Molecular Docking Studies of substituted 3-methyl-4-oxo-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile derivatives

 

Holam M. R.¹, Komala M.²*

¹Ph.D. Research Scholar, VEL’s Institute of Science, Technology and Advanced Studies (VISTAS),

Pallavaram, Chennai, Tamilnadu, 600117, India.

²Department of Pharmaceutics, School of Pharmaceutical Sciences, VELS Institute of Science,

Technology and Advanced Studies (VISTAS), Pallavaram, Chennai, Tamilnadu, 600117, India.

 

ABSTRACT:

A molecular docking study is advance technique of structure based drug discovery and help to develop more heterocyle with promising pharmacological activity. In the present study molecular docking analysis was carried out for the various pyrimidine fused heterocycle derivatives (6a-y and 7a-r)which are planned, using the C-Docker protocol. Roscovitine-complexed X-ray crystallographic enzyme (CDK2) substrate.The result of molecular docking studies showed that 6r, 6l and 6p compounds showed higher docking scores compared to those in the series. Compound 6rexhibited one H-bonding interaction between the nitrogen of Cyanide group of pyrimidine at 5^th position with LYS89 (1.80 Å) and four Pi-Alkyl bond with LEU134, ILE10, VAL18 and ALA144 (4.47, 4.46, 5.29, 5.04 Å respectively) one carbon-hydrogen bond with LEU83 (2.73 Å), one Pi-Donor Hydrogen Bond interaction with GLU12 (3.18 Å) and one Pi-Anion interaction with Asp145 (4.00 Å).All synthesized derivatives (6a-y and 7a-r) will be confirmed by the TLC, IR, NMR and MASS spectroscopy. Molecular docking studies give idea regarding the interaction of synthesized compound with protein of interest. The series of 6a-y and 7a-r will be synthesized, confirmed and tested for the in-vitro anticancer activity using human cancer cell line using MTT assay.

 

 

 

INTRODUCTION: 

Cellular Apoptosis is the responsible for the maintaining the cell population. The importance factor regulating this apoptosis process is mitochondrial outer membrane permeabilization, cytochrome C and cellular tress. B-cell lymphoma -2 protein family is the main protein responsible for the apoptosis process.¹ The various type of family of these proteins was identified and is responsible for pre apoptotic and anti-apoptotic group. In the different type of cancer cell anti apoptotic B cell Lymphoma cell 2 family protein are expressed. In the year 2000, the first drug was developed acting on Bcl-2 protein family. In 2010, the Eribulinmesylate was developed as antineoplastic agent.²

 

One carbon metabolism pathway of cancer cell is another target for the cancer drug development to minimize the adverse drug effect. Mitochondrial one carbon metabolism including serine hydroxyl methyltransferase-2 and methylenetetrahydrofolate dehydrogenase-2 are new target for the drug discovery of anticancer agents.³ Two compound MIT and MIN were discovered by using structure based drug designing method and showed good interactions with SHMT2 and MTHFD2 target.⁴

 

 

Now a day the use of biomarker for the finding of drug target, to know the mechanism of action increases the accuracy of anticancer agents. Various protein, metabolic derivatives, immunological agents can be used as biomarker for the development of efficient anticancer agents.⁵

 

Drug repositioning is the recently used tool for the identification of anticancer agents instead of de novo synthesis. In the drug repositioning new indications of already existing drug molecule will be find out for the treatment of another diseases.⁶ Ex the drug sildenafile first discovered for the used as cGMP specific phosphodiesterase 5 inhibitor, after II phase clinical trial fails it as antianginal use. The side effect of the drug like penile erection found in clinical trial first it the sildenafil was directed to use as erectile dysfuntion.⁷

 

Anticancer activity of substituted pyrimidine derivativesl:

Mohamed M. Mohamed synthesized the novel dihydropyrimidine derivatives containing thiouracilecarbonitrile ring system. The activity was predicted by molecular docking studies on three compounds (7, 9 and 2d). This studies showed that compound no 7 had greater affinity for the enzyme thymidilate synthase, as it forms 6 hydrogen bond with His256, Asp218, ala312, Val 313, Try258 of the enzyme.⁸ The synthesized compounds were tested for their anticancer activity by using MTT assay. And all compound shown significant result when tested using HepG2 & MCF-7 cell line. All the derivatives had shown inhibition of cell growth as compared to reference standard 5-fluorouracil.^9,10

 

Experimental:

Molecular Docking:

Discovery Studio 2019 Software, molecular docking analysis was carried out using the C-Docker protocol. Roscovitine-complexed X-ray crystallographic enzyme (CDK2) substrate (was downloaded from the protein database (http://www. rcsb. org/-pdb)) (PDB ID: 2A4L). The structures of the enzymes were checked for missing atoms, bonds, contacts, and cleaned. The enzyme structure was reinforced with hydrogen atoms. Manually deleted water molecules and bound ligand.¹¹

 

The receptor was prepared by a protein preparation wizard in Macromolecules Tools. Missing loops of lengths less than or equal to the Maximal Loop Length are inserted and initially refined using Modeler. Further refinement was done using CHARMm minimization.¹² The structures of compounds were sketched using Chem3D 18.1 and MM2 minimization was done.  Ligands were loaded in Discovery Studio and full minimization was carried out using CHARMm force field and steepest Descent algorithm with 2000 iterations, RMS Gradient 0.01, Nonbond List radius 18.0 Å. The binding site was defined by selecting the co-crystal ligand. CDOCKER protocol was carried out for docking studies.¹³

 

The “-Cdocker_Energy” and  “-Cdocker_Interaction_ Energy” was used as an indicator for the quality of molecular docking. The high positive value of those indicators presented a good interaction between the ligand and the receptor.¹⁴

 

Validation of the docking protocol:

By performing the RMSD calculation between the docked pose and the crystal structure, we validated the adopted docking protocol to confirm the reliability of the chosen docking system.

 

Table:1: CDOCKER scores, Binding Energy of Compounds

Sl. No	Compounds	Binding Energy	-CDOCKER Energy	CDOCKER Interaction Energy
1	6l.mol	-145.309	22.732	64.6716
2	6o.mol	-131.973	8.00179	61.7941
3	7m.mol	-128.598	16.6847	62.4351
4	6j.mol	-115.698	12.5751	54.4978
5	6x.mol	-115.595	14.0755	53.7318
6	7j.mol	-111.618	26.8672	52.7312
7	7k.mol	-110.725	5.90587	58.5525
8	6k.mol	-101.612	-20.745	50.97
9	7r.mol	-97.7653	19.3198	55.1374
10	7l.mol	-95.8146	29.5319	63.332
11	6m.mol	-87.777	1.37079	61.1818
12	6g.mol	-85.1675	-0.6733	58.4209
13	7n.mol	-84.5601	29.4313	54.2698
14	7e.mol	-83.2624	25.3973	56.9623
15	6w.mol	-82.7588	-16.2075	55.9064
16	6e.mol	-82.6398	10.6211	55.1391
17	7q.mol	-82.6202	30.3449	53.6438
18	6f.mol	-81.8044	17.7161	58.578
19	6s.mol	-81.6328	1.89556	50.151
20	6n.mol	-80.4302	20.0373	63.134
21	7f.mol	-80.1716	23.5191	57.3463
22	6t.mol	-75.2251	7.95145	52.4143
23	7c.mol	-75.1488	29.7852	60.5161
24	6c.mol	-71.3769	9.87398	62.8858
25	7d.mol	-71.3297	24.7238	50.2561
26	6v.mol	-69.2969	0.099794	45.3188
27	7o.mol	-68.5716	36.7504	47.2178
28	7a.mol	-68.5637	26.3762	47.6893
29	6y.mol	-68.1353	3.22574	47.0092
30	6a.mol	-65.253	14.5933	52.1768

 

Table:2: Cdocker scores, Binding Energy of Compounds

Sl. No	Compounds	Binding Energy	-CDOCKER Energy	-CDOCKER Interaction Energy
31	6u.mol	-60.7606	14.5579	45.1366
32	6p.mol	-59.5702	9.01891	64.4786
33	6i.mol	-57.0807	5.8324	50.2873
34	6r.mol	-56.0522	7.01405	65.0607
35	6q.mol	-54.3708	-13.4914	50.2317
36	6d.mol	-51.9712	12.9644	53.476
37	7h.mol	-50.9594	25.5813	55.4637
38	6b.mol	-43.6385	3.17672	56.7422
39	7g.mol	-40.8907	13.2772	55.9446
40	7i.mol	-27.4081	25.3914	49.5519
41	7c.mol	-12.7953	28.1627	53.4633
42	6h.mol	-10.2356	-15.1572	54.6314
43	7b.mol	-11.7253	-9.6878	45.6985

 

 

Figure-1:3D Interaction of compound 6r at the binding site of the enzyme (PDB ID: 2A4L) (A) Interaction with Protein2A4L, (C) Hydrophobic interaction, (D) Hydrogen bond interaction, (E) 2D Interaction of the compound 6r at the active site of the enzyme 2A4L

 

Figure-2: 3D Interaction of compound 6l at the binding site of the enzyme (PDB ID: 2A4L) (A) Interaction with Protein2A4L, (C) Hydrophobic interaction, (D) Hydrogen bond interaction, (E) 2D Interaction of the compound 6r at the active site of the enzyme 2A4L

 

Figure-3: 3D Interaction of compound 6p at the binding site of the enzyme (PDB ID: 2A4L) (A) Interaction with Protein2A4L, (C) Hydrophobic interaction, (D) Hydrogen bond interaction, (E) 2D Interaction of the compound 6r at the active site of the enzyme 2A4L

 

Figure - 4: RMSD of docked pose of Cocrystal ligand of 2A4L between before docking and after docking

 

RESULT AND DISCUSSION:

Molecular Docking Studies:

Using the CDOCKER algorithm, detailed intermolecular interaction was analyzed between the ligands and protein. The targeted protein's 3D structural details were collected with an entry code PDB ID 2A4L from the PDB Databank. The inhibitors were docked to the targeted protein's active site and binding energies were measured. This showed that 6r, 6l and 6p compounds showed higher docking scores compared to those in the series. Compound 6r exhibited one H-bonding interaction between the nitrogen of Cyanide group of pyrimidine at 5^th position with LYS89 (1.80 Å) and four Pi-Alkyl bond with LEU134, ILE10, VAL18 and ALA144 (4.47, 4.46, 5.29, 5.04 Å respectively) one carbon-hydrogen bond with LEU83 (2.73 Å), one Pi-Donor Hydrogen Bond interaction with GLU12 (3.18 Å) and one Pi-Anion interaction with Asp145 (4.00 Å) as shown in (Fig. 1). As depicted in Fig. 2, compound 6l exhibited five H-bonding interaction with ASP86, GLU12, LYS89, HIS84 (2.04, 2.03, 1.81, 3.08 Å respectively) and LEU83 (2.81, 2.26, 1.92 Å), two pi-Alkyl interaction with ILE10, LEU134 (5.0, 4.66 Å) and two carbon-hydrogen bond with GLY13, GLY11 (2.75, 2.40 Å). Compound 6p exhibited four Hydrogen bond interaction with THR14, LYS33, ILE10, LEU83 (2.63, 1.86,2.79, 2.31 Å respectively), three pi-Alkyl interaction with ALA31, VAL18, LEU134 (5.19, 4.75, 4.94 Å respectively), four carbon-hydrogen bond with GLY13, ASP145, PHE82, LYS89 (2.35, 2.5, 2.68,2.89 Å) as shown in (Fig. 3)

 

Validation and selection of the docking method:

To determine the precision of the docking procedure, cocrystal ligand RMSD values were calculated. The lowest RMSD value results from the CDOCKER protocol combined with the CDK2 protein model (1.54 Å) (Fig. 4).

 

CONCLUSION:

All the synthesized derivatives will be confirmed by IR, NMR and MASS spectroscopy. In the given series of derivatives compound 6l, 6p, 6r showed good result in molecular docking studies and exhibit better interaction with maximum docker interaction energy of 64.6716 for 6l, 64.4786 for 6p and 65.0607 for 6r respectively.The in-vitro anticancer activity will be carried out for the synthesized derivatives of pyrimidine fused compound by using MTT assay using reference standard compound for the different human cancer cell line of various type of cancer.

 

ACKNOWLEDGMENTS:

The author would like to express my gratitude to the Vel’s University, Chennai, Tamilnaduand Shivaji University, Kolhapur (SUK) for support to conduct this study.

 

CONFLICT OF INTEREST:

The author declared that there is no conflict of interest.

 

REFFERENCES:

1.      Sidram AN, Sachin GL, Kalyane NV. Design, Synthesis and Study of Pharmacological and Biological Evaluation of some novel 1-2-4 Triazolo containing Thiosemicarbazide Derivatives. Research Journal of Pharmacy and Technology. 2011;4(9):1400-03.

2.      Pankaj K, Abhishek K, Jean SP et al. Synthesis and Biological Evaluation of Pyrimidine Derivatives via PyrrolylChalcones. Research Journal of Pharmacy and Technology. 2017;10(5):1392-94.doi: 10.5958/0974-360X.2017.00248.7

3.      Suman K, Vinita G, Sanchita S et al. Synthesis, Characterization and Antimicrobial Activities of Some New Amino-Pyrimidine Derivatives. Research J Pharm and Tech. 2019;12(1):167-71.doi: 10.5958/0974-360X.2019.00031.3

4.      Debarshi KM, Ruchi SS, Pranesh K. Murrayanine-Chalcone Transformed into Novel Pyrimidine Compounds Demonstrated promising Anti-Inflammatory Activity. Asian Journal of Pharmaceutical Research 2018; 8(1):6-10.DOI: 10.5958/2231-5691.2018.00002.3

5.      Kalpana D, RekhaS, Murugan et al. Synthesis, Characterization and Evaluation of some newer Pyrimidine derivatives as Anti-inflammatory Agents.Research Journal of Pharmacy and Technology. 2021 May 1;14(5):2519-34.doi: 10.52711/0974-360X.2021.00445

6.      Khedkar SA,Patil JS,Sabale PM. Design and Synthesis, In Silico Analysis of Condensed Pyrimidine derivatives as Potent Antimicrobial Agents. Research Journal of Pharmacy and Technology. 2022;15(6):2422-26.doi: 10.52711/0974-360X.2022.00403

7.      Shakila B,Krishnamoorthy, Senthamarai et al. Synthesis, Spectral Characterization and Anticancer activity of Novel Pyrimidine Derivatives. Research Journal of Pharmacy and Technology. 2020;13(12):6243-47.doi: 10.5958/0974-360X.2020.01088.4

8.      Vivek BP,Santosh RB, Parag GI.Synthesis, characterization and molecular docking studies on some new N-substituted 2-phenylpyrido[2,3-d]pyrimidine derivatives. Research Journal of Pharmacy and Technology. 2021;14(7):3846-54.doi: 10.52711/0974-360X.2021.00667

9.      Almakaiev MS, Dvinskikh NV,Almakaieva LG. Development of a combined solution of pyrimidine nucleotides with vitamin B6. Research Journal of Pharmacy and Technology. 2021;14(12):5384-87.DOI: 10.52711/0974-360X.2021.01078

10.   Prerana AC, Shailaja BJ. Docking Studies, Synthesis and Evaluation of Novel Pyrimidin-2-one Derivatives as a Dipeptidyl Peptidase IV Inhibitors. Research Journal of Pharmacy and Technology. 2021;14(11):5973-77.doi: 10.52711/0974-360X.2021.01037

11.   Nadia SM, Nada AS, Radhiyah AB. Preparation,Characterization and Study of Biological Activity for some new derivatives Mannich's bases derived from Shiff's bases. Research Journal of Pharmacy and Technology. 2021;14(11):6025-32.doi: 10.52711/0974-360X.2021.01047

12.   Khedkar SA,Patil JS,Sabale PM. Virtual Analysis of Condensed Pyrimidine Derivatives as COX II Inhibitors Potential Anti-inflammatory Agents. Research Journal of Pharmacy and Technology 2021;14(10):5423-26.doi: 10.52711/0974-360X.2021.00945

13.   Mandeep S, Prasad DN, Supriya A. Synthesis, Characterization and Biological Evaluation of Novel Triazolyl - Acridine Derivatives as Cytotoxic Agents. Research Journal of Pharmacy and Technology. 2021;14(10):5101-07.DOI: 10.52711/0974-360X.2021.00889 

14.   Kavitha K, Srinivasan N, Mohan S et al. Insilco Design and Potential Cytotoxic agents EGFR Inhibitors of 4(3H) Quinazolinone Derivatives. Research Journal of Pharmacy and Technology. 2021;14(9):4849-55.doi: 10.52711/0974-360X.2021.00842

 

 

 

Accepted on 29.09.2023           © RJPT All right reserved

Research J. Pharm. and Tech 2023; 16(10):4825-4830.