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Natural Products-based drug design from Bahia Semi-Arid region against SARS-CoV-2 Mpro (3Clpro)

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), receives global attention due to the serious threat that affect public health. Since December 2019, its incidence affecting millions of patients and its rapid dissemination on a worldwide scale have led the searching for its treatment. To discover hit compounds that can be used alone or in combination with repositioned drugs, we initiated a structure-assisted drug design program including Virtual Screening, Docking, pharmacokinetic and toxicological analysis (ADMET) and Molecular Dynamics Simulation (MD) from Natural Products Database of the Bahia Semi-Arid region (NatProDB). We also aimed to identify novel scaffolds that target the SARS-CoV-2 Main Protease (Mpro, 3Clpro) since this protein plays a pivotal role in mediating viral replication and transcription, which makes it an attractive drug target for coronaviruses. Here, we selected 10 molecules that could be studied in vitro to lead discovery in response to this infectious diseases. The best SARS-CoV-2 Mpro complexes interactions revealed that some enzyme sites were accessed thereby confirming that this method can be employed as a suitable starting method for the identification of novel SARS-CoV-2 Mpro inhibitors. Two compounds (b01 and b02) suggest a better potential for interaction with SARS-CoV-2 main protease (Mpro) and could be further studied.