Haley, John D. ;

Iwata, Kenneth K. ;

Gibson, Neil W. ;

Griffin, Graeme .

MOLECULAR CANCER THERAPEUTICS, 2006, 5 (11) :2676-2684

[9] Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase [J].

Fan, KQ ;

Wei, P ;

Feng, Q ;

Chen, SD ;

Huang, CK ;

Ma, L ;

Lai, B ;

Pei, JF ;

Liu, Y ;

Chen, JG ;

Lai, LH .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (03) :1637-1642

[10]

FILION LG, 1993, CLIN INVEST MED, V16, P339

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