The SUMMIT supercomputer has very recently screened thousands of potential compounds that might interrupt the binding of the virus to its human target receptor, ACE2, to point to possible experimental directions for research. Which of these compounds are readily available?
The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally
Docking Results for the Host-Virus Interface (S-protein-ACE2 Receptor Complex)
Of the top 41 ranked compounds, we highlight four (with scores ranging from -7.4 to - 7.1) based on their poses, which are represented in figure 2. These highlighted compounds are pemirolast41-42 (ZincID: 5783214), isoniazid pyruvate (ZincID: 4974291), nitrofurantoin (ZincID: 3875368), and eriodictyol (ZincID: 58117). Of the four small-molecules shown in figure 2, the top-ranked, pemirolast, is an anti-allergy medication or for use in treating chronic asthma41-42, while the second and third of the highlighted hits are related to well-known antibiotics, with nitrofurantoin an antibiotic for use against urinary tract infections43 and isoniazid pyruvate being a metabolite of the tuberculous antibiotic Isoniazid44. The last, Eriodictyol, is a flavanone found in Herba Santa and is a traditional herbal remedy used for asthma and treating colds45
Docking Results for the Isolated Virus S-protein Host Recognition Domain
The three top-scoring ligands (with ZINC15 annotations denoting regulatory data available) for the isolated S-protein were: Cepharanthine, Ergoloid, and Hypericin. Cepharanthine and Hypericin are both natural products with both having been the subject of multiple studies on their ability to act as antiviral46-49 agents (including against coronaviruses47, 49), while Ergoloid is an FDA approved50 drug component of interest in dementia therapies51-53