Discovery of SARS-CoV-2 3CLPro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein–Ligand Interactions

Abstract

As the etiological agent for the coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges the ongoing efforts of vaccine development and drug design. Due to the accumulating cases of breakthrough infections, there are urgent needs for broad-spectrum antiviral medicines. Here, we designed and examined five new tetrapeptidomimetic anti-SARS-CoV-2 inhibitors targeting the 3C-Like protease (3CLPro), which is highly conserved among coronaviruses and essential for viral replications. We significantly improved the efficacy of a ketoamide lead compound based on high-resolution co-crystal structures, all-atom simulations, and binding energy calculations. The inhibitors successfully engaged the catalytic dyad histidine residue (H41) of 3CLPro as designed, and they exhibited nanomolar inhibitory capacity as well as mitigated the viral loads of SARS-CoV-2 in cellular assays. As a widely applicable design principle, our results revealed that the potencies of 3CLPro-specific drug candidates were determined by the interplay between 3CLPro H41 residue and the peptidomimetic inhibitors.

The SARS‐CoV‐2 main protease (Mpro): Structure, function, and emerging therapies for COVID‐19

“…Moreover, five tetrapeptidomimetic anti‐3CL pro inhibitors, similar to the backbone of 13a , were successfully involved in the design of the catalytic dyad histidine residue (His41) of 3CL pro . Among them, TPM16 and TPM19 exhibited nanomolar inhibition and attenuated the cellular viral loads of SARS‐CoV‐2 114 . Compound 15l with novel α‐acyloxymethylketone warhead mimetic compounds was described by Bai et al., 94 which was identified to have potent SARS‐CoV‐2 3CL pro and viral replication inhibition in vitro.…”

“…Among them, TPM16 and TPM19 exhibited nanomolar inhibition and attenuated the cellular viral loads of SARS-CoV-2. 114 Compound 15l with novel α-acyloxymethylketone warhead mimetic compounds was described by Bai et al, 94 which was identified to have potent SARS-CoV-2 3CL pro and viral replication inhibition in vitro. Moreover, co-crystallization of 15l with SARS-CoV-2 3CL pro confirmed the formation of covalent adducts.…”

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

“…Homologs are similar proteins found in different species, and the presence of human homologs of 3CLpro could increase the risk of adverse effects during administration in humans. By employing the Basic Local Alignment Search Tool (BLASTP) and Position-Specific Iterated BLAST (PSIBLAST) tools on the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, accessed on 20 May 2024), considering the sequence of 3CLpro from SARS-CoV-2 (PDB ID 7WOF) [31], we examined the sequence of 3CLpro from SARS-CoV-2 and restricted the search only to Homo sapiens (taxid:9606). Although we did not find human proteins with sequence similarity to 3CLpro of SARS-CoV-2, it is possible that some human proteins share structural similarities.…”

Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2’s Main Protease (Mpro)

“…Table S3: Tabular representation of conventional hydrogen bonding and its bond length for top-ranked protein-ligand complexes. Table S4: Selection of top-ranked SARS-CoV-2 infection-causing ten key proteins/proteases identified by the literature review of 57 articles [1][2][3][4][5][6]44,.…”