Limits...
A computational approach to evaluate the androgenic affinity of iprodione, procymidone, vinclozolin and their metabolites.

Galli CL, Sensi C, Fumagalli A, Parravicini C, Marinovich M, Eberini I - PLoS ONE (2014)

Bottom Line: We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking.Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three).The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia.

ABSTRACT
Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking. Three different classes of molecules with well-known endocrine activity (iprodione, procymidone, vinclozolin, and a selection of their metabolites) were evaluated. Our approach was demonstrated useful as the first step of chemical safety evaluation since ligand-target interaction is a necessary condition for exerting any biological effect. Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three). This evidence suggests that, in order not to over-/under-estimate the risks connected with the use of a chemical entity, further in vitro and/or in vivo tests should be carried out only after an accurate evaluation of the most suitable cellular system or animal species. The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.

Show MeSH

Related in: MedlinePlus

Low-mode molecular dynamics simulations.Superposition of the starting conformation (helix 12) and the most energetically favoured open conformations for the agonist-bound LBD (A), the apo LBD (B), and the antagonist-bound LBD (C).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4128724&req=5

pone-0104822-g006: Low-mode molecular dynamics simulations.Superposition of the starting conformation (helix 12) and the most energetically favoured open conformations for the agonist-bound LBD (A), the apo LBD (B), and the antagonist-bound LBD (C).

Mentions: During the molecular dynamics simulations, helix 12 keeps a closed conformation when the human AR binds an agonist (DHT), whereas it opens when the LBD is empty or bound to an antagonist (cyproterone acetate). Starting from a common closed conformation of helix 12 in all the three setups, only the apo and the antagonist-bound structures rapidly evolve towards helix 12 opening. Figure 6 shows the three closed starting conformations (helix 12), superposed to the most energetically favoured open conformation for the apo (Figure 6, panel B) and the antagonist-bound LBD (Figure 6, panel C). On the contrary, helix 12 does not open (1,000 generated and analysed conformations) when LBD is bound to an AR agonist, such as DHT (Figure 6, panel A). In spite of the ability of molecular dynamics to correctly sample the reported helix 12 conformational transition, the differences between experimental and computational dissociation constant values for natural agonists cannot yet be compensated for. Indeed, as shown in Table 5, the binding affinities of the natural hormones for the three investigated LBDs, computed applying LigX to the lowest energy complex out of 400 obtained from the low-mode molecular dynamics simulations, are very close to the affinities obtained from our rapid docking procedure. The experimental issue is connected with the definition of Ki as the ratio koff/kon, where koff is the dissociation rate constant in min−1 and kon is the association rate constant in M−1 min−1. The closed conformation of helix 12 induced by the binding of an agonist produces a decrease in koff values, thus reducing the apparent dissociation constant. The discrepancy between experimental and computational Ki for the tested natural agonists is strictly connected with this phenomenon. The analysis of the interactions between helix 12 and DHT, carried out on a crystallographic complex (RCSB PDB code: 3L3X), shows only one weak and non-specific interaction between the ligand and the side chain of Met 895, in helix 12 (see Figure S3 in File S1), corroborating a kinetic more than a thermodynamic effect as the reason for the discrepancy between computed and experimental Kis.


A computational approach to evaluate the androgenic affinity of iprodione, procymidone, vinclozolin and their metabolites.

Galli CL, Sensi C, Fumagalli A, Parravicini C, Marinovich M, Eberini I - PLoS ONE (2014)

Low-mode molecular dynamics simulations.Superposition of the starting conformation (helix 12) and the most energetically favoured open conformations for the agonist-bound LBD (A), the apo LBD (B), and the antagonist-bound LBD (C).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4128724&req=5

pone-0104822-g006: Low-mode molecular dynamics simulations.Superposition of the starting conformation (helix 12) and the most energetically favoured open conformations for the agonist-bound LBD (A), the apo LBD (B), and the antagonist-bound LBD (C).
Mentions: During the molecular dynamics simulations, helix 12 keeps a closed conformation when the human AR binds an agonist (DHT), whereas it opens when the LBD is empty or bound to an antagonist (cyproterone acetate). Starting from a common closed conformation of helix 12 in all the three setups, only the apo and the antagonist-bound structures rapidly evolve towards helix 12 opening. Figure 6 shows the three closed starting conformations (helix 12), superposed to the most energetically favoured open conformation for the apo (Figure 6, panel B) and the antagonist-bound LBD (Figure 6, panel C). On the contrary, helix 12 does not open (1,000 generated and analysed conformations) when LBD is bound to an AR agonist, such as DHT (Figure 6, panel A). In spite of the ability of molecular dynamics to correctly sample the reported helix 12 conformational transition, the differences between experimental and computational dissociation constant values for natural agonists cannot yet be compensated for. Indeed, as shown in Table 5, the binding affinities of the natural hormones for the three investigated LBDs, computed applying LigX to the lowest energy complex out of 400 obtained from the low-mode molecular dynamics simulations, are very close to the affinities obtained from our rapid docking procedure. The experimental issue is connected with the definition of Ki as the ratio koff/kon, where koff is the dissociation rate constant in min−1 and kon is the association rate constant in M−1 min−1. The closed conformation of helix 12 induced by the binding of an agonist produces a decrease in koff values, thus reducing the apparent dissociation constant. The discrepancy between experimental and computational Ki for the tested natural agonists is strictly connected with this phenomenon. The analysis of the interactions between helix 12 and DHT, carried out on a crystallographic complex (RCSB PDB code: 3L3X), shows only one weak and non-specific interaction between the ligand and the side chain of Met 895, in helix 12 (see Figure S3 in File S1), corroborating a kinetic more than a thermodynamic effect as the reason for the discrepancy between computed and experimental Kis.

Bottom Line: We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking.Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three).The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano, Italia.

ABSTRACT
Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking. Three different classes of molecules with well-known endocrine activity (iprodione, procymidone, vinclozolin, and a selection of their metabolites) were evaluated. Our approach was demonstrated useful as the first step of chemical safety evaluation since ligand-target interaction is a necessary condition for exerting any biological effect. Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three). This evidence suggests that, in order not to over-/under-estimate the risks connected with the use of a chemical entity, further in vitro and/or in vivo tests should be carried out only after an accurate evaluation of the most suitable cellular system or animal species. The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.

Show MeSH
Related in: MedlinePlus