Rational repurposing, synthesis, in vitro and in silico studies of chromone-peptidyl hybrids as potential agents against Leishmania donovani

Figures & data

Figure 1. Chemical structures of cysteine protease inhibitors with potential antileishmanial activity and the design rational of chromone-peptidyl hybrids as new antileishmanial agents.

Scheme 1. Synthesis of target chromone-peptidyl hybrids (7a–q). Reagents and conditions: (i) EDC, HOBt, DMF, stir 0 °C-rt, 2h; (ii) Dess-Martin periodinane, DMF, 0 °C-rt, 10% Na₂S₂O₃ solution, 2h (7a–l); (iii) 1% methanolic HCl, 70 °C, 2 h (7m–q).

Table 1. % Growth inhibition of L. donovani promastigotes elicited by chromone peptidyl hybrids (7a–q).

Compound	R^1	R^2	R^3	% Inhibition at 50 µM^a	% Inhibition at 25 µM^a
7a	CH3O-	H-	H	92	80
7b	CH3O-	H-	Benzyl	39	5
7c	CH3O-	H-	4-methoxyphenethyl	100	99
7d	CH3OCH2O-	H-	Benzyl	41	27
7f	CH3O-	CH3O-	H	12	NI^b
7g	CH3O-	CH3O-	Benzyl	34	8
7h	CH3O-	CH3O-	4-methoxyphenethyl	103	100
7i	CH3O-	CH3OCH2O-	Benzyl	98	55
7j	CH3O-	CH3OCH2O-	4-methoxyphenethyl	98	87
7k	CH3OCH2O-	CH3OCH2O-	Benzyl	70	58
7l	CH3OCH2O-	CH3OCH2O-	4-methoxyphenethyl	51	28
7m	HO-	H-	Benzyl	40	13
7n	HO-	H-	4-methoxyphenethyl	99	97
7o	CH3O-	HO-	Benzyl	98	96
7p	CH3O-	HO-	4-methoxyphenethyl	100	94
7q	HO-	HO-	Benzyl	58	NI
Miltefosine				100	100
Erufosine				108	106

^a% Inhibition of growth of L. donovani promastigotes after incubation with the specified concentration for 3 days relative to control. ^bNI = No Inhibition.

Table 2. Determined IC₅₀ values against L. donovani promastigotes for the most active chromone peptidyl hybrids.

Compound	R^1	R^2	R^3	IC50 (µM)^a
7a	CH3O-	H-	H	>100
7c	CH3O-	H-	4-methoxyphenethyl	9.8
7h	CH3O-	CH3O-	4-methoxyphenethyl	12.0
7j	CH3O-	CH3OCH2O-	4-methoxyphenethyl	42.0
7n	HO-	H-	4-methoxyphenethyl	10.0
7o	CH3O-	HO-	Benzyl	>100
7p	CH3O-	HO-	4-methoxyphenethyl	43.0
Miltefosine				3.5
Erufosine				9.8

^aIC₅₀: The concentration that inhibits L. donovani promastigotes by 50% relative to control after incubation for 3 days as calculated from the dose-response curves.

Table 3. In vitro evaluation of cytotoxicity on THP-1 cell of compounds 7c, 7h, and 7n.

Compound	R^1	R^2	R^3	THP-1 cell CC50 (µM)
7c	CH3O-	H-	4-methoxyphenethyl	>100
7h	CH3O-	CH3O-	4-methoxyphenethyl	29.1
7n	HO-	H-	4-methoxyphenethyl	>100
Miltefosine				>40
Erufosine				19.4

Figure 2. Sequence alignment and Ramachandran plot of the generated homology model of CALP of L. donovani (A) Sequence alignment against calpain I protease core (PDB code: 1TL9); (B) Ramachandran plot of amino acid residues of the generated homology model indicated that most of them are in the favoured regions.

Figure 3. Position of active site in three-dimensional protein structure showing co-crystallized inhibitor leupeptin in the active site.

Figure 4. Predicted binding modes of compounds 7c, 7h, and 7n as well as the reference ligand MDL28170 with LdCALP: (A) Calculated docking pose of the reference compound MDL28170 (1) in 3D (left) and 2D view (right) into the substrate pocket of LdCALP; (B) Calculated docking pose of compound 7c in 3D (left) and 2D view (right) into the substrate pocket of LdCALP; (C) Calculated docking pose of compound 7h in 3D (left) and 2D view (right) into the substrate pocket of LdCALP; (D) Calculated docking pose of compound 7n in 3D (left) and 2D view (right) into the substrate pocket of LdCALP.