3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials

Author(s)

Amorim, Vitor Martins de Freitas ; Soares, Eduardo Pereira ; Ferrari, Anielle Salviano de Almeida ; Merighi, Davi Gabriel Salustiano ; de Souza, Robson Francisco ; Guzzo, Cristiane Rodrigues ; de Souza, Anacleto Silva

• Document type: Journal article
• Source: Viruses-Basel; v. 16, n. 6, p. 22-pg., 2024-06-01.

Abstract

Proteases represent common targets in combating infectious diseases, including COVID-19. The 3-chymotrypsin-like protease (3CLpro) is a validated molecular target for COVID-19, and it is key for developing potent and selective inhibitors for inhibiting viral replication of SARS-CoV-2. In this review, we discuss structural relationships and diverse subsites of 3CLpro, shedding light on the pivotal role of dimerization and active site architecture in substrate recognition and catalysis. Our analysis of bioinformatics and other published studies motivated us to investigate a novel catalytic mechanism for the SARS-CoV-2 polyprotein cleavage by 3CLpro, centering on the triad mechanism involving His41-Cys145-Asp187 and its indispensable role in viral replication. Our hypothesis is that Asp187 may participate in modulating the pKa of the His41, in which catalytic histidine may act as an acid and/or a base in the catalytic mechanism. Recognizing Asp187 as a crucial component in the catalytic process underscores its significance as a fundamental pharmacophoric element in drug design. Next, we provide an overview of both covalent and non-covalent inhibitors, elucidating advancements in drug development observed in preclinical and clinical trials. By highlighting various chemical classes and their pharmacokinetic profiles, our review aims to guide future research directions toward the development of highly selective inhibitors, underscore the significance of 3CLpro as a validated therapeutic target, and propel the progression of drug candidates through preclinical and clinical phases. (AU)

• FAPESP's process: 21/10577-0 - Biology of Bacteria and Bacteriophages Research Center
• Grantee: Shaker Chuck Farah
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 22/08730-7 - Protein structural biology applied in the study of c-di-GMP signaling and bacterial secretion systems
• Grantee: Cristiane Rodrigues Guzzo Carvalho
• Support Opportunities: Regular Research Grants
• FAPESP's process: 19/00195-2 - Understanding the c-di-GMP signaling networks and the Type II secretion system present into the human pathogen Leptospira interrogans Copenhageni
• Grantee: Cristiane Rodrigues Guzzo Carvalho
• Support Opportunities: Regular Research Grants
• FAPESP's process: 21/00070-5 - Annual resource application plan for supporting institutional research infrastructure (ICB-USP 2018-2019)
• Grantee: Carlos Pelleschi Taborda
• Support Opportunities: Research Grants - Technical Reserve for Institutional Research Infrastructure
• FAPESP's process: 23/13894-1 - CryoEM study of the adsorption of a phage to a type IV pilus
• Grantee: Davi Gabriel Salustiano Merighi
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 16/09047-8 - Comparative genomics of bacterial toxins associated with type IV secretion systems
• Grantee: Robson Francisco de Souza
• Support Opportunities: Regular Research Grants
• FAPESP's process: 20/04680-0 - Design of different fragments of SARS-CoV-2 surface protein spike for the development of fast diagnostic test and vaccine
• Grantee: Cristiane Rodrigues Guzzo Carvalho
• Support Opportunities: Regular Research Grants