Limits...
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.

Show MeSH

Related in: MedlinePlus

(A) Structure of the co-crystallized cruzain inhibitor K11777 and (B–D) examples of complex structures predicted by our molecular docking (Glide XP).Figure prepared using CCP4mg software [43].
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3750009&req=5

pntd-0002370-g003: (A) Structure of the co-crystallized cruzain inhibitor K11777 and (B–D) examples of complex structures predicted by our molecular docking (Glide XP).Figure prepared using CCP4mg software [43].

Mentions: The criteria used for selection of compounds based on visual inspection were: (i) the occupation of the site, mainly in subsites S1, S2 and S3, (ii) hydrogen bonding, emphasizing the Gly66 H-bonding interaction set up as constraint in molecular docking and (iii) chemical structure diversity, where we prioritized compounds with similar shape to known inhibitors. Figure 3A shows the binding mode of K11777 inhibitor to the enzyme cruzain in the crystal structure conformation, which was also used as reference in the 3D similarity search; Figure 3B to Figure 3D are the docking poses predicted by Glide XP for three compounds selected for in vitro assays. As can be seen, the occupation of the active site by these compounds is similar to that of the co-crystalized inhibitor, appropriately filling the focused pockets and fulfilling the requirements imposed through H-bonding constraint. [43]


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) Structure of the co-crystallized cruzain inhibitor K11777 and (B–D) examples of complex structures predicted by our molecular docking (Glide XP).Figure prepared using CCP4mg software [43].
© Copyright Policy
Related In: Results  -  Collection

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

pntd-0002370-g003: (A) Structure of the co-crystallized cruzain inhibitor K11777 and (B–D) examples of complex structures predicted by our molecular docking (Glide XP).Figure prepared using CCP4mg software [43].
Mentions: The criteria used for selection of compounds based on visual inspection were: (i) the occupation of the site, mainly in subsites S1, S2 and S3, (ii) hydrogen bonding, emphasizing the Gly66 H-bonding interaction set up as constraint in molecular docking and (iii) chemical structure diversity, where we prioritized compounds with similar shape to known inhibitors. Figure 3A shows the binding mode of K11777 inhibitor to the enzyme cruzain in the crystal structure conformation, which was also used as reference in the 3D similarity search; Figure 3B to Figure 3D are the docking poses predicted by Glide XP for three compounds selected for in vitro assays. As can be seen, the occupation of the active site by these compounds is similar to that of the co-crystalized inhibitor, appropriately filling the focused pockets and fulfilling the requirements imposed through H-bonding constraint. [43]

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