Abstract:
The SARS-CoV-2 virus, a member of the β-coronavirus family, first emerged in Wuhan, China, in December 2019. This resulted in a pandemic with unprecedented socio-economic damage, with over 760 million people infected worldwide and 6.9 million deaths. Infection via droplet transmission is the primary means of transmission, resulting in the development of the disease known as COVID-19. This disease can lead to life-threatening respiratory complications and multi-organ failure. The main protease (Mpro) represents a promising pharmacological target in the treatment of coronavirus diseases, such as COVID-19. This is due to the fact that the Mpro cleaves the substrate in an unique manner. Moreover, Mpro plays a pivotal role in viral transcription (cleavage of non-structural proteins 5-16), which is essential for replication.
In this work, two different structural classes of Mpro inhibitors were synthesized, characterized and optimized. For this purpose, the nucleophilic Cys145 of the catalytically active Cys-His dyad of Mpro should be addressed by using a covalent design approach. The successful covalent addressing of Cys145 was verified by X-ray crystallography on three structures, which provided valuable insights into the unique binding mode. Furthermore, in a broad structure-activity relationship (SAR) study (138 compounds), important parameters for the identification of several promising Mpro inhibitors with IC50 values in the single-digit nanomolar range were derived and the knowledge gained was applied by sequential optimization of the P1-P3 residues or the P1' residue. Moreover, a number of selected potent inhibitors, demonstrated remarkable inhibitory activity at the cellular level against a range of naturally occurring nirmatrelvir-resistant mutants, such as His172Gln. Furthermore, potent inhibitors against the related coronaviruses SARS-CoV-1 , MERS-CoV, and HCoV-NL63 were successfully developed. In addition, the identification of compounds with dual (CatL + Mpro, Scaffold A) or selective (Mpro, Scaffold B) inhibitory properties led to the their antiviral properties. These observations were corroborated by robust in vitro antiviral activity against the wild-type strain of SARS-CoV-2 (in Calu-3 cells) and its variants, such as omicron (in Vero-E6 TMRSS2 cells). Due to their advantageous metabolic stability in human liver microsomes (HLM) and favorable pharmacokinetic properties, some representatives are suitable for further preclinical development.
SARS-CoV-2