Targeting Sars-Cov-2 main protease in the treatment of COVID-19: Focus on covalent inhibition

Abstract

The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a highly transmissible and pathogenic b-coronavirus, that emerged in late 2019, leading to the global pandemic known as COronaVIrus Disease 2019 (COVID-19). This disease poses a significant threat to both human health and public safety. Despite the remarkable contribution of various vaccines in containing the COVID-19 pandemic, the application and ongoing research of new pharmacological antiviral therapies can help to manage the progression of viral infections, particularly in severe cases in "fragile" patients. Antiviral strategies for the treatment of SARS-CoV-2 infection continue to be a topic of great interest and importance to the scientific community. Among the druggable targets against SARSCoV-2, the main protease (Mpro) plays a crucial role in the processing of the viral polyproteins into functional units necessary for viral replication.5 The ability of this nonstructural protein to recognize the glutamine (Gln) cleavage site is unique and not found in any other human protease. This distinct feature reduces the likelihood of off-target effects, making Mpro an attractive drug target. Structurally, Mpro is a homodimeric cysteine protease. Each protomer (A and B) consists of 306 amino acids, divided into 3 domains. The catalytic domains for each homodimer consist of β-sheets forming a substrate binding cleft, the C-terminal domain involves α-helices that function as dimerization platforms by interacting with N-terminal residues of the second protomer. The binding pocket is organized into four subsites, S1’, S1, S2, and S3/S4, which are occupied by the P1’, P1, P2, and P3 portions of the native polyproteins, respectively.2,3 In region S1’, between domains I and II, is located the catalytic site, characterized by the catalytic dyad (Cys145 and His41). During the hydrolysis of the peptide bond, His41 activates the thiol side chain of Cys145 by deprotonation, with subsequent stabilization of the adduct by the so-called “oxyanion hole”. The S1 subregion is highly specific for the glutamine residue. The S2 subregion is highly plastic and consists of hydrophobic amino acids. The S3/S4 are particularly exposed to the solvent.3 Covalent inhibition of the Cys145 residue of SARS-CoV-2 Mpro with selective antiviral drugs can disrupt the replication process and effectively stop SARS-CoV-2 infection, without affecting human catalytic pathways. Compared to conventional non-covalent agents, the covalent inhibitors provide better efficacy, higher potency, longer residence time in the receptor binding site, sustained pharmacological effect, and the ability to overcome resistance.4-6 The overall efficiency of covalent inhibition is described by the second-order rate constant Kinact/Ki: this value combines the affinity of the initial reversible interaction and the maximum potential rate of covalent bond formation. In the development of covalent inhibitors, it is crucial to achieve an exergonic process for the formation of the enzymeinhibitor complex (E-I), along with minimizing the activation energy barriers. Additionally, the energy barriers at the transition from E-I back to the reactants (E:I) control whether the inhibition is reversible or irreversible. The right balance between irreversibility and reversibility is essential to optimize both the efficacy and the safety profiles of the inhibitors.3,5,7 From the perspective of covalent drugs, this presentation aims to provide an overview of the most representative covalent inhibitors of SARS-CoV-2 Mpro. The Protein Data Bank (PDB) currently lists more than two hundred structures of covalently bound competitive Mpro inhibitors, providing a rich data set for structural and mechanistic analyses. Among the molecules studied, the dipeptide and tripeptide mimetic compounds represent the largest class described so far in the literature due to their intrinsic ability to mimic t