Binding specificity of polypeptide substrates in NS2B/NS3pro serine protease of dengue virus type 2: A molecular dynamics Study

• Binding specificity of polypeptide substrates in DV2 NS2B/NS3 protease is ranked as capsid. > intNS3 > 2A/2B > 4B/5 > 3/4A > 2B/3.
• Basic residues at P1 and P2 subsites of substrate are a vital role in the binding with NS2B/NS3pro.
• The polar and charged NS3 residues within S1 (D129, G133 and S135), S2 (D75 and N152) and S3 (G153 and Y161) pockets are preserved for important interaction with the substrate, while the binding of prime site with S1′, S2′and S4′ pockets is possessed by hydrophobic interaction.

The pathogenic dengue virus (DV) is a growing global threat, particularly in South East Asia, for which there is no specific treatment available. The virus possesses a two-component (NS2B/NS3) serine protease that cleaves the viral precursor proteins. Here, we performed molecular dynamics simulations of the NS2B/NS3 protease complexes with six peptide substrates (capsid, intNS3, 2A/2B, 4B/5, 3/4A and 2B/3 containing the proteolytic site between P1 and P1′ subsites) of DV type 2 to compare the specificity of the protein-substrate binding recognition. Although all substrates were in the active conformation for cleavage reaction by NS2B/NS3 protease, their binding strength was somewhat different. The simulated results of intermolecular hydrogen bonds and decomposition energies suggested that among the ten substrate residues (P5–P5′) the P1 and P2 subsites play a major role in the binding with the focused protease. The arginine residue at these two subsites was found to be specific preferential binding at the active site with a stabilization energy of <−10 kcal mol−1. Besides, the P3, P1′, P2′ and P4′ subsites showed a less contribution in binding interaction (<−2 kcal mol−1). The catalytic water was detected nearby the carbonyl oxygen of the P1 reacting center of the capsid, intNS3, 2A/2B and 4B/5 peptides. These results led to the order of absolute binding free energy (ΔGbind) between these substrates and the NS2B/NS3 protease ranked as capsid > intNS3 > 2A/2B > 4B/5 > 3/4A > 2B/3 in a relative correspondence with previous experimentally derived values.

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