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Non-peptidic cruzain inhibitors with trypanocidal activity discovered by virtual screening and in vitro assay.

Wiggers HJ, Rocha JR, Fernandes WB, Sesti-Costa R, Carneiro ZA, Cheleski J, da Silva AB, Juliano L, Cezari MH, Silva JS, McKerrow JH, Montanari CA - PLoS Negl Trop Dis (2013)

Bottom Line: Affinity values were in a similar range (4-80 µM), yielding poor selectivity towards cruzain but raising the possibility of investigating such inhibitors for their effect on cell proliferation.Two compounds were found to have trypanocidal activity.The IC50 value for compound Nequimed42 acting against the trypomastigote form of the Tulahuen lacZ strain was found to be 10.6±0.1 µM, tenfold lower than that obtained for benznidazole, which was taken as positive control.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.

ABSTRACT
A multi-step cascade strategy using integrated ligand- and target-based virtual screening methods was developed to select a small number of compounds from the ZINC database to be evaluated for trypanocidal activity. Winnowing the database to 23 selected compounds, 12 non-covalent binding cruzain inhibitors with affinity values (K i) in the low micromolar range (3-60 µM) acting through a competitive inhibition mechanism were identified. This mechanism has been confirmed by determining the binding mode of the cruzain inhibitor Nequimed176 through X-ray crystallographic studies. Cruzain, a validated therapeutic target for new chemotherapy for Chagas disease, also shares high similarity with the mammalian homolog cathepsin L. Because increased activity of cathepsin L is related to invasive properties and has been linked to metastatic cancer cells, cruzain inhibitors from the same library were assayed against it. Affinity values were in a similar range (4-80 µM), yielding poor selectivity towards cruzain but raising the possibility of investigating such inhibitors for their effect on cell proliferation. In order to select the most promising enzyme inhibitors retaining trypanocidal activity for structure-activity relationship (SAR) studies, the most potent cruzain inhibitors were assayed against T. cruzi-infected cells. Two compounds were found to have trypanocidal activity. Using compound Nequimed42 as precursor, an SAR was established in which the 2-acetamidothiophene-3-carboxamide group was identified as essential for enzyme and parasite inhibition activities. The IC50 value for compound Nequimed42 acting against the trypomastigote form of the Tulahuen lacZ strain was found to be 10.6±0.1 µM, tenfold lower than that obtained for benznidazole, which was taken as positive control. In addition, by employing the strategy of molecular simplification, a smaller compound derived from Nequimed42 with a ligand efficiency (LE) of 0.33 kcal mol(-1) atom(-1) (compound Nequimed176) is highlighted as a novel non-peptidic, non-covalent cruzain inhibitor as a trypanocidal agent candidate for optimization.

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Molecular structure and cruzain inhibition of compound Neq42 analogs selected for SAR investigation.Molecules drawing and figure generated with MarvinSketch software (www.chemaxon.com).
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pntd-0002370-g006: Molecular structure and cruzain inhibition of compound Neq42 analogs selected for SAR investigation.Molecules drawing and figure generated with MarvinSketch software (www.chemaxon.com).

Mentions: The structure of Neq42 was resolved into two main scaffolds: the first containing the 2-acetamidothiophene-3-carboxamide moiety, and the other the triazole ring moiety substituted in positions 1 and 2 with the benzyl and piperidine, respectively, as can be seen in Figure 6. Based on the predicted mode of binding obtained by molecular docking, a series of structures was selected from commercial databases to investigate the SAR of this compound (Figure 6). When the 2-acetamidothiophene-3-carboxamidegroup was maintained, the piperidine and benzyl groups were removed to assess their contribution to the potency. On the other hand, when the triazole moiety was kept, three substances were selected by replacing the 2-acetamidothiophene-3-carboxamide group to a phenyl group (hydrophobic), a nitrile (which might covalently bind to the catalytic cysteine) and a cyclic sulfone (hydrophilic). The 2D structures and biological activity of the selected compounds are summarized in Figure 6.


Non-peptidic cruzain inhibitors with trypanocidal activity discovered by virtual screening and in vitro assay.

Wiggers HJ, Rocha JR, Fernandes WB, Sesti-Costa R, Carneiro ZA, Cheleski J, da Silva AB, Juliano L, Cezari MH, Silva JS, McKerrow JH, Montanari CA - PLoS Negl Trop Dis (2013)

Molecular structure and cruzain inhibition of compound Neq42 analogs selected for SAR investigation.Molecules drawing and figure generated with MarvinSketch software (www.chemaxon.com).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3750009&req=5

pntd-0002370-g006: Molecular structure and cruzain inhibition of compound Neq42 analogs selected for SAR investigation.Molecules drawing and figure generated with MarvinSketch software (www.chemaxon.com).
Mentions: The structure of Neq42 was resolved into two main scaffolds: the first containing the 2-acetamidothiophene-3-carboxamide moiety, and the other the triazole ring moiety substituted in positions 1 and 2 with the benzyl and piperidine, respectively, as can be seen in Figure 6. Based on the predicted mode of binding obtained by molecular docking, a series of structures was selected from commercial databases to investigate the SAR of this compound (Figure 6). When the 2-acetamidothiophene-3-carboxamidegroup was maintained, the piperidine and benzyl groups were removed to assess their contribution to the potency. On the other hand, when the triazole moiety was kept, three substances were selected by replacing the 2-acetamidothiophene-3-carboxamide group to a phenyl group (hydrophobic), a nitrile (which might covalently bind to the catalytic cysteine) and a cyclic sulfone (hydrophilic). The 2D structures and biological activity of the selected compounds are summarized in Figure 6.

Bottom Line: Affinity values were in a similar range (4-80 µM), yielding poor selectivity towards cruzain but raising the possibility of investigating such inhibitors for their effect on cell proliferation.Two compounds were found to have trypanocidal activity.The IC50 value for compound Nequimed42 acting against the trypomastigote form of the Tulahuen lacZ strain was found to be 10.6±0.1 µM, tenfold lower than that obtained for benznidazole, which was taken as positive control.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Química, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.

ABSTRACT
A multi-step cascade strategy using integrated ligand- and target-based virtual screening methods was developed to select a small number of compounds from the ZINC database to be evaluated for trypanocidal activity. Winnowing the database to 23 selected compounds, 12 non-covalent binding cruzain inhibitors with affinity values (K i) in the low micromolar range (3-60 µM) acting through a competitive inhibition mechanism were identified. This mechanism has been confirmed by determining the binding mode of the cruzain inhibitor Nequimed176 through X-ray crystallographic studies. Cruzain, a validated therapeutic target for new chemotherapy for Chagas disease, also shares high similarity with the mammalian homolog cathepsin L. Because increased activity of cathepsin L is related to invasive properties and has been linked to metastatic cancer cells, cruzain inhibitors from the same library were assayed against it. Affinity values were in a similar range (4-80 µM), yielding poor selectivity towards cruzain but raising the possibility of investigating such inhibitors for their effect on cell proliferation. In order to select the most promising enzyme inhibitors retaining trypanocidal activity for structure-activity relationship (SAR) studies, the most potent cruzain inhibitors were assayed against T. cruzi-infected cells. Two compounds were found to have trypanocidal activity. Using compound Nequimed42 as precursor, an SAR was established in which the 2-acetamidothiophene-3-carboxamide group was identified as essential for enzyme and parasite inhibition activities. The IC50 value for compound Nequimed42 acting against the trypomastigote form of the Tulahuen lacZ strain was found to be 10.6±0.1 µM, tenfold lower than that obtained for benznidazole, which was taken as positive control. In addition, by employing the strategy of molecular simplification, a smaller compound derived from Nequimed42 with a ligand efficiency (LE) of 0.33 kcal mol(-1) atom(-1) (compound Nequimed176) is highlighted as a novel non-peptidic, non-covalent cruzain inhibitor as a trypanocidal agent candidate for optimization.

Show MeSH
Related in: MedlinePlus