RESEARCH & DEVELOPMENT
Three key protein targets essential for the function of SARS-CoV-2 were used to screen a large library of ~12,000 small molecule drug candidates. The targets were the main protease of the virus, Mpro or 3CLpro, the RNA -dependent RNA polymerase (RdRp, essential for viral replication), and the helicase (also part of the virus’ replicative machinery). The docking calculations were validated by redocking drugs into the relevant protein binding sites to recapitulate the binding poses in the experimental structure. The calculations were run on large GPU cluster machines generously made available during the pandemic by Oracle Cloud Systems. The top 80-100 drug candidates identified by the docking calculations were subjected to molecular dynamics calculations to improve the estimates of the relative binding energies of drugs to proteins, and their binding poses in the protein active sites. Subsequent literature
and has a reported in vitro SARS-CoV-2 IC50 of 18.8 µM, and CC50 >20 µM.
In silico approaches to high-throughput drug screening are set to revolutionise pandemic drug discovery efforts.
searches disclosed that >30 per cent of our predicted repurposing candidates for all three SARS-CoV-2 protein targets have experimental validation data, a very impressive validation rate for the computational methods employed. SARS-CoV-2 Mpro inhibitors
Red color is the drug inside the binding pocket Blue color highlights the interacting residues in the binding pocket. Grey color is the protein Fig3: Surface binding representation of Simeprevir with MPro.
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P H A RM A F O C U S A S I A
ISSUE 48 - 2022
Mpro is a key protease essential to SARS-CoV-2 function. We therefore screened drug libraries for compounds that might bind and inhibit Mpro . Several of the top ten best binding drug candidates were antiviral agents simeprevir, sofosbuvir, lopinavir, ritonavir and remdesivir. The more interesting candidates had similar binding affinities and were of diverse activity classes. These were bemcentinib (AXL receptor kinase inhibitor), montelukast (leukotriene receptor antagonist), ergotamine and mergocriptine (ergot alkaloids with adrenergic and dopaminergic receptor agonist activities). Bemcentinib shows in vitro activity against SARS-CoV-2 with 10-40 per cent protection at 50µM in Vero cells and an IC50 of 100nM and CC50 of 4.7µM in Huh cells. Indeed, it is already an investigational treatment for COVID-19 , with a phase 2 trial underway. Montelukast another interesting hit has been shown to produce a significant reduction in SARS-CoV-2 infection in elderly asthmatic patients
SARS-CoV-2 RdRp inhibitors
Given the function of SARS-CoV-2 RdRp to bind RNA, its binding site is large. Most of the repurposed drugs in the list of 20 best binders we predicted had relatively large complex structures and substantial ligand flexibility. Antiviral drugs accounted for half of this list, the remaining compounds in being mostly natural products or their derivatives. These were of particular interest given their relative novelty and molecular diversity. Interestingly, our computational screen identified ivermectin as fitting snugly into the RdRp binding pocket. Ivermectin and other avermectins and milbemycins are broad-spectrum antiparasitic macrocyclic lactones that have shown inconsistent activity against SARS-CoV-2. Ivermectin has been widely touted as a drug against COVID-19, although the debate around its use has become highly politicized. It is interesting, therefore, that our unbiased screening methods identified Ivermectin as one of its top hits. Digoxin is a widely used cardiac drug used to treat heart arrythmias and cardiac failure and has a large complex structure that fitted well into the RdRp binding pocket. It exhibited potent in vitro antiviral effects against SARS-CoV-2 in Vero cells (IC50 37 nM). Another tightly binding natural product, silibinin, is a flavonolignan that is the major active constituent of silymarin, a standardised extract of the milk thistle seeds. It can function as an antioxidant, antineoplastic drug, and hepatoprotectant. Rapamycin, a macrolide antifungal metabolite with immunosuppressant activity that also bound tightly to RdRp, is currently in COVID-19 clinical trials. Other highly ranked natural products from our in silico screens included: carbetocin, a synthetic analogue of oxytocin;eribulin, a fully synthetic macrocyclic ketone analogue of the marine natural product halichondrin B, a potent anti-mitotic anticancer agent; novobiocin, a DNA gyrase and bacterial type IIA topoisomerase inhibitor; and