Coronaviruses main proteases and their inhibitors.

The SARS-CoV-2 main protease (Mpro) plays a pivotal role in the viral life cycle by cleaving polyproteins pp1a and pp1ab into functional non-structural proteins (NSPs), including components essential for RNA replication, such as nsp7, nsp8, and RNA-dependent RNA polymerase. The high sequence conservation across coronaviruses and absence of closely related human proteases make Mpro an attractive target for selective antiviral interventions. Recent efforts in drug discovery have led to the development of a wide spectrum of Mpro inhibitors, including covalent peptidomimetics (e.g., nirmatrelvir) and non-covalent small molecules with enhanced pharmacological profiles, such as ensitrelvir. Structure-based drug design, fragment-based drug discovery (FBDD), high-throughput screening (HTS), and in silico approaches have contributed to identification of novel scaffolds and optimization of binding interactions within the catalytic pocket. Non-covalent inhibitors offer reversible binding mechanisms that reduce off-target effects and are particularly promising for clinical translation. However, challenges such as the limited oral bioavailability of peptidomimetic compounds, metabolic instability, and emerging resistance highlight the need for further optimization. Ongoing research is exploring prodrug strategies, advanced delivery systems, and combinatorial regimens that integrate Mpro inhibitors with other antivirals to achieve synergistic effects and suppress resistance. This chapter provides a comprehensive overview of the current landscape of Mpro-targeted therapeutics and emphasizes their potential role in future pandemic preparedness.