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

Abstract 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 P 1 and P 1 ′ 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 (P 5 –P 5 ′) the P 1 and P 2 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 −1 . Besides, the P 3 , P 1 ′, P 2 ′ and P 4 ′ subsites showed a less contribution in binding interaction ( −1 ). The catalytic water was detected nearby the carbonyl oxygen of the P 1 reacting center of the capsid, intNS3, 2A/2B and 4B/5 peptides. These results led to the order of absolute binding free energy ( ΔG bind ) 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.