Docking and Database Screening Reveal New Classes ofPlasmodiumfalciparumDihydrofolate Reductase Inhibitors

Abstract

Plasmodium falciparum dihydrofolate reductase (PfDHFR) is an important target for antimalarial chemotherapy. Unfortunately, the emergence of resistant parasites has significantly reduced the efficiency of classical antifolate drugs such as cycloguanil and pyrimethamine. In this study, an approach toward molecular docking of the structures contained in the Available Chemicals Directory (ACD) database to search for novel inhibitors of PfDHFR is described. Instead of docking the whole ACD database, specific 3D pharmacophores were used to reduce the number of molecules in the database by excluding a priori molecules lacking essential requisites for the interaction with the enzyme and potentially unable to bind to resistant mutant PfDHFRs. The molecules in the resulting "focused" database were then evaluated with regard to their fit into the PfDHFR active site. Twelve new compounds whose structures are completely unrelated to known antifolates were identified and found to inhibit, at the micromolar level, the wild-type and resistant mutant PfDHFRs harboring A16V, S108T, A16V + S108T, C59R + S108N + I164L, and N51I + C59R + S108N + I164L mutations. Depending on the functional groups interacting with key active site residues of the enzyme, these inhibitors were classified as N-hydroxyamidine, hydrazine, urea, and thiourea derivatives. The structures of the complexes of the most active inhibitors, as refined by molecular mechanics and molecular dynamics, provided insight into how these inhibitors bind to the enzyme and suggested prospects for these novel derivatives as potential leads for antimalarial development.

A common feature-based 3D-pharmacophore model generation and virtual screening: identification of potential PfDHFR inhibitors

“…As described in previous sections, the identified hits show all the necessary interactions in the active site which are required by antifolate PfDHFR inhibitors for effective inhibition of this enzyme 6,7,11,18,25 . Their hydrogen bond donor features interact with Asp54 and Ile14 or/and Leu164, whereas the hydrophobic portions interact with amino acid residues Met55, Ser111, Pro113, and other amino acids via hydrophobic interactions.…”

“…The hits were selected based on their docking scores, binding orientations, and interactions with key amino acid residues in the active site (Asp54, Ile14, and Leu164) as well as their interactions in the hydrophobic region of the active site. Because of the flexible nature of their side chains, there are no potential steric clashes with Asn108, which is known to be responsible for resistance of the mutant parasite to antimalarial drugs 1 and 2 6,7,[10][11][12][13]18,25 . The hits also fulfill all the properties required by drug-like molecules 47,48 .…”

“…c Direct hit indicates whether (1) or not (0) a molecule in the training set mapped every feature in the hypothesis. 6,7,11,25 . In this inhibitor, it has been observed that two hydrogen bond donors interact with Asp54 and backbone amino acids (Ile14 or/and Leu164).…”

“…It has also been employed in the discovery of PfDHFR enzyme inhibitors 7,24 . Rastelli et al 25 employed virtual screening, which led to the identification of 12 new leads whose chemical structures are different from those of classical antifolates. Enzyme assay and inhibition studies indicated that the compounds are generally more active toward mutant enzyme than wild-type PfDHFR enzyme.…”

Refined Docking as a Valuable Tool for Lead Optimization: Application to Histamine H3 Receptor Antagonists

“…It is frequently used to minimize the size of a chemical library before a high throughput screen (HTS). Even if industrial experience with novel targets is seldom reported, many case studies relate successful uses of such methods [7,8]. For the subsequent step in the drug-discovery process, i. e. hit / lead optimization, there are fewer reports [9].…”