A Comprehensive Study of Human Serum Albumin Interaction With Trimethoprim Using Molecular Docking and Molecular Dynamics Methods: An Appropriate Tool for Drug Delivery Systems

authors:

avatar Mitra Salehi 1 , avatar hanifeh Shariatifar 2 , avatar Morteza Ghanbari Johkool 3 , avatar Alireza Farasat 4 , *

Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.
Metabolic Diseases Research Center, Research Institute for Prevention of Non-communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran.
Cellular and Molecular Research Center, Research Institute for Prevention of Non-communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran.
Journal of Inflammatory Diseases: Vol.25, issue 2; 99-104
article type: issue_documents_importer

How To Cite Salehi M, Shariatifar H, Ghanbari Johkool M, Farasat A. A Comprehensive Study of Human Serum Albumin Interaction With Trimethoprim Using Molecular Docking and Molecular Dynamics Methods: An Appropriate Tool for Drug Delivery Systems. J Inflamm Dis. 2021;25(2):e156282. 

Abstract

Background: Human Serum Albumin (HSA) is one of the most prominent proteins in human blood. Trimethoprim (TMP) is an efficient antibiotic drug for treating pneumocystis pneumonia. Patients with HIV/AIDS and cancer are highly affected by this disease due to immune system deficiency.  Objective: This study aims to evaluate the Molecular Dynamics (MD) simulation of HSA with TMP for drug delivery systems.  Methods: In the first step, the 3D structure of HSA and TMP were determined by PDB (Protein Data Bank) and PubChem, respectively. Then, the molecular docking was done via AutoDock Vina software, and the best complex was selected based on the lowest binding energy. Finally, the structural characteristics of the above complex were evaluated.  Results:  The results showed that TMP binds to the HSA molecule with a binding energy of -7.3 kcal/mol, and this binding causes changes in the third and second structures of the HSA. Thus, Root-Mean-Square Deviation (RMSD) and radius of gyration results proved the third structural change, and the results obtained from DSSP (Database of Secondary Structure assignment for all Protein entries) confirmed the second structural modification. The TMP-HSA complex formation is accompanied by hydrophobic interaction between residues of Tyr150, Ala291, His288, Leu238, Leu219, Lys199, Lys195, Glu153, and TMP. The TMP molecule had two hydrogen bonds with Arg222 residue and three with Ser192. Furthermore, the final PDB file of the MD simulation process showed that the TMP molecule reacted with HSA (IIA chain).  Conclusion: Because of the extensive application of TMP in infectious diseases and appropriate interaction with HSA, the complex could be used for the purposeful transport of nanoparticles in the future.