title: Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study.
abstract: 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.
authors.affiliation: Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Shaher Bano
authors.initials: SB
authors.lastname: Mirza
authors.affiliation: Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.
authors.forename: Ramin Ekhteiari
authors.initials: RE
authors.lastname: Salmas
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan. Electronic address: qaiser.fatmi@comsats.edu.pk.
authors.forename: M Qaiser
authors.initials: MQ
authors.lastname: Fatmi
authors.affiliation: Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey. Electronic address: serdar.durdagi@med.bahcesehir.edu.tr.
authors.forename: Serdar
authors.initials: S
authors.lastname: Durdagi
mesh_terms: D000998:Antiviral Agents / Q000737:chemistry; D001665:Binding Sites / Q000187:drug effects; D020134:Catalytic Domain / Q000187:drug effects; D003715:Dengue / Q000188:drug therapy*; D003716:Dengue Virus / Q000737:chemistry / Q000187:drug effects*; D015195:Drug Design; D006801:Humans; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011480:Protease Inhibitors / Q000737:chemistry* / Q000627:therapeutic use; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*
chemical_list: D000998:Antiviral Agents; D011480:Protease Inhibitors; D017361:Viral Nonstructural Proteins
keywords: Dengue virus; Molecular docking; Molecular dynamics (MD) simulations; Virtual screening; ZINC ligand database