Computational studies on sirtuins from Trypanosoma cruzi: structures, conformations and interactions with phytochemicals

Abstract

Background: The silent-information regulator 2 proteins, otherwise called sirtuins, are currently considered as emerging anti-parasitic targets. Nicotinamide, a pan-sirtuin inhibitor, is known to cause kinetoplast alterations and the arrested growth of T. cruzi, the protozoan responsible for Chagas disease. These observations suggested that sirtuins from this parasite (TcSir2rp1 and TcSir2rp3) could play an important role in the regulation of the parasitic cell cycle. Thus, their inhibition could be exploited for the development of novel anti-trypanosomal compounds.

Methods: Homology modeling was used to determine the three-dimensional features of the sirtuin TcSir2rp1 from T. cruzi. The apo-form of human SIRT2 and the same structure solved in complex with its co-substrate NAD(+) allowed the modeling of TcSir2rp1 in the open and closed conformational states. Molecular docking studies were then carried out. A library composed of fifty natural and diverse compounds that are known to be active against this parasite, was established based on the literature and virtually screened against TcSir2rp1 and TcSir2rp3, which was previously modeled by our group.

Results: In this study, two conformational states of TcSir2rp1 were described for the first time. The molecular docking results of compounds capable of binding sirtuins proved to be meaningful when the closed conformation of the protein was taken into account for calculations. This specific conformation was then used for the virtual screening of antritrypanosomal phytochemicals against TcSir2rp1 and TcSir2rp3. The calculations identified a limited number of scaffolds extracted from Vismia orientalis, Cussonia zimmermannii, Amomum aculeatum and Anacardium occidentale that potentially interact with both proteins.

Conclusions: The study provided reliable models for future structure-based drug design projects concerning sirtuins from T. cruzi. Molecular docking studies highlighted not only the advantages of performing in silico interaction studies on their closed conformations but they also suggested the potential mechanism of action of four phytochemicals known for their anti-trypanosomal activity in vitro.

Figure 1. Hypothetical roles of NAD⁺ dependent deacetylases (sirtuin family) in the T. cruzi parasite.

Figure 2. Sequence alignment between TcSir2rp1 and hSIRT2.

Conserved amino acids are highlighted in yellow.

Figure 3. Molecular docking results in the productive pocket of TcSIR2rp1.

(A) Superimposition of A5dPR crystal (yellow-capped sticks) and best-ranked docking poses in hSIRT2 (green-capped sticks, cyan ribbons) and TcSIR2rp1 (white-capped sticks, dark pink ribbons). (B) NAD⁺ best-ranked docking pose in the TcSIR2rp1 productive form (purple-capped sticks, dark pink ribbons). (C) Nicotinamide best-ranked docking pose in the TcSIR2rp1 productive form (purple -capped sticks, dark pink ribbons). (D) AGK2 best-ranked docking pose in the TcSIR2rp1 productive form (purple-capped sticks, dark pink ribbons).

Figure 4. Superimposition of ten NAD⁺ docking poses in the TcSIR2rp1 productive (A) and non-productive (B) forms.

NAD⁺ molecules are represented in brown-capped sticks. Protein structures are represented as ribbons and colored in dark pink and green representing the TcSIR2rp1 productive and non-productive form, respectively. Pocket surfaces were generated with MOE (MOE 2012.10; Chemical Computing Group, Montreal, Canada) and are colored in gray.

Figure 5. Molecular docking results from the virtual screening of the productive conformational state of TcSIR2rp1.

(A) Anacardic acid best-ranked docking pose in the TcSIR2rp1 productive form. (B) Aculeatin D best-ranked docking pose in the TcSIR2rp1 productive form. (C) 16-acetoxy-11-hydroxyoctadeca-17-ene-12,14-diynylethanoate best-ranked docking pose in the TcSIR2rp1 productive form. (D) Vismione D best-ranked docking pose in the TcSIR2rp1 productive form. Protein structures are represented as dark pink ribbons. Amino acids participating in protein-ligand interactions are indicated bylight gray sticks. Ligands are represented in capped sticks and are colored in orange. GRID surface are also reported in the active site pockets and are colored as yellow, blue and red to highlight the hydrophobic, electron-donor and electron-acceptor properties, respectively.