Dans le cadre d’un projet de drug design, l’amélioration de la prédiction de l’affinité représente toujours un défi malgré les nombreux efforts déployés dans ce sens. De plus, les constantes cinétiques d’association et de dissociation sont d'un intérêt majeur pour la découverte de nouveaux médicaments, notamment au stade précoce de l'optimisation des molécules afin de mieux évaluer leurs tolérances et efficacités. De par la récente émergence des études de constantes cinétiques, il existe peu de méthodes de prédiction de ces dernières et aucune approche efficace n'a encore été développée pour estimer correctement ces paramètres cinétiques.En relevant ces deux défis, le premier volet de cette thèse consiste au développement de nouvelles méthodes qui permettent dans un premier temps d’améliorer la prédiction de l’affinité par docking flexible et dans un deuxième temps la prédiction des constantes cinétiques d’association et de dissociations (kon et koff) grâce à des simulations de dynamique moléculaire accélérées.Dans le second volet de cette thèse, nous avons conçu de nouveaux inhibiteurs des LIM kinases, cibles émergentes impliquées dans plusieurs physiopathologies incluant la neurofibromatose et le cancer. Nos composés ont de bonnes affinités et sélectivités in vitro, et d’excellentes activités et tolérances évaluées sur des tests cellulaires. / In a drug design project, improving the prediction of affinity is still an issue despite the considerable efforts made in this direction. In addition, binding kinetic constants are of major interest for the discovery of new drugs, in particular at the early stage of molecules optimization to better evaluate their tolerance and efficacy. Due to the recent emergence of the importance of binding kinetics, methods of kinetic rates prediction remain scarce and no efficient computational approach has still been developed to correctly estimate kinetic parameters.In order to challenge these two problematics, the first part of this thesis consists in the development of new methods that allow, first, to improve the prediction of affinity by a flexible docking and, second, to predict the ligand binding/unbinding pathways and binding kinetic rates (kon and koff) by enhanced molecular dynamics simulations.In the second part of this thesis, we have designed novel inhibitors of LIM kinases, emerging targets involved in several pathophysiologies including neurofibromatosis and cancer. Our compounds have good affinities and selectivities in vitro, and excellent activities and tolerances evaluated on cellular tests.

Neurofibromatosis type 2 (NF2) is a benign tumor disease of the nervous system. Development of bilateral vestibular schwannomas is characteristic of NF2; however patients frequently present schwannomas on other nerves, as well as meningiomas and ependymomas. Currently, there are no drug therapies for NF2. There is an urgent need for development of NF2 therapeutics and this dissertation presents two independent potential therapeutic targets. The disease is caused by mutations in the NF2 gene that encodes a tumor suppressor called merlin. Loss of merlin function is associated with increased activity of Rac and p21-activated kinases (PAK) and deregulation of cytoskeletal organization. LIM domain kinases (LIMK1 and 2) are substrates for Cdc42/Rac-PAK, and modulate actin dynamics by phosphorylating cofilin, an actin severing and depolymerizing agent. LIMKs also translocate into the nucleus and regulate cell cycle progression. Here we report that mouse Schwann cells (MSCs) in which merlin function is lost as a result of Nf2 exon2 deletion (Nf2ΔEx2) exhibited increased levels of LIMK1, LIMK2, and active phospho-Thr508/505-LIMK1/2, as well as phospho-Ser3-cofilin, compared to wild-type normal MSCs. Similarly, levels of LIMK1 and 2 total protein and active phosphorylated forms were elevated in human vestibular schwannomas compared to normal human Schwann cells (SCs). Reintroduction of wild-type NF2 into Nf2ΔEx2 MSC reduced LIMK1 and LIMK2 levels. Pharmacological inhibition of LIMK with BMS-5, decreased the viability of Nf2ΔEx2 MSCs in a dose-dependent manner, but did not affect viability of iv control MSCs. Similarly, LIMK knockdown decreased viability of Nf2ΔEx2 MSCs. The decreased viability of Nf2ΔEx2 MSCs was due to inhibition of cell cycle progression as evidenced by accumulation of cells in G2/M phase. Inhibition of LIMKs arrest cells in early mitosis by decreasing Aurora A activation and cofilin phosphorylation. To increase the search for NF2 therapeutics, we applied an alternative approach to drug discovery with an unbiased pilot high-throughput screen of the Library of Pharmacologically Active Compounds. We assayed for compounds capable of reducing viability of Nf2ΔEx2 MSC as a cellular model for human NF2 schwannomas. AGK2, a SIRT2 (sirtuin 2) inhibitor, was identified as a candidate compound. SIRT2, a mammalian sirtuin, is a NAD+ -dependent protein deacetylase. We show that Nf2ΔEx2 MSC have higher expression levels of SIRT2 and lower levels of overall lysine acetylation than wild-type control MSC. Pharmacological inhibition of SIRT2 decreases Nf2ΔEx2 MSC viability in a dose dependent manner without substantially reducing wildtype MSC viability. Inhibition of SIRT2 activity in Nf2ΔEx2 MSC causes cell death accompanied by release of the necrotic markers lactate dehydrogenase and high mobility group box 1 protein into the medium in the absence of significant apoptosis, autophagy, or cell cycle arrest. Overall this work uncovered two novel potential therapeutic targets, LIMK and SIRT2 for NF2 and tumors associated with merlin deficiency.