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Abdul-Hammed M, Adedotun IO, Akinboade MW, Adegboyega TA, Salaudeen OM. Antibacterial activities, PASS prediction and ADME analysis of phytochemicals from Curcubita moschata, Curcubita maxima, and Irvingia gabonensis: insights from in silico studies. In Silico Pharmacol 2024; 12:65. [PMID: 39035102 PMCID: PMC11254879 DOI: 10.1007/s40203-024-00234-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Microbial infection management and treatment are crucial as a result of the prevalent antimicrobial resistance issue. Progressive studies are being carried out on how to develop drugs that can mitigate the resistance trends of these microorganisms. Secondary metabolites of plants can also be employed and accessed for this role, as the current study examines the antibacterial activities of phytochemicals from three (3) plants (Cucubita moschata, Cucubita maxima, and Irvingia gabonesis) through computational approaches. Molecular docking studies were carried out to show the binding affinities of the phytochemicals against two target receptors (DNA gyrase and Penicillin Binding Protein 3). In addition, drug likeness analysis, bioactivity and oral-bioavailability properties, absorption, distribution, metabolism, and excretion (ADME) profiling, as well as prediction of activity spectra for substances (PASS) using online tools like SwissADME, PASS online, AdmetSAR2, and Discovery Studio, were also performed. The results obtained identified isochlorogenic acid and apigenin-7-O-glucoside for DNA gyrase (1KZN) and apigenin-7-O-glucoside for Penicillin Binding Protein 3 (4BJP), which were further subjected to molecular dynamics simulation (MDS) and therefore recommended as the lead compounds.
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Affiliation(s)
- Misbaudeen Abdul-Hammed
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Ibrahim Olaide Adedotun
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
- Insilico Scientific Inventions and Development Limited (ISID), Ibadan, Nigeria
| | - Modinat Wuraola Akinboade
- Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Timilehin Adekunle Adegboyega
- Department of Chemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA 24061 USA
| | - Oladele Muheez Salaudeen
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
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Yu J, Liu JM, Chen HY, Xiong WM. Interaction mechanism of oseltamivir phosphate with bovine serum albumin: multispectroscopic and molecular docking study. BMC Chem 2024; 18:126. [PMID: 38970054 PMCID: PMC11227190 DOI: 10.1186/s13065-024-01232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
Oseltamivir phosphate (OP) is an antiviral drug with potential risks to human health due to overuse, leading to serious consequences such as gastrointestinal disturbances, abnormal neuropsychiatric symptoms, and sudden death. Therefore, gaining an in-depth understanding of its interaction with proteins is crucial. We investigated the interaction between OP and bovine serum albumin (BSA) utilizing multispectral methods (i.e., fluorescence, ultraviolet absorption, circular dichroism) combined with molecular docking techniques. Fluorescence spectroscopy indicated that OP quenched BSA fluorescence by forming the OP-BSA complex. The Stern-Volmer constants (KSV) between OP and BSA were determined to be 3.06 × 103 L/mol, 2.36 × 103 L/mol, and 1.86 × 103 L/mol at 293 K, 298 K, and 303 K, respectively. OP occupies exclusively one binding site on BSA, and the fluorescent probe displacement measurements revealed that this is BSA site I. Thermodynamic data (∆H, ∆S, and ∆G) obtained by fitting the van't Hoff equation were - 77.49 kJ/mol, -176.54 J/(mol∙K), and - 24.88 kJ/mol, respectively, suggesting that hydrogen bonding and van der Waals forces mainly participate in OP-BSA complex stabilization. Moreover, the reaction occurs spontaneously at room temperature. Synchronous fluorescence spectra indicated that OP interacts with tryptophan residue of BSA. The results of ultraviolet (UV) and 3D fluorescence spectroscopy indicated that the OP-BSA complex formation altered the microenvironment around amino acid residues. Circular dichroism spectra revealed that the addition of OP decreased the α-helix content of BSA by 7.13%. Docking analysis confirmed that OP binds to BSA site I through hydrogen bonding with amino acids VAL342, SER453, and ASP450. Finally, ADMET studies were conducted to explore the pharmacokinetics of OP as an antiviral drug.
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Affiliation(s)
- Jing Yu
- School of Chemistry and Civil Engineering, Shaoguan University, Shaoguan, 512005, China
| | - Jian-Ming Liu
- School of Chemistry and Civil Engineering, Shaoguan University, Shaoguan, 512005, China
| | - Hui-Yi Chen
- School of Chemistry and Civil Engineering, Shaoguan University, Shaoguan, 512005, China
| | - Wei-Ming Xiong
- School of Physical Science & Technology, Guangxi University, Nanning, 530004, China.
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Saputro AH, Amelia T, Mahardhika AB, Widyawaruyanti A, Wahyuni TS, Permanasari AA, Artarini AA, Tjahjono DH, Damayanti S. Alpha-mangostin, piperine and beta-sitosterol as hepatitis C antivirus (HCV): In silico and in vitro studies. Heliyon 2023; 9:e20141. [PMID: 37809693 PMCID: PMC10559922 DOI: 10.1016/j.heliyon.2023.e20141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 09/02/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Hepatitis C is still a serious liver case of health. Up to now the development of anti-Hepatitis C Virus (HCV) drugs is challenging, especially the development of natural material compounds as anti-HCV. In the present study, we evaluated the probability of α-mangostin, piperine, and β-sitosterol as anti-HCV with the in silico and in vitro approaches. Molecular docking was performed between nonstructural protein 5B (NS5B, PDB ID 3FQL) with α-mangostin, piperine, and β-sitosterol by Autodock Tools® and BIOVIA Discovery Studio®. Subsequently, molecular dynamics simulations were conducted for 200 ns, evaluating the dynamic interaction between the ligands and the viral protein NS5B. Furthermore, compound characterization at the hepatocarcinoma cell line was employed. α-Mangostin with NS5B complex demonstrated the most negative binding free energy value based on MM-PBSA calculation with a value of -9.13 kcal/mol. In vitro test showed that IC50 of α -mangostin was 2.70 ± 0.92 μM, IC50 of piperine was 52.18 ± 3.21 μM, IC50 of β-sitosterol was >100 μM. α-Mangostin can serve as a valuable lead compound for further development of the anti-HCV.
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Affiliation(s)
- Anjar Hermadi Saputro
- Department of Pharmacochemistry, School of Pharmacy, Institut Teknologi Bandung, 40132, Indonesia
- Department of Pharmacy, Institut Teknologi Sumatera, 35365, Indonesia
| | - Tasia Amelia
- Department of Pharmacochemistry, School of Pharmacy, Institut Teknologi Bandung, 40132, Indonesia
| | | | - Aty Widyawaruyanti
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, 60115, Indonesia
- Center for Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, 60115, Indonesia
| | - Tutik Sri Wahyuni
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, 60115, Indonesia
- Center for Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, 60115, Indonesia
| | - Adita Ayu Permanasari
- Center for Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, 60115, Indonesia
| | - Aluicia Anita Artarini
- Department of Pharmaceutics, School of Pharmacy, Institut Teknologi Bandung, 40132, Indonesia
| | - Daryono Hadi Tjahjono
- Department of Pharmacochemistry, School of Pharmacy, Institut Teknologi Bandung, 40132, Indonesia
| | - Sophi Damayanti
- Department of Pharmacochemistry, School of Pharmacy, Institut Teknologi Bandung, 40132, Indonesia
- University Center of Excellence on Artificial Intelligence for Vision, Natural Language Processing & Big Data Analysis (U-CoE AI-VLB), Institut Teknologi Bandung, Indonesia
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Moharana M, Pattanayak SK, Khan F. Computational efforts to identify natural occurring compounds from phyllanthus niruri that target hepatitis B viral infections: DFT, docking and dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Missioui M, Mortada S, Guerrab W, Demirtaş G, Mague JT, Ansar M, El Abbes Faouzi M, Essassi E, Mehdar YT, Aljohani FS, Said MA, Ramli Y. Greener Pastures in Evaluating Antidiabetic Drug for a Quinoxaline Derivative: Synthesis, Characterization, Molecular Docking, in Vitro and HSA/DFT/XRD Studies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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