[Home ] [Archive]   [ فارسی ]  
:: Main :: About :: Current Issue :: Archive :: Search :: Submit :: Contact ::
Main Menu
Home::
Journal Information::
About the Journal
Editorial Board
Aims& Scopes
Journal News
Articles archive::
All Issues
Current Issue
Publication Ethics::
Peer Review Process::
Indexing Databases::
For Authors::
Authors Guideline
Call for Papers
Submission Instruction
Review Process
Research Ethics Statements
Ethical issues
Author Complaint Process
For Reviewers::
Reviewers Section
Subscription::
Registration Information
Subscription Form
Contact us::
Contact Information
Contact us
Site Facilities::
Site map
Search contents
FAQ
Top 10 contents
Inform to friends
::
Google Scholar Metrics

Citation Indices from GS

AllSince 2019
Citations68504087
h-index2722
i10-index20699
..
Search in website

Advanced Search
..
Receive site information
Enter your Email in the following box to receive the site news and information.
..
Registered in

AWT IMAGE

AWT IMAGE
..
:: Volume 31, Issue 4 (10-2023) ::
Journal of Ilam University of Medical Sciences 2023, 31(4): 79-89 Back to browse issues page
Investigating the effect of Ciprofloxacin on rhodopsin protein structure using the molecular docking calculation method
Mahdieh Sadeghpour * 1, Monir Shalbafan2 , Khadijeh Alviri3
1- Dept of Chemistry, Qazvin Branch, Islamic Azad University, Qazvin, Iran , m.sadeghpour@tiau.ac.ir
2- Dept of Chemistry, Imam Khomeini International University, Qazvin, Iran
3- Dept of Pharmacology, School of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
Abstract:   (808 Views)
Introduction: Ciprofloxacin antibiotic is used in the treatment of retinal toxicity or retinopathy. The present study aimed to assess the effect of ciprofloxacin on rhodopsin protein structure and the stability or instability of this protein in the presence of this medicine. The type of drug and protein binding is effective in the elimination or interaction of the medicine with the target tissues.
Material & Methods: Thermodynamic components can be obtained in the interactions between rhodopsin protein and ciprofloxacin using docking software. Docking studies were performed by AutoDock 4.2 software. Pymol, Ligplot, and VMD graphic software packeages were used to observe the docking performed.
Findings: Based on the results obtained from docking studies, the most important bond involved in the binding of ciprofloxacin drug with rhodopsin protein is hydrophobic bonds and hydrogen bonds. The estimate of Gibbs free energies (kcal/mol) for the best docking model is equal to -6.5. This model with the lowest level of binding energy has the greatest tendency to bind to rhodopsin amino acids, and negative values of ΔG° are indicative of a spontaneous process.
Discussion & Conclusion: Based on the docking results, the A position of the rhodopsin protein is a suitable place for ciprofloxacin to bind to this protein, and the complex of ciprofloxacin with the rhodopsin protein can cause rhodopsin to regenerate so that it can start the process of seeing normally. In fact, the strong hydrogen bond between the nitrogen atom in the ciprofloxacin structure and the amino acid arginine plays a key role in stabilizing the complex.
Keywords: Binding constant, Binding free energy, Ciprofloxacin, Molecular docking, Rhodopsin
Full-Text [PDF 836 kb]   (407 Downloads)    
Type of Study: Research | Subject: pharmacology
Received: 2023/03/1 | Accepted: 2023/07/4 | Published: 2023/10/7
References
1. Torres PHM, Sodero ACR, Jofily P, Silva-Jr FP. Key Topics in Molecular Docking for Drug Design. Int J Mol Sci 2019; 20:4574. doi: 10.3390/ijms20184574.
2. Wang G, Zhu W. Molecular docking for drug discovery and development: a widely used approach but far from perfect. Future Med Chem 2016; 8:1707-1710. doi.org/10.4155/fmc-2016-0143.
3. Sethi A, Khusbhoo J, Sasikala K, Alvala M. Molecular Docking in Modern Drug Discovery: Principles and Recent Applications. Book Published 2019. doi: 10.5772/intechopen.85991.
4. De Ruyck J, Brysbaert G, Blossey R, Lensink M. Molecular docking as a popular tool in drug design, an in-silico travel. Adv Appl Bioinform Chem 2016; 9:1-11. doi: 10.2147/AABC.S1052895.
5. Jakhar R, Dangi M, Khichi A, Chhillar A K. Relevance of molecular docking studies in drug designing. Current Bioinformatics 2020; 15:270-8. doi: 10.2174/1574893615666191219094216.
6. Mares-Sámano S, Garduño-Juárez R. Computational modeling of the interactions of drugs with human serum albumin (HSA). Compute y Sist 2018; 22: 1123-35. doi:10.13053/cys-22-4-3085.
7. Heydargoy MH. Investigation of antiviral drugs with direct effect on RNA polymerases and simulation of their binding to SARS-CoV-2 RNA dependent RNA polymerase by molecular docking method. Iran J Microbiol 2020; 14:342-7. doi: 10.30699/ijmm.14.4.342.
8. Collins I, Workman P. New approaches to molecular cancer therapeutics. Nat Chem Biol 2006; 2: 689-700. doi. 10.1038/nchembio840.
9. Wadood A, Ahmed N, Shah L, Ahmad A, Hassan H, Shams S. In-silico drug design: An approach which revolutionarised the drug discovery process. Drug Des Devel 2013; 1:3-7. doi: 10.13172/2054- 4057-1-1-1119.
10. Parsa NZ, Mukherjee AB, Gaidano G, Hauptschein RS, Dallafavera R, Lenoir G. Cytogenetic and molecular analyis of 6q deletions in Burkitt΄s lymphoma cell lines. Genes Chromosomes cancer 1994; 9: 13-8. doi: 10.1002/gcc.2870090104.
11. Christensen SH, Roest B, Besselink N, Janssen R, Boymans S, Artens JWM, et al. 5-Fluorouracil treatment induces characteristic T>G mutations in human cancer. Nat Commun 2019; 10: 4571-82. doi: 10.1038/s41467-019-12594-8.
12. Yanamala N, Gardner E, Riciutti A, Klein-Seetharaman J. The Cytoplasmic Rhodopsin-Protein Interface: Potential for Drug Discovery. Curr Drug Targets 2012; 13:3-14. doi: 10.2174/138945012798868461.
13. Chen S, Getter T, Salom D, Wu D, Quetschlich D, Chorev DS, et al. Rhodopsin signaling study could present new opportunities for GPCR drug discovery. Nature 2022:1-7. doi: 10.1038/s41586-022-04547-x.
14. Yuzlenko O, Kieć-Kononowicz K. Molecular modeling of A1 and A2A adenosine receptors: Comparison of rhodopsin- and β2-adrenergic-based homology models through the docking studies. J Comput Chem 2009; 30:14-32. doi: 10.1002/jcc.21001.
15. Kanwal S, Nishat S, Irfan Khan M. Docking of human rhodopsin mutant (Gly90→Asp) with beta-arrestin and cyanidin 3-rutinoside to cure night blindness. Bioinformation 2012; 8:128-33. doi: 10.6026/97320630008128.
16. Sinha A, Brunette AMJ, Fay JF, Schafer CT, Farrens DL. Rhodopsin TM6 can interact with two separate and distinct sites on arrestin: evidence for structural plasticity and multiple docking modes in arrestin-rhodopsin binding. Biochemistry 2014; 53:3294-3307. doi.10.1021/bi401534y.
17. Kataoka C, Sugimoto T, Shigemura S, Katayama K, Tsunoda SP, Inoue K, et al. TAT rhodopsin is an ultraviolet-dependent environmental pH sensor. Biochemistry 2021; 60:899-907. doi: 10.1021/acs.biochem.0c00951.
18. Mattle D, Kuhna B, Aebia J, Bedouchaa M, Kekillib D, Grozingera N, et al. Ligand channel in pharmacologicallystabilized rhodopsin. Proc Natl Acad Sci USA 2018; 115:3640-45. doi: 10.1073/pnas.1718084115.
19. Razzaghi N, Fernandez-Gonzalez P, Mas-Sanchez A, Vila-Julià G, Perez JJ, Garriga P. Effect of Sodium Valproate on the Conformational Stability of the Visual G Protein-Coupled Receptor Rhodopsin. Molecules 2021; 26:3032-48. doi: 10.3390/molecules26103032.
20. Yuriev E, Holien J, Ramsland PA. Improvements, trends and new ideas in molecular docking 2012- 2013 in review. J Mol Recognit 2015; 28:581-604. doi: 10.1002/jmr.2471.
21. Dratz EA, Hargrave PA. The structure of rhodopsin and the rod outer segment disk membrane. Trends Biochem Sci 1983; 8: 128-31. doi: 10.1016/0968-0004(83)90235-9.
22. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera—A Visualization system for exploratory research and analysis. J Comput Chem 2004; 25:1605-12. doi:10.1002/jcc.20084.
23. Ritchie DW, Kemp GJL. Protein docking using spherical polar fourier correlations. Proteins 2000; 39:178-94.
24. Cosconati S, Forli S, Perryman AL, Harris R, David S, Olson Arthur J. Virtual screening with AutoDock: theory and practice. Expert Opin Drug Discov 2010; 5:597-607. doi:10.1517/17460441.2010.484460.
25. Smith SO. Mechanism of activation of the visual receptor rhodopsin. Annu Rev Biophys 2023; 52: 301-17. doi:10.1146/annurev-biophys-083122-094909.
26. Kesi´c AS, Milenkovi´c D, Antonijevi´c M, Petrovi´c B, Markovi´c Z. Molecular docking study on the interaction of rhodopsin-like receptors with tetracoordinated gold (III) complexes. Biol Life Sci Forum 2021; 7:17-23. doi:10.3390/ECB2021-10264.
27. Jain A. Computer aided drug design. J Phys Conf Ser 2017; 884:1-23. doi:10.1088/1742-6596/884/1/012072.
28. Motaharinia M, Sadeghpour M, Shalbafan M. Study of human albumin protein interaction with fluorouracil anticancer drug using molecular docking method. J Ilam Uni Med Sci 2022; 30:32-40. doi: 10.52547/sjimu.30.2.32.
29. Parvizi Fard G, Solouki L, Zakariazadeh M, Haghaei H, Soltani S. Study of interaction between nicotinamide and human serum albumin using spectroscopic techniques and molecular docking simulation simulation. Nova Biologica Reperta 2022; 9:153-68. doi: 10.29252/nbr.9.3.153.
30. Asghar BH, Arshad M. Ciprofloxacin analogues: drug likeness, biological and molecular docking studies. J Umm Al-Qura Uni Applied Sci 2023; doi: 10.1007/s43994-023-00061-6.
31. Akhtar R, Noreen R, Raza Z, Rasul A, Zahoor AF. Synthesis, anticancer evaluation, and in Silico modeling study of some N-acylated ciprofloxacin derivatives. Russ J Org Chem 2022; 58: 541-8. doi:10.1134/S107042802204011X.
32. Marciniec K, Beberok A, Pęcak P, Boryczka S, Wrześniok D. Ciprofloxacin and moxifloxacin could interact with SARS-CoV-2 protease: preliminary in silico analysis. Pharmacol Rep 2020; 72:1553-61. doi:10.1007/s43440-020-00169-0.
Send email to the article author

Add your comments about this article
Your username or Email:

CAPTCHA

Ethics code: 1

XML   Persian Abstract   Print

Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
Sadeghpour M, Shalbafan M, Alviri K. Investigating the effect of Ciprofloxacin on rhodopsin protein structure using the molecular docking calculation method. J. Ilam Uni. Med. Sci. 2023; 31 (4) :79-89
URL: http://sjimu.medilam.ac.ir/article-1-7903-en.html
Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Volume 31, Issue 4 (10-2023) Back to browse issues page
مجله دانشگاه علوم پزشکی ایلام Journal of Ilam University of Medical Sciences
Persian site map - English site map - Created in 0.15 seconds with 41 queries by YEKTAWEB 4670