Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening and in vitro assays

Abstract

The emergence of SARS/MERS drug-resistant SARS-CoV2 comes with higher rates of transmission and mortality. Like all coronaviruses, SARS-CoV-2 is a relatively large virus consisting of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs by identifying potential drugs that are predicted to effectively inhibit critical enzymes. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral multiplication cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2’-O-MT. For virtual screening, the energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard(Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs (n=5903) that are approved by worldwide regulatory bodies. The screening was performed against viral targets using three sequential docking modes (i.e. HTVS, SP, and XP). Our in-silico virtual screening identified ~290 potential drugs based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. Herein we report the evaluation of in-vitro efficacy of selected hit drug molecules on SARS-CoV-2 inhibition. Among eight molecules included in our evaluation, we found inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), as the potent inhibitor of SARS-CoV-2 in-vitro. Further, in-silico predicted target validation through enzymatic assays confirmed 3CLpro to be the target. Therefore, our data support advancing BIM IX for clinical evaluation as a potential treatment for COVID-19. This is the first study that has showcased the possibility of using bisindolylmaleimide IX to treat COVID-19 through this pipeline.

Heparin: A simplistic repurposing to prevent SARS-CoV-2 transmission in light of its in-vitro nanomolar efficacy

“…In the present study, through the application of in-silico based virtual screening of FDA and world approved drugs [ 23 ] and specific in-vitro validations, we found that UFH had a sub-nanomolar activity and a potential to block receptor-binding domain (RBD) of SARS-CoV-2, thus pointing to its immense potential as a transmission-blocking agent. Collectively, the current findings emphasize the possible beneficial use of heparin, both as a transmission-blocking agent and treatment for coagulopathy/DIC associated symptoms in severe COVID-19 patients.…”

Therapeutic and Vaccine Options for COVID-19: Status after Six Months of the Disease Outbreak

“…Nonstructural uridylate-specific endoribonuclease (NendoU) is another nonstructural protein worth investigating as an antiviral target since its endoribonuclease is suspected to be similar in all coronaviruses. 23,24 Angiotensin-converting enzyme 2 (ACE2) is an antigen receptor recognition enzyme that is located on the host cell surface. To gain entry into a target cell, the SARS-CoV S protein binds to the ACE2 receptor.…”

Antiviral evaluation of hydroxyethylamine analogs: Inhibitors of SARS-CoV-2 main protease (3CLpro), a virtual screening and simulation approach

“…As per the viral cycle, upon entry into the host cell, the incoming viral genome is initially translated to produce two large precursor polyproteins 1a (pp1a) and 1ab (pp1ab), that are processed by ORF 1a-encoded viral proteinases, papain-like protease (PLpro), and the 3-chymotrypsin-like cysteine protease (Mpro or 3CLpro) into 16 mature non-structural proteins (NSP1-NSP16) 22 . Many of the NSPs perform essential functions in viral RNA replication and translation 22 , 23 , 24 . The 3CLpro enzyme, a.k.a.…”