Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study
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...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-01-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/27/3/653 |
| _version_ | 1827659896621891584 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Mst. Sharmin Sultana Shimu |
| collection | DOAJ |
| description | 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-<i>O</i>-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. |
| first_indexed | 2024-03-09T23:30:43Z |
| format | Article |
| id | doaj.art-e58ff17638ef47bca6649c0328c519d3 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T23:30:43Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-e58ff17638ef47bca6649c0328c519d32023-11-23T17:10:16ZengMDPI AGMolecules1420-30492022-01-0127365310.3390/molecules27030653Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics StudyMst. Sharmin Sultana Shimu0Shafi Mahmud1Trina Ekwati Tallei2Saad Ahmed Sami3Ahmad Akroman Adam4Uzzal Kumar Acharjee5Gobindo Kumar Paul6Talha Bin Emran7Shahriar Zaman8Md. Salah Uddin9Md. Abu Saleh10Sultan Alshehri11Mohammed M Ghoneim12Maha Alruwali13Ahmad J. Obaidullah14Nabilah Rahman Jui15Junghwan Kim16Bonglee Kim17Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshMicrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshDepartment of Biology, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado 95115, IndonesiaDepartment of Pharmacy, University of Chittagong, Chittagong 4331, BangladeshDentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, IndonesiaDepartment of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshMicrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshDepartment of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, BangladeshMicrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshMicrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshMicrobiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, BangladeshDepartment of Pharamaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi ArabiaDepartment of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi ArabiaDrug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi ArabiaDepartment of Biochemistry and Biotechnology, University of Science and Technology, Chittagong 4202, BangladeshDepartment of Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02447, KoreaDepartment of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, KoreaThe 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-<i>O</i>-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.https://www.mdpi.com/1420-3049/27/3/653phytochemicalsDengue virusNS2B/NS3 proteinmolecular dockingmolecular dynamics |
| spellingShingle | 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 Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study Molecules phytochemicals Dengue virus NS2B/NS3 protein molecular docking molecular dynamics |
| title | Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study |
| title_full | Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study |
| title_fullStr | Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study |
| title_full_unstemmed | Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study |
| title_short | Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study |
| title_sort | phytochemical compound screening to identify novel small molecules against dengue virus a docking and dynamics study |
| topic | phytochemicals Dengue virus NS2B/NS3 protein molecular docking molecular dynamics |
| url | https://www.mdpi.com/1420-3049/27/3/653 |
| work_keys_str_mv | AT mstsharminsultanashimu phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT shafimahmud phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT trinaekwatitallei phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT saadahmedsami phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT ahmadakromanadam phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT uzzalkumaracharjee phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT gobindokumarpaul phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT talhabinemran phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT shahriarzaman phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT mdsalahuddin phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT mdabusaleh phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT sultanalshehri phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT mohammedmghoneim phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT mahaalruwali phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT ahmadjobaidullah phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT nabilahrahmanjui phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT junghwankim phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy AT bongleekim phytochemicalcompoundscreeningtoidentifynovelsmallmoleculesagainstdenguevirusadockinganddynamicsstudy |