Identification of FDA approved drugs against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and 3-chymotrypsin-like protease (3CLpro), drug repurposing approach

Abstract

The RNA-dependent RNA polymerase (RdRp) and 3C-like protease (3CLpro) from SARS-CoV-2 play crucial roles in the viral life cycle and are considered the most promising targets for drug discovery against SARS-CoV-2. In this study, FDA-approved drugs were screened to identify the probable anti-RdRp and 3CLpro inhibitors by molecular docking approach. The number of ligands selected from the PubChem database of NCBI for screening was 1760. Ligands were energy minimized using Open Babel. The RdRp and 3CLpro protein sequences were retrieved from the NCBI database. For Homology Modeling predictions, we used the Swiss model server. Their structure was then energetically minimized using SPDB viewer software and visualized in the CHIMERA UCSF software. Molecular dockings were performed using AutoDock Vina, and candidate drugs were selected based on binding affinity (∆G). Hydrogen bonding and hydrophobic interactions between ligands and proteins were visualized using Ligplot and the Discovery Studio Visualizer v3.0 software. Our results showed 58 drugs against RdRp, which had binding energy of -8.5 or less, and 69 drugs to inhibit the 3CLpro enzyme with a binding energy of -8.1 or less. Six drugs based on binding energy and number of hydrogen bonds were chosen for the next step of molecular dynamics (MD) simulations to investigate drug-protein interactions (including Nilotinib, Imatinib and dihydroergotamine for 3clpro and Lapatinib, Dexasone and Relategravir for RdRp). Except for Lapatinib, other drugs-complexes were stable during MD simulation. Raltegravir, an anti-HIV drug, was observed to be the best compound against RdRp based on docking binding energy (-9.5 kcal/mole) and MD results. According to the MD results and binding energy, dihydroergotamine is a suitable candidate for 3clpro inhibition (−9.6 kcal/mol). These drugs were classified into several categories, including antiviral, antibacterial, anti-inflammatory, anti-allergic, cardiovascular, anticoagulant, BPH and impotence, antipsychotic, antimigraine, anticancer, and so on. The common prescription-indications for some of these medication categories appeared somewhat in line with manifestations of COVID-19. We hope that they can be beneficial for patients with certain specific symptoms of SARS-CoV-2 infection, but they can also probably inhibit viral enzymes. We recommend further experimental evaluations in vitro and in vivo on these FDA-approved drugs to assess their potential antiviral effect on SARS-CoV-2.

The dual role of phytochemicals on SARS-CoV-2 inhibition by targeting host and viral proteins

“…Control drugs such as Arbidol (spike), Disulfiram (PL pro ), Lopinavir (M pro ) and Hydroxychloroquine (ACE2), Ivermectin (importin-alpha-5 and importin-beta-1) were considered to systematically compare the reactivity of the resulting plant based bioactive compounds. 25 Finally, DFT based reactivity properties were calculated and molecular dynamics simulations were also performed to understand the protein-ligand interaction.…”

Potential therapeutic options for COVID-19: an update on current evidence

“…As developing a novel drug is a lengthy, expensive and risky process, to discover a cure for this pandemic, the emergency of the pandemic considered to first attempts to identify possible treatments between approved or marketed drugs. Drug repurposing is the best approach to recognize therapeutic options for COVID‑19 in a limited time [ 14 , 15 ]. The great benefit of this approach is the available science about the metabolic profile of drugs, dosages requirement, possible risks, complications and side effects.…”

“…The great benefit of this approach is the available science about the metabolic profile of drugs, dosages requirement, possible risks, complications and side effects. The drawback of these classes of medicines is their inadequate selectivity and, mostly, weak utility among families of viruses [ 15 ].…”

Rational approaches to discover SARS-CoV-2/ACE2 interaction inhibitors: from pharmacophore-based virtual screening to molecular dynamics

“…The pandemic also has tremendous economic damage in most countries around the world [4]. For these reasons, the researchers' efforts are globally trying to discover effective drugs and vaccines to tackle the SARS-CoV-2 infection [5].…”