3
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Xie X, Lan Q, Zhao J, Zhang S, Liu L, Zhang Y, Xu W, Shao M, Peng J, Xia S, Zhu Y, Zhang K, Zhang X, Zhang R, Li J, Dai W, Ge Z, Hu S, Yu C, Wang J, Ma D, Zheng M, Yang H, Xiao G, Rao Z, Lu L, Zhang L, Bai F, Zhao Y, Jiang S, Liu H. Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1. Signal Transduct Target Ther 2024; 9:54. [PMID: 38443334 PMCID: PMC10914734 DOI: 10.1038/s41392-024-01758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Respiratory disease caused by coronavirus infection remains a global health crisis. Although several SARS-CoV-2-specific vaccines and direct-acting antivirals are available, their efficacy on emerging coronaviruses in the future, including SARS-CoV-2 variants, might be compromised. Host-targeting antivirals provide preventive and therapeutic strategies to overcome resistance and manage future outbreak of emerging coronaviruses. Cathepsin L (CTSL) and calpain-1 (CAPN1) are host cysteine proteases which play crucial roles in coronaviral entrance into cells and infection-related immune response. Here, two peptidomimetic α-ketoamide compounds, 14a and 14b, were identified as potent dual target inhibitors against CTSL and CAPN1. The X-ray crystal structures of human CTSL and CAPN1 in complex with 14a and 14b revealed the covalent binding of α-ketoamide groups of 14a and 14b to C25 of CTSL and C115 of CAPN1. Both showed potent and broad-spectrum anticoronaviral activities in vitro, and it is worth noting that they exhibited low nanomolar potency against SARS-CoV-2 and its variants of concern (VOCs) with EC50 values ranging from 0.80 to 161.7 nM in various cells. Preliminary mechanistic exploration indicated that they exhibited anticoronaviral activity through blocking viral entrance. Moreover, 14a and 14b exhibited good oral pharmacokinetic properties in mice, rats and dogs, and favorable safety in mice. In addition, both 14a and 14b treatments demonstrated potent antiviral potency against SARS-CoV-2 XBB 1.16 variant infection in a K18-hACE2 transgenic mouse model. And 14b also showed effective antiviral activity against HCoV-OC43 infection in a mouse model with a final survival rate of 60%. Further evaluation showed that 14a and 14b exhibited excellent anti-inflammatory effects in Raw 264.7 mouse macrophages and in mice with acute pneumonia. Taken together, these results suggested that 14a and 14b are promising drug candidates, providing novel insight into developing pan-coronavirus inhibitors with antiviral and anti-inflammatory properties.
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Affiliation(s)
- Xiong Xie
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoshuai Lan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Jinyi Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yumin Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Maolin Shao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jingjing Peng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Keke Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Xianglei Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ruxue Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jian Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Wenhao Dai
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Ge
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Shulei Hu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Changyue Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dakota Ma
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gengfu Xiao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Leike Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Yao Zhao
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
| | - Hong Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China.
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4
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Flury P, Breidenbach J, Krüger N, Voget R, Schäkel L, Si Y, Krasniqi V, Calistri S, Olfert M, Sylvester K, Rocha C, Ditzinger R, Rasch A, Pöhlmann S, Kronenberger T, Poso A, Rox K, Laufer SA, Müller CE, Gütschow M, Pillaiyar T. Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity. ACS Pharmacol Transl Sci 2024; 7:493-514. [PMID: 38357286 PMCID: PMC10863444 DOI: 10.1021/acsptsci.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024]
Abstract
Cathepsins (Cats) are proteases that mediate the successful entry of SARS-CoV-2 into host cells. We designed and synthesized a tailored series of 21 peptidomimetics and evaluated their inhibitory activity against human cathepsins L, B, and S. Structural diversity was realized by combinations of different C-terminal warhead functions and N-terminal capping groups, while a central Leu-Phe fragment was maintained. Several compounds were identified as promising cathepsin L and S inhibitors with Ki values in the low nanomolar to subnanomolar range, for example, the peptide aldehydes 9a and 9b (9a, 2.67 nM, CatL; 0.455 nM, CatS; 9b, 1.76 nM, CatL; 0.512 nM, CatS). The compounds' inhibitory activity against the main protease of SARS-CoV-2 (Mpro) was additionally investigated. Based on the results at CatL, CatS, and Mpro, selected inhibitors were subjected to investigations of their antiviral activity in cell-based assays. In particular, the peptide nitrile 11e exhibited promising antiviral activity with an EC50 value of 38.4 nM in Calu-3 cells without showing cytotoxicity. High metabolic stability and favorable pharmacokinetic properties make 11e suitable for further preclinical development.
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Affiliation(s)
- Philipp Flury
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Julian Breidenbach
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Rabea Voget
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Laura Schäkel
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Yaoyao Si
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Vesa Krasniqi
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Sara Calistri
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Matthias Olfert
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Katharina Sylvester
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Raphael Ditzinger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Alexander Rasch
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Thales Kronenberger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
- Excellence
Cluster “Controlling Microbes to Fight Infections” (CMFI), Tübingen 72076, Germany
| | - Antti Poso
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), Braunschweig 38124, Germany
- Partner
Site Hannover-Braunschweig, German Center
for Infection Research (DZIF), Braunschweig 38124, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Michael Gütschow
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Thanigaimalai Pillaiyar
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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