Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal

Abstract

We report the discovery of a novel small-molecule inhibitor of the dengue virus (DENV) protease (NS2B-NS3pro) using a newly constructed Web-based portal (DrugDiscovery@TACC) for structure-based virtual screening. Our drug discovery portal, an extension of virtual screening studies performed using IBM's World Community Grid, facilitated access to supercomputer resources managed by the Texas Advanced Computing Center (TACC) and enabled druglike commercially available small-molecule libraries to be rapidly screened against several high-resolution DENV NS2B-NS3pro crystallographic structures. Detailed analysis of virtual screening docking scores and hydrogen-bonding interactions between each docked ligand and the NS2B-NS3pro Ser135 side chain were used to select molecules for experimental validation. Compounds were ordered from established chemical companies, and compounds with established aqueous solubility were tested for their ability to inhibit DENV NS2B-NS3pro cleavage of a model substrate in kinetic studies. As a proof-of-concept, we validated a small-molecule dihydronaphthalenone hit as a single-digit-micromolar mixed noncompetitive inhibitor of the DENV protease. Since the dihydronaphthalenone was predicted to interact with NS2B-NS3pro residues that are largely conserved between DENV and the related West Nile virus (WNV), we tested this inhibitor against WNV NS2B-NS3pro and observed a similar mixed noncompetitive inhibition mechanism. However, the inhibition constants were ∼10-fold larger against the WNV protease relative to the DENV protease. This novel validated lead had no chemical features or pharmacophores associated with adverse toxicity, carcinogenicity, or mutagenicity risks and thus is attractive for additional characterization and optimization.

Thioguanine-based DENV-2 NS2B/NS3 protease inhibitors: Virtual screening, synthesis, biological evaluation and molecular modelling

“…Nevertheless, many peptidic or modified peptidic molecules have been discovered to have good NS2B/NS3pro inhibition activities [15,[24][25][26][27][28][29][30]. In addition, there are also reports of potent small molecule NS2B/ NS3pro inhibitors from natural products (panduratin [31], agathisflavone and quercetin [32]), from synthetic medicinal chemistry (dehydronaphthalene [33], benzimidazole [34], and thiadiazoloacrylamide [35]) or from the utilisation of computational methods [36][37][38][39].…”

In silicoidentification of potential inhibitors against human 2’-5’-oligoadenylate synthetase (OAS) proteins

“…Virtual screenings against the donor and acceptor binding sites of OAS proteins were performed using the DrugDiscovery@TACC virtual portal [43], [44]. This web portal executed the Autodock Vina program on the “Lonestar” supercomputer at TACC (Texas Advanced Computing Center).…”

“…While the protein structures in the “active-Mg 2+ -donor” state were used for screening on the acceptor binding site, the remaining targets were employed for screening on the donor binding site (Table 1). The chemical library used was a subset of the ZINC database termed the “ZINC (Lrg)” library [42], [43]. This library includes 642,769 small molecules with “clean, drug-like” constraints such as molecular weight between 150 and 500 Da, clogP ≤ 5, five or fewer hydrogen-bond donors, and ten or fewer hydrogen-bond acceptors.…”

The Burden of Dengue and Chikungunya Worldwide: Implications for the Southern United States and California

“…Most work is focused on identifying inhibitors of the NS3 multifunctional non-structural protein, NS2B/NS3 protease, and NS5 polymerase through cell culture-based high- or low-throughput approaches and in silico screening. 55–60 Host proteins required for viral replication or egress are also being explored as possible targets for drug development. 61,62 For an excellent review of dengue drug development, see Lim et al, 2013.…”