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Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study.
Molecules. 2022 Jan 20; 27(3)M

Abstract

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.

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Authors+Show Affiliations

Shimu MSS
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Mahmud S
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Tallei TE
Department of Biology, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado 95115, Indonesia.
Sami SA
Department of Pharmacy, University of Chittagong, Chittagong 4331, Bangladesh.
Adam AA
Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia.
Acharjee UK
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Paul GK
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Emran TB
Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh.
Zaman S
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Uddin MS
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Saleh MA
Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh.
Alshehri S
Department of Pharamaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
Ghoneim MM
Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia.
Alruwali M
Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia.
Obaidullah AJ
Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia. Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
Jui NR
Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong 4202, Bangladesh.
Kim J
Department of Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea.
Kim B
Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea.

MeSH

Antiviral AgentsDengueDengue VirusHigh-Throughput Screening AssaysHumansMolecular Docking SimulationMolecular Dynamics SimulationPhytochemicalsProtease InhibitorsSerine EndopeptidasesViral Nonstructural Proteins

Pub Type(s)

Journal Article

Language

eng

PubMed ID

35163918

Citation

Shimu, Mst Sharmin Sultana, et al. "Phytochemical Compound Screening to Identify Novel Small Molecules Against Dengue Virus: a Docking and Dynamics Study." Molecules (Basel, Switzerland), vol. 27, no. 3, 2022.
Shimu MSS, Mahmud S, Tallei TE, et al. Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. Molecules. 2022;27(3).
Shimu, M. S. S., Mahmud, S., Tallei, T. E., Sami, S. A., Adam, A. A., Acharjee, U. K., Paul, G. K., Emran, T. B., Zaman, S., Uddin, M. S., Saleh, M. A., Alshehri, S., Ghoneim, M. M., Alruwali, M., Obaidullah, A. J., Jui, N. R., Kim, J., & Kim, B. (2022). Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. Molecules (Basel, Switzerland), 27(3). https://doi.org/10.3390/molecules27030653
Shimu MSS, et al. Phytochemical Compound Screening to Identify Novel Small Molecules Against Dengue Virus: a Docking and Dynamics Study. Molecules. 2022 Jan 20;27(3) PubMed PMID: 35163918.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. AU - Shimu,Mst Sharmin Sultana, AU - Mahmud,Shafi, AU - Tallei,Trina Ekwati, AU - Sami,Saad Ahmed, AU - Adam,Ahmad Akroman, AU - Acharjee,Uzzal Kumar, AU - Paul,Gobindo Kumar, AU - Emran,Talha Bin, AU - Zaman,Shahriar, AU - Uddin,Md Salah, AU - Saleh,Md Abu, AU - Alshehri,Sultan, AU - Ghoneim,Mohammed M, AU - Alruwali,Maha, AU - Obaidullah,Ahmad J, AU - Jui,Nabilah Rahman, AU - Kim,Junghwan, AU - Kim,Bonglee, Y1 - 2022/01/20/ PY - 2021/12/15/received PY - 2022/01/10/revised PY - 2022/01/14/accepted PY - 2022/2/15/entrez PY - 2022/2/16/pubmed PY - 2022/2/25/medline KW - Dengue virus KW - NS2B/NS3 protein KW - molecular docking KW - molecular dynamics KW - phytochemicals JF - Molecules (Basel, Switzerland) JO - Molecules VL - 27 IS - 3 N2 - 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. SN - 1420-3049 UR - https://www.unboundmedicine.com/medline/citation/35163918/Phytochemical_Compound_Screening_to_Identify_Novel_Small_Molecules_against_Dengue_Virus:_A_Docking_and_Dynamics_Study_ DB - PRIME DP - Unbound Medicine ER -