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.

*Corresponding Author E-mail: komala.sps@velsuniv.ac.in

 

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 5th 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.

 

KEYWORDS: Substituted tetrahydropyridine, Cyclin dependent kinase2, Thin Layer Chromatography, glutamic acid12.

 

 


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 5th 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.

 

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Received on 15.06.2021            Modified on 19.08.2022

Accepted on 29.09.2023           © RJPT All right reserved

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

DOI: 10.52711/0974-360X.2023.00782