Structure-based design, and development of amidinyl, amidoximyl and hydroxamic acid based organic molecules as novel antimalarial drug candidates

Abstract

Malaria remains a significant global health concern causing numerous fatalities and the emergence of antimalarial drug resistance highlights the urgent need for novel therapeutic options with innovative mechanisms of action and targets. This study aimed to design potential inhibitors of Plasmodium falciparum 6-pyruvoyltetrahydropterin synthase (PfPTPS), synthesize them, and experimentally validate their efficacy as antimalarial agents. A structure-based approach was employed to design a series of novel derivatives, including amidinyl, amidoximyl and hydroxamic acid analogs (1c, 1d, 2b, and 3b), with a focus on their ability to bind to the Zn²⁺ present in the active site of PfPTPS. The syntheses of these compounds were accomplished through various multi-step synthetic pathways and their structural identities were confirmed using ¹H and ¹³C NMR spectra, mass spectra, and elemental analysis. The compounds were screened for their antiplasmodial activity against the NF54 strain of P. falciparum and in vitro cytotoxicity testing was performed using L-6 cells. The in vivo acute toxicity of the compounds was evaluated in mice. Docking studies of the compounds with the 3D structure of PfPTPS revealed their strong binding affinities, with compound 3b exhibiting notable metal-acceptor interaction with the Zn²⁺ in the protein binding pocket thereby positioning it as a lead compound for PfPTPS inhibition. The in vitro antiplasmodial studies revealed moderate efficacies against the Pf NF54 strain, particularly compounds 1d and 3b which displayed IC₅₀ < 0.2 μM. No significant cytotoxicity was noted on the L-6 rat cell line. Moreover, in vivo studies suggested that compound 3b exhibited both safety and efficacy in treating rodent malaria. The identified lead compound in this study represents a possible candidate for antimalarial drug development and can be further explored in the search for alternative antifolate drugs to combat the malaria menace.

Keywords: Acute toxicity; Cytotoxicity; Hydroxamic acids; Malaria; Suppression.

Fig. 1.

Known antifolate antimalarials that are active-site inhibitors of the P. falciparum dihydrofolate reductase, a common target in the de novo folate synthesis pathway.

Fig. 2.

The active site of PfPTPS (PDB 1D: 1Y13) and the native ligand biopterin.

Fig. 3.

2D interactions with the amino acid residues in the binding site of the protein target (PDB ID: 1Y13) (A) co-crystallized biopterin (B) redocked biopterin.

Fig. 4.

Molecular docking interactions between 3b and the binding sites of PfPTPS: (A) 3D model (B) 2D model.

Fig. 5.

Graph describing the increase in weight based on the concentration.

Fig. 6.

Histology of kidney sections from test animals treated with benzamide compound (9b): (A) 100 mg/kg, (B) 200 mg/kg, (C) 400 mg/kg, (D) 2000 mg/kg, (E) Control (Magnification ×400).

Fig. 7.

Histology of liver sections from test animals treated with benzamide compound (9b): (A) 100 mg/kg, (B) 200 mg/kg, (C) 400 mg/kg, (D) 2000 mg/kg, (E) Control (Magnification ×400).

Scheme 1.

Synthetic pathway for achieving the designed amidinyl- compound (1c) and amidoximyl- compound (1d).

Scheme 2.

Synthetic pathway for achieving the designed amidoximyl- analog, 2b.

Scheme 3.

Synthetic pathway for achieving the designed amidoximyl- analogs, 3b.