Molecular docking of the designed compounds with the target
The designed compounds after optimization were subjected to molecular docking simulation to validate the improvement in the interaction of the lead compound for a better inhibition of the DENV NS-5 protease. The results of the docking scores of the designed compounds (34a, 34b, 34c, 34d, 34e, 34f, 34g, 34h, 34i, and 34j) obtained from the Molsoft IC-M-Pro are presented in Tables 2 and 3 shown to be − 26.54, − 29.612, − 22.652, − 23.644, − 23.594, − 19.992, − 23.943, − 19.292, − 20.121, − 19.091, − 22.347 kcal/mol, respectively.
The interaction of the designed compounds with protease amino acid residues indicating the individual residues’ interaction distance as well as the nature and the type of the interactions is presented in Table 3. From Table 2, it could be observed that the docking score of the designed compounds ranged between − 19.091 and − 29. 61 kcal/mol; the lead compound has been reported to have a binding/docking score of − 19.10 kcal/mol (Adawara et al. 2021). The designed compound-protease interactions, as well as those of the standard inhibitors, are illustrated in Fig. 3a–d and Additional file 1: SF1.
Compound 34a (binding score − 26.54 kcal/mol) was observed to form three conventional hydrogen bonds (C HB) with SER763, CYS780, and SER885 (1.852, 1.799, and 2.084 Å) amino acid residues and one carbon-hydrogen bond (C–H-B) with ARG773 amino acid residue. About eight hydrophobic interactions were also formed with TYR882, ASN777, TRP833, TRP833, TYR882, and HIE786 A: CYS780 and MET809 residues through Pi–Sulfur, Pi–Lone Pair, Pi–Pi Stacked, Pi–Pi Stacked, Pi–Pi T-shaped, Pi–Alkyl, Pi–Alkyl, and Pi–Alkyl, respectively. The conventional hydrogen bond formation in compound 34a involved oxygen and nitrogen at position 2 of the oxadiazole core, as well as the –HO group at the para position in which it interacted with SER885 amino residue where it acts as hydrogen bond donor.
Compound 34b with the best docking score of − 29. 61 kcal/mol was observed to participate in the interactions involving four C HB with ASN777, TRP833, SER885, SER885 (1.858, 2.164, 1.836, and 2.123 Å) amino acid residues where the two –OH group at the ortho and meta position of the phenyl ring both donated hydrogen to SER885 residue, while the oxygen of the –OH group at the para position of the phenyl ring and the nitrogen at position 2 of the oxadiazole account for the other two C HB interactions involving ASN777 and TRP833 residues where they act as donors. There was no C–H-B interaction observed in compound 34b, other than the four C BH and nine hydrophobic interactions involving MET809, MET809, CYS780, TYR882, ASN777, TRP833, TRP833, TYR882, and HIE786 amino acid residues through Pi–Donor Hydrogen Bond, Pi–Sigma, Pi–Sulfur, Pi–Sulfur, Pi–Lone Pair, Pi-Pi Stacked, Pi–Pi Stacked, Pi–Pi Stacked, and Pi-Alkyl.
Ribavirin formed eight favourable conventional hydrogen bond interactions involving LYS756, SER763, CYS780, CYS780, ASN777, GLN760, GLN760, and THR806 (1.690, 1.853, 2.536, 2.467, 2.799, 2.896, 2.208, and 2.554 Å) were observed as well as five C–H-B with THR806, SER785, THR806, GLU807, GLN760 amino acid residue, whereas the MET809, CYS780, MET809 residues were involved in hydrophobic interactions through Pi–Donor Hydrogen Bond, Pi–Alkyl, and Pi–Alkyl.
SAH has the highest hydrogen bond interaction energy of − 10.4372 and formed six C HB interactions with LYS756, ASN777, CYS780, MET809, GLN760, GLN760 (2.325, 1.871, 1.840, 2.925, 2.099, 2.047 Å) amino acid residues, and formed seven C–H-B interactions with SER763, ASP808, GLN760, SER785, THR806, ASP808, HIE786, with other two hydrophobic interaction TYR882, HIE786 residues through Pi–Sulfur, Pi–Pi T-shaped, respectively. The higher hydrogen bond energy observed in SAH could be due to majorly C–H-B interaction because it has the highest amount of C–H-B interaction but a lower binding score of − 16.536 kcal/mol.
The co-crystal ligand of the protease demonstrated a binding score of − 25.0433 kcal/mol (Table 2), but despite having such a higher binding score was observed to form some unfavourable bond (Additional file 1: Fig. SF2b) which entail instability of the complex. The 2D binding interactions of the native ligand-protease presented in Additional file 1: Fig. SF2 were viewed before and after docking (Additional file 1: Fig. SF2a, b) to understand the significance of optimizing the co-crystal ligand in terms of how it interacts with the protease.
In summary, the hydroxyl group of the phenyl moiety, as well as those of the methylamine and methoxy groups, formed conventional hydrogen bond interaction with some important amino acid residues of the protease. This observation could be responsible for the higher hydrogen bond energy interactions obtained for the designed compounds which are important for the ligand-protease complex stability. More so, the nitrogen at position two of the oxadiazole core was observed to be stabilized through conventional hydrogen in all the designed compounds, this highlights the importance of nitrogen at position two in conferring the stability of the ligand protease complexes.
The compounds all formed favourable interactions with the protease which entails the good potential of the compounds as inhibitors. Among the designed compounds, compounds 34a and 34b showed remarkable docking scores far much better than the lead as well as the standard inhibitor, although, none of the inhibitors had a docking score close to the lead talk more of the improved derivatives of the lead.
The stabilization of the complexes of the designed compound-protease was majorly through conventional hydrogen bond and hydrophobic bond interactions involving residues at the allosteric sites of the protease. All the designed compounds have a better hydrogen bond energy (− 3.402 to − 9.0128 kcal/mol) than the template (− 3.1 kcal/mol) which entails favourable interactions with the protease than the template and were all found to be in a similar manner as the standard inhibitors. This could bring about better stability of the complexes, hence better inhibitory activity.
D-L, pharmacokinetics, and ADME prediction of the designed compounds
D-L of any potential drug candidate is essential in the drug development process. The D-L properties for potential drug candidate proposed by Lipinski implemented in the Swiss-ADME web tool were utilized. The obtained D-L parameters are presented in Table 4. It could be observed that all the designed compounds perfectly obeyed the rules suggested by Lipinski characterized by their molecular weight of not less than 500, logP value of not greater than 5, hydrogen-bond donors of not greater than 5; hydrogen-bond acceptors of not greater than 10, and topological polar surface area (TPSA) of less than 140 recommended by Lipinski (Lipinski 2016; Daina et al. 2017), from the predicted properties presented in Table 4, it could also be seen that our designed compounds passed all Lipinski’s rule of five which also suggests good D-L and oral bioavailability (Lipinski 2016).
The estimation of the ease of synthesis (synthetic-accessibility) of bioactive compounds possessing drug-likes-ness is an essential need in the drug discovery process (Ertl and Schuffenhauer 2009).
Other valuable information obtained from the ADME evaluation presented in Table 4 includes the gastro-intestinal adsorption (GIA), pan-assay interference compounds (PAINS) alert, bioavailability score, and synthetic accessibility. The designed compounds could all be seen to possess high GIA except the standards inhibitors considered, which entail easy and favourable GIA by the designed compound.
The designed compounds were predicted to possess no PAINS alert except compound 34b with one PAINS alert which depicts the true activity of the compounds in the biochemical assay (Baell and Holloway 2010).
The bioavailability scores of the designed compounds, as well as those of the standard all, fall within the range of active category as compounds with bioavailability scores in this range, are classified as highly active (Ertl and Schuffenhauer 2009; Mishra et al. 2016). The compounds have all demonstrated the ease of synthesis evidenced by their synthetic accessibility score of 3.27–3.83 which are lower than those of the standards since the smaller the value, the easier a chemical compound could be synthesized (Ertl and Schuffenhauer 2009).
The drug-metabolizing capacity of CYP450 enzymes, clinically relevant CYP450 genetic polymorphisms, cytochrome P450 CYP-1A2, CYP-2C9, CYP-2C19, and CYP-2D6 were also evaluated. The compounds including the standard are all non-Pgp substrate, as well as CYP2D6, a CYP3A4 inhibitor, whereas only compound 34j was found to be non-inhibitor of CYP-2C9, respectively (Table 4) (Hollenberg 2002; Serretti et al. 2009).
The toxicity of the designed compounds was assessed using the pkCSM webpage tool, with the results presented in Table 5. The results revealed that the designed compounds all had no AMES toxicity, no skin sensitization, and were all non-inhibitors of the human ether-a-go-go-related gene (hERG) cardiovascular toxicity, making them safer. Except for compounds 34c, all of the compounds' hepatotoxicity potential was assessed to be positive. The proposed compounds' Oral Rat Acute Toxicity (LD50) ranged from 1.894 to 2.674, while SAH Ribavirin and Fenretinide had 2.485, 1.481, and 2.696, respectively, indicating that they are in the same range as Ribavirin and are even safer. Based on the toxicity profile of the developed compounds, it may be reasonable to classify them as non-toxic, and they have been demonstrated to have good D-L.