Receptor-guided 3D-QSAR approach for the discovery of c-kit tyrosine kinase inhibitors

Studies of the the three-dimensional quantitative structure–activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a cocrystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to validate the selected pharmacophore model. The best pharmacophore model consisted of five features: one hydrogen-bond donor and four aromatic rings. Reliable statistics were obtained (R2=0.95, Rpred 2=0.75), and the model was validated by using it to select c-kit inhibitors from a database; 82.1% of the hits it retrieved were active. Accordingly, our model can be reliably used to identify new c-kit inhibitors, and can provide useful information when designing new inhibitors

Studio del ruolo delle mutazioni “gatekeeper” V654A e T670I di c-kit kinase nell’interazione con inibitori attraverso un approccio misto Dinamica Molecolare/Docking

La sovraespressione del proto-oncogene c-kit è stata riscontrata nelle cellule ematopoietiche, nel cancro a piccole cellule del polmone e nei tumori stromali gastrointestinali1-3. L’importanza clinica dell’espressione di c-kit nei tumori ha indirizzato la ricerca verso inibitori di questa tirosina chinasi. Imatinib (Gleevec®) (in figura) è stato il primo farmaco utilizzato in terapia, ma la comparsa di mutazioni su c-kit ha portato ad una riduzione dell’efficacia o a completa resistenza a questo trattamento. In alternativa, altri composti si sono mostrati attivi anche nei confronti dei mutanti come ad esempio Sunitinib (Sutent®)4, ma la necessità di nuovi e più efficaci inibitori contro i mutanti rimane ancora un punto critico della ricerca. Si riporta uno studio misto Dinamica Molecolare/Docking (IFD) con lo scopo di svelare i meccanismi molecolari coinvolti nella resistenza a Imatinib, Sunitinib e altri inibitori contro le mutazioni “gatekeeper” V654A e T670I, provando ad evidenziare i punti forti e deboli degli attuali inibitori (Nilotinib, Sorafenib, Motesanib, PKC412, una tienopirimidina TPD, un aminobenzoisossazolo ABIOZ). Questo approccio in silico può consentire di identificare le linee guida per la progettazione di nuovi farmaci attivi contro i mutanti

Study of the role of “gatekeeper” mutations V654A and T670I of c-kit kinase in the interaction with inhibitors by means mixed molecular dynamics/docking approach

The over-expression of c-kit proto-oncogene has been reported in hematopoietic cells, small cell lung cancer, and gastrointestinal stromal tumors. The clinical importance of c-kit expression in tumors focused the research towards inhibitors of this tyrosine kinase. Imatinib (Gleevec®) was the first compound used in therapy, but mutations on c-kit led to reduced effectiveness or ineffectiveness of this treatment. Other compounds are likely to be effective against mutants, such as Sunitinib (Sutent®), but the need for new and most effective inhibitors against mutants is still critical. We report mixed Molecular Dynamics/Docking study with the aim to unveil the molecular mechanism involved in the resistance of Imatinib, Sunitinib, and other known compounds against the “gatekeeper” mutants V654A and T670I. We tried to evidence strong and weak features of actual inhibitors in order to identify the guidelines to design new and most potent inhibitors against c-kit mutants

Discharge Coefficients for Sluice Gates Set in Weirs at Different Upstream Wall Inclinations

Laboratory experiments and numerical simulations are performed to measure discharge coefficients in the case of a gate located on the upstream wall of a weir for flood storage. The effect of the gate slope and the side contraction have been taken into account. The study was first performed experimentally, when three series of tests were carried out with (and without) a broad crested weir located under the gate, at different values of the inclination angle of the weir upstream wall, and at different values of the shape ratio and the relative opening. In order to provide useful suggestions for those involved in sluice gate construction and management, three equations were obtained based on multiple regression, relating the discharge coefficient to different parameters that characterize the phenomenon at hand, separating the case when the broad-crested weir was present. Then numerical simulations were executed by means of the Reynolds-averaged Navier–Stokes (RANS) equations with the k-ε turbulence closure model and in conjunction with the volume of fluid (VOF) method, to validate the numerical results against the experimental and to possibly investigate phenomena not caught by the experimental measurements. Simulated discharges were very close to the observed ones showing that the proposed three-dimensional numerical procedure is a favorable option to correctly reproduce the phenomenon

Molecular Dynamics studies on Mdm2 complexes: an analysis of the inhibitor influence

p53 is a powerful anti-tumoral molecule frequently inactivated by mutations or deletions in cancer. However, half of all human tumors expresses wild-type p53, and its activation, by antagonizing its negative regulator Mdm2, might offer a new strategy for therapeutic protocol. In this work, we present a molecular dynamics study on Mdm2 structure bound to two different known inhibitors with the aim to investigate the structural transitions between apo-Mdm2 and Mdm2-inhibitor complexes. We tried to gain information about conformational changes binding a benzodiazepine derivative inhibitor with respect the known nutlin and the apo form. The conformational changes alter the size of the cleft and were mainly in the linker regions, suggesting that the overall dynamic nature of Mdm2 is related to dynamic movements in these regions

Pharmacophore modelling as useful tool in the lead compounds identification and optimization

The goal of computer-aided molecular design methods in modern medicinal chemistry is to reduce the overall cost and time associated to the discovery and development of a new drug by identifying the most promising candidates to focus the experimental efforts on. Very often, many drug discovery projects have reached already a well-advanced stage before detailed structural data on the protein target have become available. A possible consequence is that often, medicinal chemists develop novel compounds for a target using preliminary structure–activity information, together with the theoretical models of interactions. Only responses that are consistent with the working hypothesis contribute to an evolution of the used models. Within this framework, the pharmacophore approach has proven to be successful, allowing the perception and understanding of key interactions between a receptor and a ligand[1]. In recent years, our research group exploited this useful modeling tool with the aim to identify new chemical entities and/or optimizing known lead compounds to obtain more active drugs in the field of antitumor, antiviral, and antibacterial drugs. In this communication, we present an overview of our recent works in which we used the pharmacophore modelling approach combined with induced fit docking, 3D-QSAR approach, and HTVS for the analysis of drug-receptor interactions and the discovery of new inhibitors of IKKβ, Bcl-xl, and c-kit tyrosine kinase, all targets involved into the initiation and the development of different types of cancer[2-5]