IDENTIFICATION AND OPTIMIZATION OF BINDING SITE FOR AN ACTIVE METABOLITE OF CLOPIDOGREL, PRASUGREL AND TICLOPIDINE ON RECEPTOR P2Y12
HTML Full TextIDENTIFICATION AND OPTIMIZATION OF BINDING SITE FOR AN ACTIVE METABOLITE OF CLOPIDOGREL, PRASUGREL AND TICLOPIDINE ON RECEPTOR P2Y12
Parmeshwar R. Devhare * 1, Shirish Jain 2, Gajanan Sonwane 1, Vijay Borkar 1 and Rushikesh Diwre 1
Department of Pharmaceutical Chemistry 1, Department of Pharmacology 2, Rajarshi Shahu College of Pharmacy, Buldhana - 443001, Maharashtra, India.
ABSTRACT: In this article, an attempt was made to develop molecular docking studies on active metabolites of Prasugrel, Clopidogrel, and Ticlopidine acting as protein P2Y12 inhibitors. Molecular docking analysis was performing by using autodock version 4.3 adjoin with discovery studio to better understand the interactions between P2Y12 targets and inhibitors in this series. Hydrophobic and hydrogen bond interactions lead to the identification of active binding sites of P2Y12 protein in the docked complex, signifying the affection of active Metabolite of Prasugrel is more than other active metabolites of ticlopidine and clopidrogrel. The present study may lead to the discovery of therapeutically potent agents against clinically very important cardiovascular disorders, including arterial thrombosis, Hypertension, embolism etc. cardiac diseases. Hence the computer-aided drug design docking model proposed in this work can be employed to design the metabolites of Clopidogrel, Prasugrel, and Ticlopidine with specific P2Y12 inhibitory activity and futuristic active metabolites possibilities.
Keywords: |
Molecular docking, P2Y12, Clopidogrel, Prasugrel, Ticlopidine
INTRODUCTION: Molecular modeling and computational tools have become a close matching part of experimenting in the understanding of molecular aspects of genetic systems 1-4. The computational strategies like molecular docking and quantitative structure-activity relationship (QSAR) are utilized to find the new hits for different helpful targets 5-7. The ongoing report featured the interface between computational methodologies and experiments as an essential tool in the drug discovery technology 8, 9.
Using the prominent rising interest in the design of ligand-enzyme inhibitors, this present study is to elucidate the molecular docking study of active metabolites of clopidogrel, prasugrel, and ticlopidine as P2Y12 inhibitor using computational tools that can be applied to understand interactions between inhibitors and their target proteins.
P2Y12 Crystal structures of the human P2Y12 receptor shown in figure 1 have as of late been settled. Structures of the receptor in a complex with the agonists 2-methylthio-adenosine diphosphate (2MeS-ADP) and 2-methylthio-adenosine tri-phosphate (2MeS-ATP) 10, 11 and with the non-nucleotide antagonist ethyl 6-(4-[(benzylsulfonyl) carbamoyl] piperidin-1-yl)-5- cyano-2-methyl-nicotinate (AZD1283) were obtained 12, 13. The P2Y12 receptor represents a successful drug target, with several clinical drugs on the market, including clopidogrel, prasugrel, ticlopidine, cangrelor, and ticagrelor, and more drugs in clinical trials 14. Along these lines, the advancement of P2Y12 antagonist has been a functioning region of medication improvement, and endeavors have been founded on dynamic metabolites of clopidogrel, prasugrel, and ticlopidine with the plan to maintain a strategic distance from biotransformation of the prodrug.
Docking considers as the structures of progressively potential medication target are explained the open door for the computer to perform beginning binding studies is expanding. By computationally docking a ligand to a protein, one point of confinement worries about examine intricacy, for example, compound solvency and the requirements to keep up broad physical compound libraries.
The goal of computational docking is to decide how atoms of realized structure will collaborate. The molecule may bind to the receptor and modify its function. The docking considers performed between receptor (P2Y12, PDB code: 4NTJ) and ligands by utilizing PyRx-Python solution (adaptation 0.8). 4NTJ Fig. 1, recovered from RCSB and arranged by Discovery Studio visualizer rendition 16.1.01
FIG. 1 STRUCTURE OF 4NTJ
Experimental Methods: 3D structure of the enzyme P2Y12 with PDB code: 4NTJ by Zhang et al., and active metabolites are shown in Fig. 2 of clopidogrel, prasugrel, and ticlopidine were taken from literature 15, 16. The protein structure was downloaded from the information base online Protein Data Bank (PDB) 17, 18. Two and three-dimensional structure of metabolites drawn utilizing program package ChemDraw Ultra v12.0.2, 2010.
FIG. 2: ACTIVE METABOLITE OF TICLOPIDINE, CLOPIDOGREL AND PRASUGEL
Preparation of Protein Structure: The 3D coordinates of the crystal structure of P2Y12 (PDB ID: 4NTJ) were downloaded from the Protein Data Bank 19–21. 4NTJ (chains A) were picked for the docking reenactments. Before docking, all water atoms are ousted from protein document 4NTJ. In the wake of ousting the water molecules, H atom was added to protein for right ionization and tautomeric states of amino corrosive, such as ARG, CYS, LYS, PHE TYR, and VAL.
Preparation of Ligand Structures: The ligands used for the docking study were selected from the literature 22–24. The ligand structures were generated using the tool ChemDraw ultra v12.0.2. Three-dimensional optimizations of the ligand structures were done and saved as 'PDB file'. Geometry optimizations of the ligands were performed using the Steepest descent calculation method using Avagdro software. The compounds included in the study are active metabolites of clopidogrel, prasugrel, and ticlopidine; the bioactive compounds considered for the study are listed in Fig. 2.
Protein-ligand Interaction using PyRx (Autodock Vina): The docking studies were conceded by PyRx (Autodock vina) tools 25, 26 version v 0.8 programs. The looking through lattice reached out over the favoured objective proteins; polar hydrogen was added to the ligand moieties. Kollman charges were assigned, and atomic solvation parameters were added. Polar hydrogen charges of the Gasteiger-type were assigned, and the non-polar hydrogen was merged with the carbons, and the internal degrees of freedom and torsions were set. Active metabolites were docked to target protein complex (4NTJ), with the molecule considered as a rigid body and the ligand being flexible. The search was extended over the whole receptor protein used as blind docking. Affinity maps for all the atom types present, as well as an electrostatic map, were computed with a grid spacing of 0.375 Å. The search was carried out with the Lamarckian Genetic Algorithm; populations of 150 individuals with a mutation rate of 0.02 were evolved for 9 generations. Evaluation of the results was done by sorting the different complexes concerning the predicted binding energy. A cluster analysis based on root mean square deviation values concerning the starting geometry was subsequently performed, and the lowest energy conformation of the more populated cluster was considered as the most trustable solution.
RESULTS AND DISCUSSION: In this present study, to understand the formation of hydrogen bond interactions between the active metabolites and active sites of the crystal structure of P2Y12 (PDB code: 4NTJ) was used to explore their binding mode, and a docking study was performed by using PyRx (Autodock vina) 27, 28. Three active metabolites of clopidogrel, prasugrel and ticlopidine were retrieved from literature 29. The 3D structure and energy minimization was done by Avogadro software. All these chemical compounds. To date, three crystal structures of P2Y12 in complex with agonist and antagonist have been reported in the literature. In the present study, we have used X-ray crystallography structure of P2Y12 (PDB code: 4NTJ) Fig. 1 in ternary complex with the non-nucleotide antagonist ethyl 6-(4-[(benzylsulfonyl) carbamoyl] piperidine-1-yl)-5- cyano-2-methylnicotinate (AZD1283) is used for the docking study.
Binding Site of the Protein: The detection of ligand-binding sites is often the starting point for protein function identification and drug discovery 30, 31. In our study, PyRx (autodock vina) predicted the active site of the receptor P2Y12 (4NTJ) with higher average precision. P2Y12 (4NTJ) 's active site comprises amino acid residues such as CYS97, VAL102, TYR105, PHE106, TYR109, MET152, LEU155, SER156, ASN159, HIS187, VAL190, ASN191, CYS194, PHE252, ALA255, ARG256, TYR259, LEU276, AND VAL279. As most of the amino acid residues in the active site are hydrophobic, so they are the main contributors to the receptor and ligand-binding interaction. Amino acid interaction of active metabolite of Ticlopidine, Clopidogrel, and Prasugrel shown in Fig. 3, 4, and 5 respectively, and standard drug ethyl 6- (4-((benzylsulfonyl) carbamoyl) piperidin- 1- yl)- 5-cyano-2-methylnicotinate amino acid interaction shown in Fig. 6.
Interaction between Active Metabolites and 4ntj:
TABLE 1: DOCKING ENERGY OF ACTIVE METABOLITES OF COLPIDOGREL, PRASUGREL, AND TICLOPIDINE
Ligand | Binding Affinity | rmsd/ub | rmsd/lb |
Metabolite of Ticlopidine | -7 | 6.94 | 1.496 |
Metabolite of Colpidogrel | -5.7 | 30.813 | 29.362 |
Metabolite of Prasugrel | -7.1 | 2.378 | 2.126 |
Std | -6.8 | 12.349 | 11.335 |
FIG. 3: AMINO ACID INTERACTION WITH TICLODIPINE LIGAND
CONCLUSION: The P2Y12 receptor is a significant objective of antithrombotic treatment. In PCI patients, new P2Y12 inhibitors decrease all-cause mortality and major ischemic conditions, specifically in PCI for STEMI patients.
These further backings that a more significant level of platelet inhibition than clopidogrel (600 mg) is required for, by far, most of the patients. This study based on binding energy for receptor P2Y12 (4NTJ) of the metabolite of Prasugrel ligand showed better activity than Metabolite of Ticlopidine Metabolite of Colpidogrel, which may show a better dose regimen with lesser side effects. This research will help for further wetlab Pharmacological investigation of Prasugrel ligand as compared to a metabolite of Ticlopidine and metabolite of Clopidogrel.
ACKNOWLEDGEMENT: Authors are thankful to the Principal, Dr. S.P Jain Sir, Rajarshi Shahu College of Pharmacy, Buldhana (MS), India, for providing the necessary facilities.
CONFLICTS OF INTEREST: Nil
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How to cite this article:
PR Devhare, Jain S, Sonwane G, Borkar V and Diwre R: Identification and optimization of binding site for an active metabolite of clopidogrel, prasugrel and ticlopidine on receptor P2Y12. Int J Pharm Sci & Res 2021; 12(8): 4365-70. doi: 10.13040/IJPSR.0975-8232. 12(8).4365-70.
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Article Information
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English
IJPSR
P. R. Devhare *, S. Jain, G. Sonwane, V. Borkar and R. Diwre
Department of Pharmaceutical Chemistry, Rajarshi Shahu College of Pharmacy, Buldhana, Maharashtra, India.
parme1717@gmail.com
20 August 2019
28 January 2021
19 May 2021
10.13040/IJPSR.0975-8232.12(8).4365-70
01 August 2021