Design, Synthesis, and Development of Broad Spectrum Coronaviral 3C‐Like Protease Inhibitors to Target Emerging Human Pathogens: A Phylochemical Approach
Authors: St. John Sarah Emma , Mesecar Andrew D 
Published: November 2023

In 2002, the human coronavirus severe acute respiratory syndrome (SARS) caused the first pandemic of the 21st century, infecting over 8,000 people in 32 countries with a case fatality rate near 10%. In 2012, a new human coronavirus emerged, Middle East respiratory syndrome (MERS), and has since infected over 1200 individuals causing at least 450 deaths. Coronaviruses are zoonotic viruses with many animal hosts and reservoirs. As a result, there are a variety of coronaviral strains, which are categorized into phylogenetic groups and subgroups. The human pandemics caused by coronaviruses have emerged as a result of zoonotic shifts, or spillover events, where humans become infected with coronaviral strains from animal reservoirs. Despite the deadly nature of these viruses, the development of anti‐coronaviral therapeutics has been largely unsuccessful. It is crucial to investigate not only the known human coronaviral strains, but also to study the strains of coronaviruses residing in animal reservoirs because of the likelihood of future spillover events.Our goal is to design and develop a small molecule therapeutic against coronaviral infection with efficacy toward multiple coronaviral strains. An attractive target for drug development is the main coronaviral protease, the 3C‐like protease (3CLpro), which is responsible for the cleavage of the viral polyprotein and is essential for the coronavirus lifecycle. The coronaviral 3CLpro is architecturally conserved across phylogenetic groups and subgroups; therefore, the development of broad‐spectrum inhibitors of coronaviral 3CLpro's gives a mechanism to target emerging human coronaviruses from zoonotic reservoirs. We have designed, synthesized, and tested a small library of 48 molecules that show broad‐spectrum inhibition of ten coronaviral 3CLpro's from different phylogenetic origin. From this library, we have identified five compounds that inhibit every coronaviral 3CLpro against which they have been tested and elucidated structure‐activity relationships for broad‐spectrum inhibition of coronaviral 3CLpro's. We are in the process of crystallizing the most promising inhibitors in complex with 3CLpro's from each phylogenetic subgroup and have determined seven inhibitor:3CLpro X‐ray crystal structures, including two X‐ray crystal structures of coronaviral 3CLpro's not yet reported. Recently, we advanced our most promising inhibitors for in vivo anti‐viral assays and have been met with encouraging results.Support or Funding InformationThis work was supported in part by grants to A.D.M. from the National Institutes of Health via the National Institute of Allergy and Infectious Diseases. A.D.M. also acknowledges partial support from the Walther Cancer Foundation. Crystallization and DNA sequencing were partially supported by the Purdue Center for Cancer Research Macromolecular Crystallography and DNA Sequencing Shared Resources which are partially supported by an NIH grant. The authors acknowledge the 220 LS‐CAT beamline staff for their help in acquiring X‐ray data. Use of the Advanced Photon Source, an Office of Science User Facility operated for the U.S. Department of Energy Office of Science by Argonne National Laboratory. Use of the LS‐CAT Sector 21 was supported by the Michigan Economic Development Corporation and the Michigan Technology Tri‐Corridor.