A team of scientists from the USA and Sweden has recently screened 8 million small molecule inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the crystal structure of spike receptor-binding domain (RBD)/angiotensin-converting enzyme 2 (ACE2) complex, they have identified one inhibitor, which is highly synergistic with antiviral medicine remdesivir and can inhibit both SARS-CoV-2 replication and host cell entry at sub-micromolar concentration. The study is currently available on the bioRxiv* preprint server.

Background

Since its emergence in December 2019 in China, SARS-CoV-2, the causative pathogen of coronavirus disease 2019 (COVID-19), has infected 130 million people and claimed 2.8 million lives globally. Within one year of the pandemic, several vaccines have been developed to battle the viral spread. Some of these vaccines are currently under clinical trials, and some are rolling out globally with the primary aim of saving susceptible individuals. Simultaneously, many antiviral medicines have been repurposed to treat severe COVID-19 patients. One such repurposed medicine is remdesivir, which has received emergency use approval in many countries for treating hospitalized COVID-19 patients.

However, because of the discrepancy in results demonstrating the actual benefits of remdesivir, the USA government has restricted the use of remdesivir only for critically ill COVID-19 patients requiring oxygen supplementation. Given the overshooting trajectory of the COVID-19 pandemic, it is thus necessary to develop potent therapeutic inhibitors against SARS-CoV-2 together with developing prophylactic vaccines.

In the current study, the scientists have used a computer-aided drug design approach to screen 8 million small molecule inhibitors against SARS-CoV-2. Specifically, using the crystal structure of the RBD/ACE2 complex, they have docked these inhibitors within the pockets present at the RBD/ACE2 interface. Depending on the docking scores, they initially selected 5 candidates and tested their efficacy in inhibiting SARS-CoV-2 replication and viral entry using in vitro cell-based assays. This led to the identification of two inhibitors (MU-UNMC-1 and MU-UNMC-2) with the highest antiviral efficacy.

Important observations

Using a human bronchial epithelial cell line and Vero-STAT1 knockout cells, the scientists investigated the antiviral efficacy of MU-UNMC-1 and MU-UNMC-2 against wildtype SARS-CoV-2. The findings revealed that both MU-UNMC-1 and MU-UNMC-2 were capable of significantly inhibiting viral replication inside host cells. Of these two compounds, MU-UNMC-2 showed strong antiviral effects against both wildtype SARS-CoV-2 and lentiviral-based pseudovirus expressing SARS-CoV-2 spike protein. Specifically, MU-UNMC-2 robustly inhibited the entry of SARS-CoV-2 into the host cell, whereas only a moderate inhibitory effect was observed for MU-UNMC-1.     

While examining the biophysical properties of all tested compounds using the SwissADME web portal, the scientists observed a synergistic effect MU-UNMC-2 with antiviral medicine remdesivir. Moreover, the compound exhibited high permeability, moderate solubility, and low toxicity levels.

Given the synergy between MU-UNMC-2 and remdesivir, the scientists investigated the combined efficacy of two compounds using in vitro cell-based assays. The findings revealed that the combination of MU-UNMC-2 and remdesivir had more potent antiviral efficacy than the individual compounds alone.

Study significance

The study identifies a potent small molecule inhibitor (MU-UNMC-2) against SARS-CoV-2 that acts at the spike RBD/ACE2 interface to inhibit both viral entry and replication. The compound also exhibits synergistic effects with antiviral medicine remdesivir.

Because of the better pharmacokinetic profile, stability, and easy logistic chain shipment process, small molecule inhibitors are generally considered more effective than therapeutic macromolecules in treating SARS-CoV-2 infection. Because the compound identified in the study targets the RBD/ACE2 interface and not ACE2 directly, treatment with this inhibitor is not expected to disrupt the renin-angiotensin system and impair cardiovascular and renal functions.

Another potential advantage is that a combination treatment with MU-UNMC-2 and remdesivir has been found to significantly reduce the dosage requirement, which in turn reduces the cytotoxicity profile and risk of developing drug resistance. An enhanced antiviral potency of the combination treatment over monotherapies highlights the importance of simultaneously targeting different stages of the viral life-cycle, with MU-UNMC-2 targeting the viral entry and remdesivir targeting the viral replication.      

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.