How missense mutations in receptors tyrosine kinases impact constitutive activity and alternate drug sensitivity: insights from molecular dynamics simulations

The fundamental oncology-related research is required for a deeper understanding of the molecular mechanisms associated with the normal and/or abnormal protein functions, which are closely related with structure and dynamics of the macromolecules involved in these process. The most common origin of oncogenic events is related to missense mutations. Mutation-induced structural effects promoted by oncogenic mutations in receptor tyrosine kinases (RTKs), are not yet fully characterized. Computational biology completes and enriches experimental data, producing a novel vision of molecular mechanisms governing RTKs activity. In series of our papers, we studied the structural and dynamical features of native and mutated RTKs from III family (KIT and CSF-1R), yielding a detailed description of their mechanisms of activation, ligand-depend for the native proteins and constitutive for the distinct mutants. The mechanisms of RTKs activation are described in terms of allosteric regulation between coupled regulating fragments of the protein, juxta-membrane region (JMR) and activation (A-) loop. As some mutations promote resistance to the clinically-used drugs, we analyzed the affinity of imatinib to these therapeutic targets. The computationally-obtained (in silico) data were correlated with in vivo and in vitro observations, thus validating our numerically-based accounts. Going forward, clinical validation of cancer-related models and simulations are cornerstones key of translation of in silico data into biomedical research, at clinical and pharmacological levels

The First 3D Model of the Full-Length KIT Cytoplasmic Domain Reveals a New Look for an Old Receptor

International audienceReceptor tyrosine kinases (RTKs) are key regulators of normal cellular processes and have a critical role in the development and progression of many diseases. RTK ligand-induced stimulation leads to activation of the cytoplasmic kinase domain that controls the intracellular signalling. Although the kinase domain of RTKs has been extensively studied using X-ray analysis, the kinase insert domain (KID) and the C-terminal are systematically missing in all reported structures. We communicate the first structural model of the full-length RTK KIT cytoplasmic domain, a crucial target for cancer therapy. This model was achieved by integration of ab initio KID and C-terminal probe models into an X-ray structure, and by their further exploration through molecular dynamics (MD) simulation. An extended (2-µs) MD simulation of the proper model provided insight into the structure and conformational dynamics of the full-length cytoplasmic domain of KIT, which can be exploited in the description of the KIT transduction processes

The G140S mutation in HIV integrases from raltegravir-resistant patients rescues catalytic defect due to the resistance Q148H mutation

Raltegravir (MK-0518) is the first integrase (IN) inhibitor to be approved by the US FDA and is currently used in clinical treatment of viruses resistant to other antiretroviral compounds. Virological failure of Raltegravir treatment is associated with mutations in the IN gene following two main distinct genetic pathways involving either the N155 or Q148 residue. Importantly, in most cases, an additional mutation at the position G140 is associated with the Q148 pathway. Here, we investigated the viral DNA kinetics for mutants identified in Raltegravir-resistant patients. We found that (i) integration is impaired for Q148H when compared with the wild-type, G140S and G140S/Q148H mutants; and (ii) the N155H and G140S mutations confer lower levels of resistance than the Q148H mutation. We also characterized the corresponding recombinant INs properties. Enzymatic performances closely parallel ex vivo studies. The Q148H mutation ‘freezes’ IN into a catalytically inactive state. By contrast, the conformational transition converting the inactive form into an active form is rescued by the G140S/Q148H double mutation. In conclusion, the Q148H mutation is responsible for resistance to Raltegravir whereas the G140S mutation increases viral fitness in the G140S/Q148H context. Altogether, these results account for the predominance of G140S/Q148H mutants in clinical trials using Raltegravir

In Silico

Most antiretroviral medical treatments were developed and tested principally on HIV-1 B nonrecombinant strain, which represents less than 10% of the worldwide HIV-1-infected population. HIV-1 circulating recombinant form CRF02_AG is prevalent in West Africa and is becoming more frequent in other countries. Previous studies suggested that the HIV-1 polymorphisms might be associated to variable susceptibility to antiretrovirals. This study is pointed to compare the susceptibility to integrase (IN) inhibitors of HIV-1 subtype CRF02_AG IN respectively to HIV-1 B. Structural models of B and CRF02_AG HIV-1 INs as unbound enzymes and in complex with the DNA substrate were built by homology modeling. IN inhibitors—raltegravir (RAL), elvitegravir (ELV) and L731,988—were docked onto the models, and their binding affinity for both HIV-1 B and CRF02_AG INs was compared. CRF02_AG INs were cloned and expressed from plasma of integrase strand transfer inhibitor (INSTI)-naïve infected patients. Our in silico and in vitro studies showed that the sequence variations between the INs of CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. The binding modes and affinities of INSTI inhibitors to B and CRF02_AG INs were found to be similar. Although previous studies suggested that several naturally occurring variations of CRF02_AG IN might alter either IN/vDNA interactions or INSTIs binding, our study demonstrate that these variations do affect neither IN activity nor its susceptibility to INSTIs

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites

Properties of Electrodeposited CuSCN 2D Layers and Nanowires Influenced by Their Mixed Domain Structure

International audienc

How missense mutations in receptors tyrosine kinases impact constitutive activity and alternate drug sensitivity: insights from molecular dynamics simulations

The fundamental oncology-related research is required for a deeper understanding of the molecular mechanisms associated with the normal and/or abnormal protein functions, which are closely related with structure and dynamics of the macromolecules involved in these process. The most common origin of oncogenic events is related to missense mutations. Mutation-induced structural effects promoted by oncogenic mutations in receptor tyrosine kinases (RTKs), are not yet fully characterized. Computational biology completes and enriches experimental data, producing a novel vision of molecular mechanisms governing RTKs activity. In series of our papers, we studied the structural and dynamical features of native and mutated RTKs from III family (KIT and CSF-1R), yielding a detailed description of their mechanisms of activation, ligand-depend for the native proteins and constitutive for the distinct mutants. The mechanisms of RTKs activation are described in terms of allosteric regulation between coupled regulating fragments of the protein, juxta-membrane region (JMR) and activation (A-) loop. As some mutations promote resistance to the clinically-used drugs, we analyzed the affinity of imatinib to these therapeutic targets. The computationally-obtained (in silico) data were correlated with in vivo and in vitro observations, thus validating our numerically-based accounts. Going forward, clinical validation of cancer-related models and simulations are cornerstones key of translation of in silico data into biomedical research, at clinical and pharmacological levels