Project #17594
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#17594 : An online database of RNA-small molecules complexes for rational drug design
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Name of Applicant : Massimiliano Bonomi
Date of application : 13-10-2021
Unit : Structural Bioinformatics
Location : Omics - 3rd floor
Phone : +33 (0)1 44 38 93 63
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Project context and summary :

The majority of approved drugs target proteins, which are encoded in a very small fraction of the human genome. When a pathology is associated with so-called undruggable proteins, an alternative strategy should be sought. In the last twenty years, non-coding RNA molecules have been shown to perform a variety of crucial biological functions, including regulating gene expression, protecting chromosomes from foreign nucleic acids, and guiding telomers synthesis. In this context, targeting either mRNA molecules that are translated into undruggable protein targets or biologically relevant non-coding RNA molecules with small molecules is emerging as a promising therapeutical approach in pathologies such as cancer, viral infections, and neurodegenerative disorders. However, the number of approved drugs that target RNA molecules is still very limited and the existing examples have mostly been found by costly and time-consuming screening experiments. In this project, we aim at building a computational framework to guide the rational design of drugs targeting RNA. To this end, we created a database containing all the experimentally-determined structures of RNA-small molecule complexes deposited in the PDB database. The entries containing drug-like compounds were selected and annotated based on the different biological entities interacting with the ligands. Our database, freely accessible via a web interface, will facilitate i) mapping the chemical space of the small molecules known to bind RNA, ii) understanding the nature of the interactions that drive ligand/RNA recognition, and iii) benchmarking existing tools for in silico protein drug design with RNA targets.

Related team publications :
Bonomi et al. Nat. Methods 16 (2019) 670.
R.-A. A. Garibsingh, et al. Proc. Natl. Acad. Sci. USA 118 (2021) e2104093118.
D. Sindhikara et al. J. Med. Chem. 63 (2020), 12100-12115.
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Project Type : Medium
Status : Closed
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