ersilia-os/sars-cov-2-chemspace

Exploration of the chemical space associated with SARS-CoV-2 using manually curated data from UB-CeDD, Cameroon. # SARS-CoV-2 Chemical Space This repository explores the chemical space associated with SARS-CoV-2 according to manually curated data at UB-CeDD (Buea, Cameroon). The project is developed in the context of a research visit of Prof. Fidele Ntie-Kang. ## Overview An important component of UB-CeDD's work is the manual curation of synthetic and natural product compounds targetting a specific pathogen. UB-CeDD has assembled a team of curators who have catalogued compounds of potential SARS-CoV-2 activity. In this project, we set up a chemoinformatics pipeline to expand the chemical space around these manually-curated compounds using tools that can work in low-resource settings. Importantly, while SARS-CoV-2 may not be a top priority globally, the pipeline is conceived such that in can be applied to other pathogens and disease areas. Therefore, this repository should be viewed as a proof-of-concept. Central to the pipeline is the Ersilia Model Hub, our resource of open source AI/ML models for drug discovery. The pipeline consists of the following steps: 1. Manual curation of SARS-CoV-2 related compounds at UB-CeDD. Both synthetic and natural products are annotated. 1. Automated characterisation of the manually-curated compounds using the Ersilia Model Hub. This includes calculation of interesting features such as synthetic-accessibility and natural-product-likeness, as well as ADME properties. 1. Ultra-large scale similarity search against Zinc and Enamine REAL databases. For this, CHEESE is used to query using 2D and 3D similarities. 1. Post-processing and aggregation of similarity search results. 1. Characterisation of the resulting chemical space based on SARS-CoV-2 predictors as provided by the REDIAL-2020 suite of models, as available from the Ersilia Model Hub. ## Data All data used in the project is publicly available. The manually curated molecules can be found under `data/original` and a compilation of both Natural Products and Synthetic Derivatives is availab …