Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study

• Published in: Journal of molecular graphics & modelling Vol. 66; pp. 99 - 107
• Main Authors: Mirza, Shaher Bano, Salmas, Ramin Ekhteiari, Fatmi, M. Qaiser, Durdagi, Serdar
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-05-2016
• Subjects: Antiviral Agents - chemistry; Binding Sites - drug effects; Catalytic Domain - drug effects; Dengue - drug therapy; Dengue virus; Dengue Virus - chemistry; Dengue Virus - drug effects; Docking; Drug Design; Drugs; Enzymes; Humans; Hydrogen Bonding; Inhibitors; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular dynamics (MD) simulations; Molecular Dynamics Simulation; Protease Inhibitors - chemistry; Protease Inhibitors - therapeutic use; Thermodynamics; Viral diseases; Viral Nonstructural Proteins - antagonists & inhibitors; Viral Nonstructural Proteins - chemistry; Virtual screening; Viruses; ZINC ligand database; Virtual screening; ZINC ligand database; Dengue virus; Molecular dynamics (MD) simulations; Molecular docking
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2016.03.008

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•There is an urgent need to discover and design better potential inhibitors against Dengue virus.•NS3 protease is one of the potential targets for antiviral drug designing against Dengue virus.•Around 18 million small compounds are used in virtual screening against NS3.•Docking results of top-five compounds show strong predicted binding affinity for the catalytically important residues of NS3.•Selected compounds were further tested at the active site of the NS3 protease helicase enzyme using MD simulations.
Dengue virus is a major issue of tropical and sub-tropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year. This issue necessitates the design of novel anti-dengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus. Therefore, approximately eighteen million compounds from the ZINC database have been virtually screened against nonstructural protein 3 (NS3). The incremental construction algorithm of Glide docking program has been used with its features high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP) and in combination of Prime module, induced fit docking (IFD) approach has also been applied. Five top-ranked compounds were then selected from the IFD results with better predicted binding energies with the catalytic triad residues (His51, Asp75, and Ser135) that may act as potential inhibitors for the underlying target protease enzyme. The top-ranked compounds ZINC95518765, ZINC44921800, ZINC71917414, ZINC39500661, ZINC36681949 have shown the predicted binding energies of −7.55, −7.36, −8.04, −8.41, −9.18kcal/mol, respectively, forming binding interactions with three catalytically important amino acids. Top-docking poses of compounds are then used in molecular dynamics (MD) simulations. In computational studies, our proposed compounds confirm promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds to work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors.