In-silico guided design, screening, and molecular dynamic simulation studies for the identification of potential SARS-CoV-2 main protease inhibitors for the targeted treatment of COVID-19

• Published in: Journal of biomolecular structure & dynamics Vol. 42; no. 4; pp. 1733 - 1750
• Main Authors: Gutti, Gopichand, He, Yiran, Coldren, William H., Lalisse, Remy F., Border, Sarah E., Hadad, Christopher M., McElroy, Craig A., Ekici, Özlem Doğan
• Format: Journal Article
• Language: English
• Published: England Taylor & Francis 03-03-2024
• Subjects: aza-peptide epoxides; COVID-19; main protease; molecular docking; molecular dynamics simulations; peptidomimetics; protease inhibitors; rational drug design; SARS-CoV-2; suicide inhibitors; COVID-19; aza-peptide epoxides; molecular dynamics simulations; rational drug design; SARS-CoV-2; molecular docking; main protease; protease inhibitors; peptidomimetics; suicide inhibitors
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2023.2202247

COVID-19, the disease responsible for the recent pandemic, is caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) of SARS-CoV-2 is an essential proteolytic enzyme that plays a number of important roles in the replication of the virus in human host cells. Blocking the function of SARS-CoV-2 Mpro offers a promising and targeted, therapeutic option for the treatment of the COVID-19 infection. Such an inhibitory strategy is currently successful in treating COVID-19 under FDA's emergency use authorization, although with limited benefit to the immunocompromised along with an unfortunate number of side effects and drug-drug interactions. Current COVID vaccines protect against severe disease and death but are mostly ineffective toward long COVID which has been seen in 5-36% of patients. SARS-CoV-2 is a rapidly mutating virus and is here to stay endemically. Hence, alternate therapeutics to treat SARS-CoV-2 infections are still needed. Moreover, because of the high degree of conservation of Mpro among different coronaviruses, any newly developed antiviral agents should better prepare us for potential future epidemics or pandemics. In this paper, we first describe the design and computational docking of a library of novel 188 first-generation peptidomimetic protease inhibitors using various electrophilic warheads with aza-peptide epoxides, α-ketoesters, and β-diketones identified as the most effective. Second-generation designs, 192 compounds in total, focused on aza-peptide epoxides with drug-like properties, incorporating dipeptidyl backbones and heterocyclic ring motifs such as proline, indole, and pyrrole groups, yielding 8 hit candidates. These novel and specific inhibitors for SARS-CoV-2 Mpro can ultimately serve as valuable alternate and broad-spectrum antivirals against COVID-19.
Communicated by Ramaswamy H. Sarma