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SARS-CoV-2, the causative agent of the disease known as Covid-19, has so farreported around 3,435,000 cases of human infections, including more than239,000 deaths in 187 countries, with no effective treatment currentlyavailable. For this reason, it is necessary to explore new approaches for thedevelopment of a drug capable of inhibiting the entry of the virus into thehost cell. Therefore, this work includes the exploration of potentialinhibitory compounds for the Spike protein of SARS-CoV-2 (PDB ID: 6VSB), whichwere obtained from The Patogen Box. Later, they were filtered through virtualscreening and molecular docking techniques, thus obtaining a top of 1000compounds, which were used against a binding site located in the ReceptorBinding Domain (RBD) and a cryptic site located in the N-Terminal Domain (NTD),resulting in good pharmaceutical targets for the blocking the infection. Fromthe top 1000, the best compound (TCMDC-124223) was selected for the bindingsite. It interacts with specific residues that intervene in the recognition andsubsequent entry into the host cell, resulting in a more favorable binding freeenergy in comparison to the control compounds (Hesperidine and Emodine). In thesame way, the compound TCMDC-133766 was selected for the cryptic site. Theseidentified compounds are potential inhibitors that can be used for thedevelopment of new drugs that allow effective treatment for the disease.

Targeting Receptor Binding Domain and Cryptic Pocket of Spike glycoprotein from SARS-CoV-2 by biomolecular modeling