Table I.
Molecular docking studies of CDK1/Cyclin B1 with metabolites/derivatives of aspirin.
| S. no. | Ligand | Receptor | PDB ID | Interacting amino acids | No. of H-bonds | Measurement (A0) | Energy value (kcal/mol) | Interactions |
|---|---|---|---|---|---|---|---|---|
| 1 | Aspirin | CDK1 | 4y72 (A Chain) | Asn133, Gln132 and Tyr15 | 3 | 2.7, 2.1 and 2.6 | −7.4 | -COOH - Asn133, Gln132 and Tyr15 |
| 2 | Salicylic acid | CDK1 | 4y72 (A chain) | Asp146 and Lys 33 | 2 | 1.8 and 2.5 | −8.6 | -OH - Lys33; -COOH - Asp146 |
| 3 | 2,3-DHBA | CDK1 | 4y72 (A Chain) | Asp146 | 1 | 2.0 | −6.8 | -COOH - Asp146 |
| 4 | 2,5-DHBA | CDK1 | 4y72 (A Chain) | Asp146 | 1 | 2.1 | −6.8 | -COOH - Asp146 |
| 5 | 2,6-DHBA | CDK1 | 4y72 (A Chain) | Asp146 | 1 | 2.0 | −7.1 | 6th -OH - Asp146 |
| 6 | 2,4,6-THBA | CDK1 | 4y72 (A Chain) | Arg123, Arg151 and Gly154 | 3 | 2.5, 2.0 and 2.4 | −5.8 | 2nd -OH - Arg151 and Gly154; -COOH -Arg123 |
| 7 | Aspirin | Cyclin B1 | 2b9r | Arg135 | 2 | 1.9 and 2.5 | −6.8 | -COOH Arg135 |
| 8 | Salicylic acid | Cyclin B1 | 2b9r | Arg135 and Tyr60 | 4 | 2.2, 2.4, 2.7 and 2.3 A | −7.4 | -OH - Arg135; -COOH - Tyr60, Arg135 |
| 9 | 2,3-DHBA | Cyclin B1 | 2b9r | Arg135, Arg38 and Asp67 | 6 | 2.1, 2.2, 2.2, 2.2, 2.4 and 2.3 | −6.8 | 2nd -OH - Asp67; 3rd - OH -COOH - Arg38; Arg135 |
| 10 | 2,5-DHBA | Cyclin B1 | 2b9r | Arg135 | 2 | 2.0 and 2.4 | −6.7 | 2nd -OH - Arg135 |
| 11 | 2,6-DHBA | Cyclin B1 | 2b9r | Arg135 | 2 | 2.1 and 2.5 | −5.4 | 6th -OH - Arg135 |
| 12 | 2,4,6-THBA | Cyclin B1 | 2b9r | Arg135, Phe175, Asp67, Arg38, Thr166 | 6 | 2.2, 2.4, 2.2, 2.2, 2.3 and 2.1 | −6.8 | 2nd -OH - Asp67; 4th -OH - Arg38, Thr166; 6th -OH - Asp67; -COOH - Arg135 |
| 13 | Aspirin | CDK1_ Cyclin B1 | 4y72 (A, B chain) | Tyr15 (CDK1) | 1 | 2.5 | −7.0 | -COOH - Tyr15 (CDK1) |
| 14 | Salicylic acid | CDK1_ Cyclin B1 | 4y72 (A, B chain) | Asp146 and Lys33 (CDK1) | 3 | 1.9, 2.5 and 2.6 | −9.6 | -OH - Asp146; -COOH - Lys33, Asp146 (CDK1) |
| 15 | 2,3-DHBA | CDK1_Cyclin B1 | 4y72 (A, B chain) | Thr329, Val336, Phe338 (Cyclin B1) | 2 | 2.4, 2.1 and 2.4 | −6.1 | 2nd and 3rd -OH - Phe338; 3rd -OH Val336; -COOH Thr329 (cyclin B1) |
| 16 | 2,5-DHBA | CDK1_ Cyclin B1 | 4y72 (A, B chain) | Arg123 (3), Leu125, and Arg151 (CDK1) | 5 | 2.2, 2.2, 2.4, 2.4 and 2.4 | −6.0 | 5th -OH - Leu125 and Arg151; -COOH - Arg123 (CDK1) |
| 17 | 2,6-DHBA | CDK1_ Cyclin B1 | 4y72 (A, B chain) | Val336 (Cyclin B1) | 1 | 2.6 | −5.6 | 6th -OH - Val336 (cyclin B1) |
| 18 | 2,4,6-THBA | CDK1_ Cyclin B1 | 4y72 (A, B chain) | Tyr223, Asp 230, and Arg201 (Cyclin B1) | 2 | 2.3, 2.5 and 2.5 | −5.4 | 2nd -OH - Asp230; 4th -OH - Tyr223; -COOH - Arg201 (cyclin B1) |
Free energy binding values and hydrogen bond lengths for the interaction of aspirin, salicylic acid, 2,3-DHBA, 2,5-DHBA, 2,6-DHBA and 2,4,6-THBA with CDK1, cyclin B1 and CDK1/cyclin B1 complex.