The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design

Abstract

The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.

Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response

“…Modulation of H3 modification itself may be transcriptionally regulated, as suggested by previous transcriptomics analyses that revealed changes in HDAC expression in L. am-infected BMDMs (Calegari-Silva et al, 2018;Osorio y Forté a et al, 2009). Likewise, the release of parasite histones (Silverman et al, 2010) may alter host H3 modification through competition with host HMEs, and host histones may be directly modified by parasite HMEs, such as SIRTUIN 2 (Ronin et al, 2018;Tavares et al, 2010;Yahiaoui et al, 1996) or various histone acetyltransferases (Chandra et al, 2017;Kumar et al, 2012;Kumar and Saha, 2015;Maity and Saha, 2012). Future studies investigating macrophage-Leishmania interactions at the systems level combining transcriptomic, epigenetic, and metabolomic analyses will shed new light on the mechanisms underlying host cell chromatin remodeling, with the potential to uncover new candidates for host-directed, anti-leishmanial therapy.…”

Identification of Inhibitors to Trypanosoma cruzi Sirtuins Based on Compounds Developed to Human Enzymes

“…Comparative models for TcSir2RP1 and TcSir2RP3 were obtained from the SWISS-MODEL web server [33]. The Leishmania infantum Sir2RP1 (PDB ID: 5OL0) [34] showing a sequence identity of 62% was selected as template for TcSir2RP1. Whereas for TcSir2RP3 the E. coli cobB (PDB ID: 1S5P) [35] was selected as a template showing a sequence identity of 60%.…”

Leishmania-Host Interactions—An Epigenetic Paradigm

“…Sirtuins of L. donovani have been validated as drug targets (81). Crystal structure of L. infantum Sir2 has been elucidated with implications for drug design (82). Sir2 has been suggested as a resistance marker for VL (21).…”