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Akash S, Bayıl I, Hossain MS, Islam MR, Hosen ME, Mekonnen AB, Nafidi HA, Bin Jardan YA, Bourhia M, Bin Emran T. Novel computational and drug design strategies for inhibition of human papillomavirus-associated cervical cancer and DNA polymerase theta receptor by Apigenin derivatives. Sci Rep 2023; 13:16565. [PMID: 37783745 PMCID: PMC10545697 DOI: 10.1038/s41598-023-43175-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
The present study deals with the advanced in-silico analyses of several Apigenin derivatives to explore human papillomavirus-associated cervical cancer and DNA polymerase theta inhibitor properties by molecular docking, molecular dynamics, QSAR, drug-likeness, PCA, a dynamic cross-correlation matrix and quantum calculation properties. The initial literature study revealed the potent antimicrobial and anticancer properties of Apigenin, prompting the selection of its potential derivatives to investigate their abilities as inhibitors of human papillomavirus-associated cervical cancer and DNA polymerase theta. In silico molecular docking was employed to streamline the findings, revealing promising energy-binding interactions between all Apigenin derivatives and the targeted proteins. Notably, Apigenin 4'-O-Rhamnoside and Apigenin-4'-Alpha-L-Rhamnoside demonstrated higher potency against the HPV45 oncoprotein E7 (PDB ID 2EWL), while Apigenin and Apigenin 5-O-Beta-D-Glucopyranoside exhibited significant binding energy against the L1 protein in humans. Similarly, a binding affinity range of - 7.5 kcal/mol to - 8.8 kcal/mol was achieved against DNA polymerase theta, indicating the potential of Apigenin derivatives to inhibit this enzyme (PDB ID 8E23). This finding was further validated through molecular dynamic simulation for 100 ns, analyzing parameters such as RMSD, RMSF, SASA, H-bond, and RoG profiles. The results demonstrated the stability of the selected compounds during the simulation. After passing the stability testing, the compounds underwent screening for ADMET, pharmacokinetics, and drug-likeness properties, fulfilling all the necessary criteria. QSAR, PCA, dynamic cross-correlation matrix, and quantum calculations were conducted, yielding satisfactory outcomes. Since this study utilized in silico computational approaches and obtained outstanding results, further validation is crucial. Therefore, additional wet-lab experiments should be conducted under in vivo and in vitro conditions to confirm the findings.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh.
| | - Imren Bayıl
- Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Md Saddam Hossain
- Department of Biomedical Engineering, Faculty of Engineering & Technology, Islamic University, Kushtia, Bangladesh
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Birulia, Ashulia, Dhaka, 1216, Bangladesh
| | - Md Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, 2325, Quebec City, QC, G1V 0A6, Canada
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, 70000, Laayoune, Morocco
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States.
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Begum MN, Mahtarin R, Ahmed S, Shahriar I, Hossain SR, Mia MW, Qadri SS, Qadri F, Mannoor K, Akhteruzzaman S. Investigation of the impact of nonsynonymous mutations on thyroid peroxidase dimer. PLoS One 2023; 18:e0291386. [PMID: 37699049 PMCID: PMC10497151 DOI: 10.1371/journal.pone.0291386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Congenital hypothyroidism is one of the most common preventable endocrine disorders associated with thyroid dysgenesis or dyshormonogenesis. Thyroid peroxidase (TPO) gene defect is mainly responsible for dyshormonogenesis; a defect in the thyroid hormone biosynthesis pathway. In Bangladesh, there is limited data regarding the genetic etiology of Congenital Hypothyroidism (CH). The present study investigates the impact of the detected mutations (p.Ala373Ser, and p.Thr725Pro) on the TPO dimer protein. We have performed sequential molecular docking of H2O2 and I- ligands with both monomers of TPO dimer to understand the iodination process in thyroid hormone biosynthesis. Understanding homodimer interactions at the atomic level is a critical challenge to elucidate their biological mechanisms of action. The docking results reveal that mutations in the dimer severely disrupt its catalytic interaction with essential ligands. Molecular dynamics simulation has been performed to validate the docking results, thus realizing the consequence of the mutation in the biological system's mimic. The dynamics results expose that mutations destabilize the TPO dimer protein. Finally, principal component analysis exhibits structural and energy profile discrepancies in wild-type and mutant dimers. The findings of this study highlight that the mutations in TPO protein can critically affect the dimer structure and loss of enzymatic activity is persistent. Other factors also might influence the hormone synthesis pathway, which is under investigation.
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Affiliation(s)
- Mst. Noorjahan Begum
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Imrul Shahriar
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shekh Rezwan Hossain
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Md. Waseque Mia
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Syed Saleheen Qadri
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Firdausi Qadri
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Mucosal Immunology and Vaccinology, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kaiissar Mannoor
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol 2022; 5:360. [PMID: 35422073 PMCID: PMC9010423 DOI: 10.1038/s42003-022-03233-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia. Noble gases are known to interact with proteins and can be good anaesthetics in hyperbaric conditions. This study identifies argon and krypton binding sites on membrane proteins and proposes as a hypothesis that noble gases, by altering protein/lipid contacts, may affect protein function.
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Hohlweg W, Wagner GE, Hofbauer HF, Sarkleti F, Setz M, Gubensäk N, Lichtenegger S, Falsone SF, Wolinski H, Kosol S, Oostenbrink C, Kohlwein SD, Zangger K. A cation-π interaction in a transmembrane helix of vacuolar ATPase retains the proton-transporting arginine in a hydrophobic environment. J Biol Chem 2018; 293:18977-18988. [PMID: 30209131 DOI: 10.1074/jbc.ra118.005276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/24/2018] [Indexed: 11/06/2022] Open
Abstract
Vacuolar ATPases are multisubunit protein complexes that are indispensable for acidification and pH homeostasis in a variety of physiological processes in all eukaryotic cells. An arginine residue (Arg735) in transmembrane helix 7 (TM7) of subunit a of the yeast ATPase is known to be essential for proton translocation. However, the specific mechanism of its involvement in proton transport remains to be determined. Arginine residues are usually assumed to "snorkel" toward the protein surface when exposed to a hydrophobic environment. Here, using solution NMR spectroscopy, molecular dynamics simulations, and in vivo yeast assays, we obtained evidence for the formation of a transient, membrane-embedded cation-π interaction in TM7 between Arg735 and two highly conserved nearby aromatic residues, Tyr733 and Trp737 We propose a mechanism by which the transient, membrane-embedded cation-π complex provides the necessary energy to keep the charged side chain of Arg735 within the hydrophobic membrane. Such cation-π interactions may define a general mechanism to retain charged amino acids in a hydrophobic membrane environment.
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Affiliation(s)
| | - Gabriel E Wagner
- the Institute of Hygiene, Microbiology, and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | - Harald F Hofbauer
- the Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Florian Sarkleti
- the Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Martina Setz
- the Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | | | - Sabine Lichtenegger
- the Institute of Hygiene, Microbiology, and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria
| | | | - Heimo Wolinski
- the Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
| | - Simone Kosol
- the Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, United Kingdom
| | - Chris Oostenbrink
- the Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Sepp D Kohlwein
- the Institute of Molecular Biosciences, BioTechMed-Graz, University of Graz, 8010 Graz, Austria
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