RP 67580 structure The molecular docking data supported the
The molecular docking data supported the potential interaction of lapachol and the synthetic naphthoquinonolyl compounds with the PfDHODH enzyme as the putative mechanism of action and the inhibition of parasite growth in vitro. In general, compounds fit well into the binding pocket of PfDHODH, the tightness of binding varying with the size of the ligand, which is expressed by the docking scores. In order to explain the binding of the studied compounds, the ligand-binding site is labeled as three pockets based on the binding of atovaquone: pocket 1 (P1) occupied by the 1,4-naphthoquinone moiety, pocket 2 (P2) accommodating cyclohexane, and pocket 3 (P3) occupied by the 4-chlorobenzene ring (Fig. 2). The 1,4-naphthoquinone, a common substructure, displayed direct interactions with R265 and Y528 in pocket P1, and its binding pose was stabilized by hydrophobic interactions with I172, I263 and V532 amino acids. The unsaturated isoprenyl moiety at position 2 of the 1,4-napthoquinone moiety occupied the proximal hydrophobic pocket P2 comprising interactions with the RP 67580 structure F188, V223, F227 and Y528. It has been shown experimentally that the side chain of F188 attains various rotameric states in P2 in order to allow the protein to accommodate ligands of variable sizes as well as to provide access to P3. Interestingly, since the binding site was kept flexible during docking studies, F188 attained a down-pointing conformation in most of the inhibitor-docked PfDHODH structures, so as to accommodate the large substituents present at position 3 of 1,4-naphthoquinone. Additionally, F188 exhibited aromatic interactions with the 1,2,3-triazole moiety in an edge-to-face manner. In addition, the 1,2,3-triazole moiety was oriented parallel to the disulfide bridge between C175 and C184, which connects the two helices α1 and α2 of PfDHODH, and exhibited hydrophobic interactions with C175, L176, C184, and other proximal amino acids. Among the studied novel molecules (1, 7, 11, 13–28), major differences were observed in the relative binding of the various substituents linked to the nitrogen N1 of the 1,2,3-triazole moiety into P3 of PfDHODH. To accommodate these substituents, F171 in the α1 helix attained distinct conformations and was found to exhibit aromatic π–π stacking or other types of hydrophobic interactions. The better activity observed for compound atovaquone (2) over lapachol (1) is apparently due to the presence of the hydrophobic propargyl group which fit better into the hydrophobic pocket. The piperidine NH moiety of 14 formed H-bonds with the OH of Y168 and the backbone C=O of F171. The piperidine ring in 13 (docking score = −12.504) exhibited bidentate H-bonding with the backbone C=O of F171 and with Y168 in pocket P3. The substitution of the acetyl group for the piperidyl nitrogen (compound 19, docking score = −10.994) reduced the binding score, due to loss of H-bonding with F171 and Y168, which could be one of the reason behind its lesser potency against P. falciparum. In comparison to 24 (docking score = −12.014), compound 25, which contains an o-methoxy group in addition to a p-nitro, showed better binding (docking score = −12.960), due to the hydrophobic contribution in pocket P3. The sulfonamide analogue 21 displayed poorer binding affinity (docking score = −10.120), which agreed with its experimentally-demonstrated lower activity (IC50). The docking study suggested 17 as the compound with the highest affinity for PfDHODH. As shown in Fig. 2, the 3-pyridyl substituent (17) exhibited aromatic π–π stacking interactions with F171 (in the α1-helix) as well as H-bonding with the backbone NH of M536 along with hydrophobic interactions. In addition, it favored the CH – π interaction between the 1,2,3-triazole and F188 (Fig. 2). Attempts of docking with 18 failed, probably because of its overall large size. Possibly the pocket P3 failed to accommodate the bulky substituent on N1 of its 1,2,3-triazole core. Therefore, compound 18 is predicted not to act through the inhibition of PfDHODH enzyme for its antimalarial activity (IC50 = 13.6 ± 3.4 μM). The quinoline analogue 7 also displayed comparatively poorer binding affinity that was apparently due to the bulkiness of its quinoline ring, leading to impaired interaction in pocket P3. Overall, the docking study suggested compound 17 as the lead against PfDHODH (score = −14.550) (IC50 = 5.2 ± 1.8 μM; SI = 197.7). The structure-activity relationships could be further explored by incorporating small substitutions on the 3-pyridyl ring. Such structural modifications are expected to enhance enzyme binding affinity and thus lead to compounds with higher potency against the parasite.