- Scientist
- Thanyada Rungrotmongkol
- Protein
- ZIKV NS2B/NS3-tetrapeptide (TGKR) complex
- Ligand
- (A) Ac-nKKR-ACC, (B) Ac-D-RKOR-ACC, (C) Ac-D-KKOR-ACC, (D) Bz-nKRR-AMC
- Simulation Duration
- 200 ns
- InChIKey
- LSDSITOZGWIHGA-IBBBAUQKSA-N
- SMILES
- CCOC1=C(C=CC(=C1)C(C)(C)C)C2=N[C@@]([C@@](N2C(=O)N3CCN(CC3)CC(=O)N4CCOCC4)(C)C5=CC=C(C=C5)Cl)(C)C6=CC=C(C=C6)Cl.Cl.Cl
- Molecular Formula
- C40H51Cl4N5O4
- Protein Details
- An attractive drug target for the ZIKV treatment is the NS2B/NS3 serine protease, which is essential for viral polyprotein processing. Herein, classical molecular dynamics (MD) simulations were performed on the ZIKV NS2B/NS3 serine protease in complex with four peptide substrates to investigate the binding recognition and protein-substrate interactions. The obtained results indicate that the P1 and P2 positions of the substrate play a significant role in binding with the protease enzyme, while the P3 and P4 positions show a minor contribution in binding interaction.
- Ligand Details
- Four fluorogenic substrates used in this study are selected from the literatures on the basis of being the recently designed substrates compared with the most commonly used substrate in the assays. All determined substrates were consisted of: (i) substrate 1, acyl-Norleucine-LysineLysine-Arginine-7-amino-4-carbamoylmethylcoumarin (Ac-nKKR-ACC); (ii) substrate 2, acylD-Arginine-Lysine-Ornithine-Arginine-7-amino-4-carbamoylmethylcoumarin (Ac-D-RKORACC); (iii) substrate 3, acyl-D-Lysine-Lysine-Ornithine-Arginine-7-amino-4- carbamoylmethylcoumarin (Ac-D-KKOR-ACC); (iv) substrate 4, benzoyl-Norleucine-LysineArginine-Arginine-aminomethylcoumarin (Bz-nKRR-AMC)
