HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR.

Fragment-based lead discovery (FBLD) is one of the most efficient methods to develop new drugs. We present here a new computational protocol called High-Throughput Supervised Molecular Dynamics (HT-SuMD), which makes it possible to automatically screen up to thousands of fragments, representing therefore a new valuable resource to prioritise fragments in FBLD campaigns. The protocol was applied to Bcl-XL, an oncological protein target involved in the regulation of apoptosis through protein-protein interactions. Initially, HT-SuMD performances were validated against a robust NMR-based screening, using the same set of 100 fragments. These independent results showed a remarkable agreement between the two methods. Then, a virtual screening on a larger library of additional 300 fragments was carried out and the best hits were validated by NMR. Remarkably, all the in silico selected fragments were confirmed as Bcl-XL binders. This represents, to date, the largest computational fragments screening entirely based on MD.

Citation

Francesca Ferrari, Maicol Bissaro, Simone Fabbian, Jessica De Almeida Roger, Stefano Mammi, Stefano Moro, Massimo Bellanda, Mattia Sturlese. HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR. Journal of enzyme inhibition and medicinal chemistry. 2021 Dec;36(1):1-14

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PMID: 33115279

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