Unveiling nicotiflorin analogs with improved oral drug-like metrics as candidates for the development of dengue virus NS2B-NS3 protease inhibitors: An in silico study

Kaempferol 3-O-β-rutinoside (nicotiflorin) has been identified as a dengue virus (DENV) NS2B-NS3 protease (NS2B-NS3pro) inhibitor. However, nicotiflorin possesses suboptimal oral drug-like metrics regarding violation of the Lipinski’s rule of five (Ro5) and low in silico-derived bioavailability score, rendering it a less favorable lead candidate for the development of oral drugs. Here, ligand-based virtual screening, structure-based virtual screening, and molecular dynamics (MD) simulation approaches were applied to identify nicotiflorin analogs with improved oral drug-like metrics, compared to those of nicotiflorin, as leads for the development of anti-DENV inhibitors targeting NS2B-NS3pro. The SwissSimilarity server was used to search chemical databases for nicotiflorin analogs, which were subsequently combined to form a small molecule library. The library was screened against DENV-2 NS2B-NS3pro, where the fitness score of nicotiflorin (control) was used to set the selection cutoff for shortlisting six compounds as screening hits. Three compounds (cpd1, cpd2, and cpd3) that remained stably bound to NS2B-NS3pro for up to 100 ns in MD simulations were identified as promising oral drug leads. Cpd1, cpd2, and cpd3 demonstrated effective binding to DENV-2 NS2B-NS3pro and obtained improved ligand efficiency scores of 0.12, 0.13, and 0.11, respectively, compared with a score of 0.09 obtained by nicotiflorin. Unlike nicotiflorin, the three analogs passed the Ro5, and each obtained an acceptable in silico-derived bioavailability score of 0.55, which is threefold better than the 0.17 score for nicotiflorin. Furthermore, the three nicotiflorin analogs exhibited RMSDs, H-bonding, binding free energies, and ADMET properties comparable to those of nicotiflorin. The overall results suggest that cpd1, cpd2, and cpd2 possess improved oral drug-like metrics compared to those of nicotiflorin and could serve as promising leads for the development of oral anti-DENV inhibitors targeting NS2B-NS3pro.