Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods

The dengue virus (DENV) infects approximately 400 million people annually worldwide causing significant morbidity and mortality. Despite advances in understanding the virus life cycle and infectivity, no specific treatment for this disease exists due to the lack of therapeutic drugs. In addition, vaccines available currently are ineffective with severe side effects. Therefore, there is an urgent need for developing therapeutics suitable for effective management of DENV infection. In this study, we adopted a drug repurposing strategy to identify new therapeutic use of existing FDA approved drug molecules to target DENV2 non-structural proteins NS3 and NS5 using computational approaches. We used Drugbank database molecules for virtual screening and multiple docking analysis against a total of four domains, the NS3 protease and helicase domains and NS5 MTase and RdRp domains. Subsequently, MD simulations and MM-PBSA analysis were performed to validate the intrinsic atomic interactions and the binding affinities. Furthermore, the internal dynamics in all four protein domains, in presence of drug molecule binding were assessed using essential dynamics and free energy landscape analyses, which were further coupled with conformational dynamics-based clustering studies and cross-correlation analysis to map the regions that exhibit these structural variations. Our comprehensive analysis identified tolcapone, cefprozil, delavirdine and indinavir as potential inhibitors of NS5 MTase, NS5 RdRp, NS3 protease and NS3 helicase functions, respectively. These high-confidence candidate molecules will be useful for developing effective anti-DENV therapy to combat dengue infection.Communicated by Ramaswamy H. Sarma.

Tissue-type plasminogen activator (tPA) homozygous Tyr471His mutation associates with thromboembolic disease

Tissue-type plasminogen activator (tPA) encoded by PLAT is a major mediator that promotes fibrinolysis and prevents thrombosis. Pathogenetic mutations in PLAT associated with venous thromboembolism have rarely been reported. Here, we report the first case of a homozygous point mutation c.1411T>C (p.Y471H) in PLAT leading to thromboembolic events and conduct related functional studies. The corresponding tPA mutant protein (tPA-Y471H) and wild-type tPA (tPA-WT) were synthesized in vitro, and mutant mice (PLATH/H mice) were constructed. The molecular docking and surface plasmon resonance results indicated that the mutation impeded the hydrogen-bonding interactions between the protease domain of tPA and the kringle 4 domain of plasminogen, and the binding affinity of tPA and plasminogen was significantly reduced with a difference of one order of magnitude. mRNA half-life assay showed that the half-life of tPA-Y471H was shortened. The inferior vena cava thrombosis model showed that the rate of venous thrombosis in PLATH/H mice was 80% compared with 53% in wild-type mice. Our data suggested a novel role for the protease domain of tPA in efficient plasminogen activation, and demonstrated that this tPA mutation could reduce the fibrinolysis function of the body and lead to an increased propensity for thrombosis.

Delineation of an epitope recognized by a chikungunya virus anti-capsid monoclonal antibody on the protease domain using an immuno-informatics approach

The capsid-protein (CP) of chikungunya virus (CHIKV) is reported to generate a primary immune response in infected individuals during disease progression. CP-specific monoclonal antibodies (mAbs) developed in our laboratory, exhibited promising potential in diagnosing recent CHIKV infection in IgM capture ELISA. In this study we focused on the molecular and structural characterization of one such representative mAb ClVE4/D9 to delineate the epitope recognized by it using an immuno-informatics approach. The antigen-antibody interacting residues were found to lie within the dimer interface region of the CP, also predicted as a conformational epitope. This implies that the mAb could interfere during the process of nucleocapsid assembly, ultimately preventing budding and egress of the virus particle. The binding specificity of the mAb highlights the possibility of using this anti-CP antibody for therapeutic or prophylactic treatment against CHIKV.Communicated by Ramaswamy H. Sarma.

Molecular details of spontaneous insertion and interaction of HCV non-structure 3 protease protein domain with PIP2-containing membrane

Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis, and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level. Our results indicated that protease domain of HCV NS3 protein can spontaneously bind and penetrate to an endoplasmic reticulum complex membrane containing phosphatidylinositol 4,5-bisphosphate (PIP2). An amphipathic helix α₀ and loop S1 show their anchoring role to keep the protein on the membrane surface. Proper orientation of the protein domain at membrane surface was identified through measuring tilt angles of two specific vectors, wherein residue R161 plays a crucial role in its final orientation. Remarkably, PIP2 molecules were observed to bind to three main sites of the protease domain via specific electrostatic contacts and hydrogen bonds. PIP2-interaction determines the protein orientation at the membrane while both hydrophobic interplay and PIP2-interaction can stabilize the NS3 - membrane complex. Simulated results provide us with a detailed characterization of insertion, orientation and PIP2-interaction of NS3 protease domain at membrane environment, thus enhancing our understanding of structural functions and mechanism for the association of HCV non-structure 3 protein with respect to ER membranes.