Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease

Abstract

Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.

A Computational Approach Applied to the Study of Potential Allosteric Inhibitors Protease NS2B/NS3 from Dengue Virus

“…In addition, an analysis of Figure 3 In addition, an analysis of Figure 3 showed that the RMSD values of the NS2B/NS3pro-ZINC000001679427 and NS2B/NS3pro-ZINC000001680989 complexes fluctuated within a range of ±1.2 Å over time, thus exhibiting the greater stability of the protein complex link during the simulation [22]. Notably, these binders presented the best PLPChem score and interacted with the essential residues for inhibition at the DENV NS2B/NS3 allosteric site [12,13,16].…”

“…Typically, the tails (N-and C-terminals) fluctuate more than any other part of the protein. Secondary structure elements such as alpha helices and beta strands are usually more rigid than the unstructured part of the protein and thus fluctuate less than the loop regions [16]. In the NS2B/NS3pro-ZINC000001680989, NS2B/NS3pro-ZINC000001684485 and NS2B/NS3pro-ZINC000006694490 complexes, the rate of fluctuation is higher at residue No.…”

“…The fact that the DENV NS3pro active site is planar and preferentially binds to peptidebased substrates, such as the competitive peptidomimetics inhibitors of NS2B/NS3pro DENV found in the literature, has conferred limited oral bioavailability and difficulties in in vivo assays in studies of potential inhibitors targeting the active site of this enzyme [13,16,17]. However, this strengthens the strategy of exploring allosteric sites that are known to be successful targets of small molecule inhibitors, as presented in the works of [13][14][15][16].…”

Loop Dynamics and Conformational Flexibility in Dengue Serine Protease Activity: Noninvasive Perturbation by Solvent Exchange

“…The enzyme is conserved among the established four serotypes of the virus viz, DENV1, DENV2, DENV3, and DENV4 that are primarily responsible for dengue hemorrhagic fever or dengue shock syndrome. 1 There are approximately 100 million annual cases of dengue virus infection seen worldwide with a fatality rate of more than 2.5%. 2 The virus is spread from a dengue patient to healthy individuals via the bite of infected female Aedes mosquitoes (Aedes aegypti and Aedes polynesiensis).…”

“…The trypsin-like NS2B/NS3 serine protease of dengue virus (DENV) is a classic example of such natural proteases. The enzyme is conserved among the established four serotypes of the virus viz, DENV1, DENV2, DENV3, and DENV4 that are primarily responsible for dengue hemorrhagic fever or dengue shock syndrome …”