ABSTRACT
Natural products and semi-synthetic compounds continue to be a significant source of drug candidates for a broad range of diseases, including coronavirus disease 2019 (COVID-19), which is causing the current pandemic. Besides being attractive sources of bioactive compounds for further development or optimization, natural products are excellent substrates of unique substructures for fragment-based drug discovery. To this end, fragment libraries should be incorporated into automated drug design pipelines. However, public fragment libraries based on extensive collections of natural products are still limited. Herein, we report the generation and analysis of a fragment library of natural products derived from a database with more than 400,000 compounds. We also report fragment libraries of a large food chemical database and other compound datasets of interest in drug discovery, including compound libraries relevant for COVID-19 drug discovery. The fragment libraries were characterized in terms of content and diversity.
Subject(s)
Biological Products/chemistry , Drug Discovery , Algorithms , Betacoronavirus/isolation & purification , Biological Products/therapeutic use , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Databases, Chemical , Humans , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , SARS-CoV-2 , Small Molecule Libraries/chemistry , Small Molecule Libraries/therapeutic useABSTRACT
The pandemic caused by SARS-CoV-2 (COVID-19 disease) has claimed more than 500 000 lives worldwide, and more than nine million people are infected. Unfortunately, an effective drug or vaccine for its treatment is yet to be found. The increasing information available on critical molecular targets of SARS-CoV-2 and active compounds against related coronaviruses facilitates the proposal (or repurposing) of drug candidates for the treatment of COVID-19, with the aid of in silico methods. As part of a global effort to fight the COVID-19 pandemic, herein we report a consensus virtual screening of extensive collections of food chemicals and compounds known as dark chemical matter. The rationale is to contribute to global efforts with a description of currently underexplored chemical space regions. The consensus approach included combining similarity searching with various queries and fingerprints, molecular docking with two docking protocols, and ADMETox profiling. We propose compounds commercially available for experimental testing. The full list of virtual screening hits is disclosed.