Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study
Mst. Sharmin Sultana Shimu,
Shafi Mahmud,
Trina Ekwati Tallei,
Saad Ahmed Sami,
Ahmad Akroman Adam,
Uzzal Kumar Acharjee,
Gobindo Kumar Paul,
Talha Bin Emran,
Shahriar Zaman,
Md. Salah Uddin,
Md. Abu Saleh,
Sultan Alshehri,
Mohammed M Ghoneim,
Maha Alruwali,
Ahmad J. Obaidullah,
Nabilah Rahman Jui,
Junghwan Kim,
Bonglee Kim
Affiliations
Mst. Sharmin Sultana Shimu
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Shafi Mahmud
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Trina Ekwati Tallei
Department of Biology, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado 95115, Indonesia
Saad Ahmed Sami
Department of Pharmacy, University of Chittagong, Chittagong 4331, Bangladesh
Ahmad Akroman Adam
Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia
Uzzal Kumar Acharjee
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Gobindo Kumar Paul
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Talha Bin Emran
Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
Shahriar Zaman
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Md. Salah Uddin
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Md. Abu Saleh
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
Sultan Alshehri
Department of Pharamaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
Mohammed M Ghoneim
Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
Maha Alruwali
Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
Ahmad J. Obaidullah
Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
Nabilah Rahman Jui
Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong 4202, Bangladesh
Junghwan Kim
Department of Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
Bonglee Kim
Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea
The spread of the Dengue virus over the world, as well as multiple outbreaks of different serotypes, has resulted in a large number of deaths and a medical emergency, as no viable medications to treat Dengue virus patients have yet been found. In this paper, we provide an in silico virtual screening and molecular dynamics-based analysis to uncover efficient Dengue infection inhibitors. Based on a Google search and literature mining, a large phytochemical library was generated and employed as ligand molecules. In this investigation, the protein target NS2B/NS3 from Dengue was employed, and around 27 compounds were evaluated in a docking study. Phellodendroside (−63 kcal/mole), quercimeritrin (−59.5 kcal/mole), and quercetin-7-O-rutinoside (−54.1 kcal/mole) were chosen based on their binding free energy in MM-GBSA. The tested compounds generated numerous interactions at Lys74, Asn152, and Gln167 residues in the active regions of NS2B/NS3, which is needed for the protein’s inhibition. As a result, the stable mode of docked complexes is defined by various descriptors from molecular dynamics simulations, such as RMSD, SASA, Rg, RMSF, and hydrogen bond. The pharmacological properties of the compounds were also investigated, and no toxicity was found in computational ADMET properties calculations. As a result, this computational analysis may aid fellow researchers in developing innovative Dengue virus inhibitors.
