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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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Related in: MedlinePlus

(A) Dose-response and (B) Linewaver-Burk curves for Neq30 from Table S1.Non-linear fit method was employed in the analysis.
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pntd-0002370-g004: (A) Dose-response and (B) Linewaver-Burk curves for Neq30 from Table S1.Non-linear fit method was employed in the analysis.

Mentions: After visual inspection, 23 compounds were selected for in vitro assays against the enzyme cruzain. First, the activity of compounds was determined through measurement of IC50 values in the presence of Triton X-100 (0.01% v/v) in order to avoid artifactual aggregate-based inhibition. Afterwards, those compounds that showed activities had their mechanism of enzyme inhibition and affinity constants determined. Dose-response curves were used for measuring the IC50 values and Michaelis-Menten curves in the presence and absence of inhibitors in three different concentrations, which allowed the determination of the mechanism of inhibition and affinity constants. Since the identified active compounds showed similar curves, representative curves are shown in Figure 4A and 4B for Neq30 of Table S1 (see Supporting Information). A similar approach for the discovery of cruzain inhibitors is described elsewhere by Ferreira et al. (see reference [44]). Using the docking strategy the authors were able to find one inhibitor out of 17 screened compounds that displayed a Ki of 32 µM, via a competitive mechanism of cruzain inhibition. Our consensus ligand-based virtual screening (LBVS) and target-based virtual screening (TBVS) approaches also using the Lineweaver-Burk plots in a similar fashion confirmed the competitive mode of action of 12 out of 23 compounds whose average IC50 value is 40.3 µM (with 3 compounds in the range of 3.5 µM) – see Table S1.


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)

(A) Dose-response and (B) Linewaver-Burk curves for Neq30 from Table S1.Non-linear fit method was employed in the analysis.
© Copyright Policy
Related In: Results  -  Collection

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

pntd-0002370-g004: (A) Dose-response and (B) Linewaver-Burk curves for Neq30 from Table S1.Non-linear fit method was employed in the analysis.
Mentions: After visual inspection, 23 compounds were selected for in vitro assays against the enzyme cruzain. First, the activity of compounds was determined through measurement of IC50 values in the presence of Triton X-100 (0.01% v/v) in order to avoid artifactual aggregate-based inhibition. Afterwards, those compounds that showed activities had their mechanism of enzyme inhibition and affinity constants determined. Dose-response curves were used for measuring the IC50 values and Michaelis-Menten curves in the presence and absence of inhibitors in three different concentrations, which allowed the determination of the mechanism of inhibition and affinity constants. Since the identified active compounds showed similar curves, representative curves are shown in Figure 4A and 4B for Neq30 of Table S1 (see Supporting Information). A similar approach for the discovery of cruzain inhibitors is described elsewhere by Ferreira et al. (see reference [44]). Using the docking strategy the authors were able to find one inhibitor out of 17 screened compounds that displayed a Ki of 32 µM, via a competitive mechanism of cruzain inhibition. Our consensus ligand-based virtual screening (LBVS) and target-based virtual screening (TBVS) approaches also using the Lineweaver-Burk plots in a similar fashion confirmed the competitive mode of action of 12 out of 23 compounds whose average IC50 value is 40.3 µM (with 3 compounds in the range of 3.5 µM) – see Table S1.

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