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High-throughput virtual screening to identify non-covalent inhibitors of CRM1 with anti-tumural potential
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Resumo(s)
The ideia of using CRM1 inhibitors to target several neoplasia is not new, with a few inhibitors already being used in the treatment of multiple myeloma. However, all known inhibitors of CERM1 bind covalently to a Cysteine in the NES-binding groove, thus making them highly toxic. In this work , we set on to use a combina tion of computational methods (namely Molecular Dynamics simulations and Molecular Docking) to sample representative conformations, alternative to the biased crystal structure, of the NES-binding groove in solution, and to identify potential non-covalent inhibitorsos of CRM1. We also aimed at studying how the C528S mutation impacts the pocket, since this mutation will be used in the experimental protocols to help identify the desired inhibitors. the MD simulations allowed for a thorough characterization on the NES-binding groove and its"mini-pockets". Two representative conformations of CERM1 with an open (ready-to-bind) NES-binding groove were selected for the Docking calculations. The C528S MD simulations suggest that, despitefavoring the more closed conformations, this mutation does not alter significantly the conformational landscape of the CRM1 NES-binding groove. A HTVS protocol was implemented using the mentioned conformations from the MD simulations and the crystal structure (PDB ID:6TVO) to screen a large compound database (~6200 compounds) provided by our collaborator, Prof. Romano Silvestri (Sapeenza University, Italy). We selected the top-10 rankedcompounds from each HTVS campaign (30 compounds) acording to their binding energies and noticedthat they do not possesss chemical groups that are susceptible to a nucleophilic attack by the Cys528thiolate. Most of these selected compounds were synthesized in Prof. Silvestri's Lab. and sent to Prof. Wolfgang Link Lab. (University of Madrid, Spain) to be tested experimentally using CRM1 inhibitionassays. The inhibition constants measured will be determinant to validate our computational approach and to help identify, at least, new lead compounds that could pave the way towards a true non-covalent inhibitor of this very important protein.
Descrição
Tese de mestrado, Bioinformática e Biologia Computacional, Universidade de Lisboa, Faculdade de Ciências, 2022
Palavras-chave
CRM1 Inibidores Dinâmica Molecular Docking Molecular Screening de Bases de Dados