- Open Access
In-silico screening of Schistosoma mansoni Sirtuin1 inhibitors for prioritization of drug candidates
© Singh et al. 2016
- Received: 26 November 2015
- Accepted: 17 February 2016
- Published: 7 March 2016
Schistosomiasis is a common, neglected parasitic disease caused by Schistosoma mansoni. Availability of two specific drug oxamniquine and praziquintel for treatment of the disease is a major concern. Recently NAD+ dependent lysine deacetylases have been identified as new drug targets in pathogens. Sirtuins are NAD+ dependent lysine deacetylases that are involved in a wide variety of vital cellular processes. Amongst them, members of sirtuin’s class1 proteins are considered to be main target of the drugs. Sirtinol and Salermide are two known inhibitors of Schistosoma mansoni Class1sirtuin which is a protein with unknown 3-D structure. Here, we investigate molecular insights of interaction between modeled sirtuin1 structure and it’s inhibitors, that were derivatives of Sirtinol and Salermide, to prioritize them for their binding affinities with target. A detailed examination of absorption, distribution, metabolism and toxicity of these inhibitors has also been included in the study. Finally we found two derivatives of Sirtinol to be most appropriate drug candidates for Schistosomiasis.
- Intestinal schistosomiasis
- Sirtuin 1
- Sirtinol 1
- Molecular docking
- ADMET profiling
Schistosomiasis, one of the most common parasitic diseases in developing countries, is caused by species of dioecious blood flukes belonging to the genus Schistosoma. After malaria, schistosomiasis is the most important tropical disease in terms of human morbidity. Under Schistosomiasis control initiative more than 40 million doses of Praziquantel have been dispensed in sub-Saharan Africa (Fenwick et al. 2009). Praziquantel is reported as the only drug used for mass treatment of schistosomiasis (Dömling and Khoury 2010) while Oxamniquine is a specific drug for Schistosomiasis mansoni (Cioli 1993; Fallon 1994). So, availability of the limited drug for the disease draws attention towards the search for new therapeutic targets as well as development of novel compounds to overcome the prospective threats from resistant strains of schistosomes (Doenhoff et al. 2008) that have been already reported and characterized in endemic areas (Melman et al. 2009).
Recently NAD+ dependent lysine deacetylases (Histone modifying enzymes) have been identified as new drug targets in several pathogen (J Pierce et al. 2012). Sirtuin1 protein in Schistosoma mansoni, a member of NAD+ dependent deacetylases family which is phylogenetically unrelated to the Zn2+-dependent deacetylase (Frye 2000), has been targeted in assays designed to study the therapeutic effect of inhibitors (Lancelot et al. 2013). Sirtuin proteins have been classified into five different classes (I, II, III, IV and U), on the basis of presence of conserved motifs in their core domain (Religa and Waters 2012). Parasitic class I sirtuins, characterized by the GAGXSXXXGIPDFRS, PS/TXXH, TQNID and HG motifs (Religa and Waters 2012) have been extensively and successfully explored as antiparasitic targets (Vergnes et al. 2002). It has been reported that these proteins have vital role in parasite survival by catalyzing the deacetylation reaction of acetylated lysine residues of nuclear histones and other substrates, with NAD+ as a cofactor (Vergnes et al. 2002). Salermide, which induces cell death in S. mansoni by targetting both Sirt1 and Sirt2 (Lara et al. 2009), is a potential anticancer agent due to it’s sirtuin inhibition property. The inhibition of sirtuins has been less explored for their therapeutic use against parasites. The molecular features of SmSirt2 as well as it use for the development of new targets for schistosomiasis were explored in a recent studies (Singh et al. 2015; Singh and Pandey 2015). In the present paper Sirt1 protein of S. mansoni has been used for the study. Due to unavailability of determined three dimensional structure of S. mansoni Sirt1 protein molecular insights of the inhibitor protein interaction or their participating residues are not known. Here we have modeled a 3-D structure of the protein by multi-template homology modeling. After that ten derivatives of salermide and sirtinol were screened against the modeled structure by docking. For sorting the inhibitors according to their druggability they were assessed on ADMET parameters.
Sequence retrieval and phylogenetic analysis
Comparison of DOPE score, quality factor determination through ERRAT and stereochemical property generated by Ramachandran plot of five models predicted through MODELLER
Residues in most favored regions
Residues in additional allowed region
Residues in generously allowed region
Residue in disallowed region
Overall quality score errat
Multi-template homology modeling of Sirt1 protein
PSI-BLAST (Altschul et al. 1997) algorithm was used against the Protein Data Bank (www.pdb.org) to search homologous sequences having 3D structure solved by experimental techniques. After PSI-BLAST search 50 protein structures were found then after three structures having PDB ID 2hjh, 4i5i and 4iao matching with different positions of query sequence were used as a template. Multi-template modeling was performed by MODELLER 9.10 (Šali and Blundell 1993). Homology modeling of was done by the steps: template selection from psi-blast, sequence multiple template alignment, multiple model building, evaluation of model, model refinement and model validation (Martí-Renom et al. 2000).
Protein structure optimization, quality assessment and visualization
MODELLER generated several preliminary models which were ranked based on their DOPE and GA scores. Models with low DOPE score were selected and stereo chemical property of each model was checked by PROCHECK. The model which having low DOPE score and least number of residues falling in disallowed region in Ramachandran plot was selected for further study. ProSA-Web server (Wiederstein and Sippl 2007) was used to check the quality of models, energy and stereochemical geometry.
Active sites prediction and ligand designing
Active site in the protein model were identified by using DoGSite sever (Volkamer et al. 2012). Scoring was based on a linear combination of the three descriptors volume, enclosure and hydrophobicity for all the pockets present in the protein.
Sirtinol and Salermide are two known lead compounds against the Sirtuin Protein. Four derivatives of salermide were generated by using Zinc database on the basis of similarity. The four derivatives of sirtinol were constructed by Chemsketch11.0.[ACD/Structure Elucidator, version 11.0, Advanced Chemistry Development, Inc., Toronto, ON, Canada, www.acdlabs.com, 2008].
Pre-docking steps were performed with the help of AutoDockTools 4.2 in which grid was generated near the active site residue Ala103 (GlyAlaGly domain) (Morris et al. 2009). Molecular docking was performed by Autodock 4.2. Flexible docking algorithm was used to check the interaction between ligand and protein. Average Grid points used in this docking were (60, 60, 60) and centre of ligand was approximately as coordinates: [−3.879 36.765 93.619]. Grid point spacing was 0.375Å. Lamarckian genetic algorithm (LGA) was used for docking.
In order to rank the putative drug candidates on the basis of Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties the structures of salermide, sirtniol and eight derivatives were done by using admetSAR (Cheng et al. 2012). First the structures of ligand PDB files were converted to SMILEs files by using Online SMILES Translator and Structure File Generator of National cancer Institute (http://www.cactus.nci.nih.gov) and these files were used as input for ADMET prediction.
The S. mansoni. Sirt1 protein is 568 amino acids long and was predicted to have a molecular weight of 63,262.3 Daltons with an isoelectric point (pI) of 4.71. Sirt 1 has a Negative GRAVY index of −0.513 which is indicative of a hydrophilic and soluble protein.
Homology modeling and structure validation
The selected template protein’s PDB IDs are 2hjh, 4i5i and 4iao. These template proteins showing 40, 46 and 46 % identity with target protein sequence, respectively. The multiple template modeling was done by using these three protein structures.
The overall protein quality and its structural deviation from the total energy were measured by Z-Score (Additional file 1: Figure S2). The black point in Additional file 1: Figure S2 represents the Z-score of the protein. Groups of structures determined from different source (NMR, X-ray) are distinguished by different color (NMR with dark blue and X-ray by light blue color). The plot of Z-Score represents value of the modeled protein of Schistosoma mansoni is (4.5) is located within the space of proteins related to NMR. The modeled protein’s Z-Score is within the acceptable range (−10 to 10, negative Z-score are good and depend on length of protein).
Modeled protein has large number of insertion in both the terminals (Fig. 1). Explicitly blast tool was used to find sequence similarity of inserted regions but it did not give any kind of similarity with existing annotated sequences.
Active site prediction
Pockets and descriptors calculation for Sirtuin1 model
Lipo surface [Å]2
Docking results of Human and pathogen Sirtinol1 proteins with 10 drug candidates
Binding affinity with host Sirt1 (kcal/mol)
Binding affinity with pathogen sirt1 (kcal/mol)
Druggability and toxicity of ten drug candidates were assessed on the basis of 23 ADMET parameters. The results of ADMET screening have been shown in Additional file 1: Table S1.
Sirtuin1 protein of S. mansoni sequence and its different homologues of species with their length and NCBI accession code
Pediculas humans coporsis
On the other hand the ADMET screening data suggest that sirtinol1 and salermide due to having AMES toxicity may not be considered as drug candidate. Salermide1 is a predicted carcinogen in the AMES tat and salermide4 is a P-glycoprotein inhibitor. Sirtinol3 has been predicted as a drug candidate which has neither blood–brain barrier crossing nor human intestine absorption capability. So, this may have prospects of being used as injection drugs that are directly mixed in blood. Further sirtinol2 is also a promising drug candidate for treatment of Schistosmiasis. Though sirtinol2 is not having blood brain carrier permeability but it is not a major issue as the location of the pathogen in host is intestine.
Aim of this study was to design and screen new drugs for treatment of Schistosomiasis which is a disease prevalent in tropical regions of the world. We have screened two drug candidates named as sirtinol2 and sirtinol3, both are derived for the structures of sirtinol, a reported inhibitor of Schistosoma mansoni. There is need to search the druggability of the screened drug candidates which may prove to be promising in the way of providing low cost and safe drugs to the needy population in the society. This study will trigger the drug development and prospective clinical trial process for schistosomiasis may prove to be a milestone to new drug discovery.
RS, BSY, SS and AM performed the experiments and manuscript writing. PNP helped in data analysis and manuscript writing. AM conceived the project. All authors read and approved the final manuscript.
BSY is thankful to DST INSPIRE for PhD fellowship. AM is thankful to MNNIT Allahabad for the computational facility.
The authors declare that they have no competing interests.
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- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410View ArticleGoogle Scholar
- Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402View ArticleGoogle Scholar
- Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y (2012) admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model 52(11):3099–3105View ArticleGoogle Scholar
- Cioli D, Pica-Mattoccia L, Archer S (1993) Drug resistance in schistosomes. Parasitol Today 9(5):162–166View ArticleGoogle Scholar
- Doenhoff MJ, Cioli D, Utzinger J (2008) Praziquantel: mechanisms of action, resistance and new derivatives for schistosomiasis. Curr Opin Infect Dis 21(6):659–667View ArticleGoogle Scholar
- Dömling A, Khoury K (2010) Praziquantel and schistosomiasis. ChemMedChem 5(9):1420–1434View ArticleGoogle Scholar
- Fallon PG, Doenhoff MJ (1994) Drug-resistant schistosomiasis: resistance to praziquantel and oxamniquine induced in Schistosoma mansoni in mice is drug specific. Am J Trop Med Hyg 51(1):83–88Google Scholar
- Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791View ArticleGoogle Scholar
- Fenwick A, Webster JP, Bosque-Oliva E, Blair L, Fleming F, Zhang Y, Garba A, Stothard J, Gabrielli AF, Clements A (2009) The Schistosomiasis control initiative (SCI): rationale, development and implementation from 2002–2008. Parasitology 136(13):1719–1730View ArticleGoogle Scholar
- Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273(2):793–798View ArticleGoogle Scholar
- Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series. 95–98Google Scholar
- Lancelot J, Caby S, Dubois-Abdesselem F, Vanderstraete M, Trolet J, Oliveira G, Bracher F, Jung M, Pierce RJ (2013) Schistosoma mansoni sirtuins: characterization and potential as chemotherapeutic targets. PLoS Negl Trop Dis 7:e2428View ArticleGoogle Scholar
- Lara E, Mai A, Calvanese V, Altucci L, Lopez-Nieva P, Martinez-Chantar M, Varela-Rey M, Rotili D, Nebbioso A, Ropero S (2009) Salermide, a sirtuin inhibitor with a strong cancer-specific proapoptotic effect. Oncogene 28(6):781–791View ArticleGoogle Scholar
- Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948View ArticleGoogle Scholar
- Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Šali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29(1):291–325View ArticleGoogle Scholar
- Melman SD, Steinauer ML, Cunningham C, Kubatko LS, Mwangi IN, Wynn NB, Mutuku MW, Karanja D, Colley DG, Black CL (2009) Reduced susceptibility to praziquantel among naturally occurring Kenyan isolates of Schistosoma mansoni. PLoS Negl Trop Dis 3(8):e504View ArticleGoogle Scholar
- Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791View ArticleGoogle Scholar
- Pierce JR, Dubois-Abdesselem F, Lancelot J, Andrade L, Oliveira G (2012) Targeting schistosome histone modifying enzymes for drug development. Curr Pharm Des 18(24):3567–3578Google Scholar
- Religa AA, Waters AP (2012) Sirtuins of parasitic protozoa: in search of function (s). Mol Biochem Parasitol 185(2):71–88View ArticleGoogle Scholar
- Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425Google Scholar
- Šali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815View ArticleGoogle Scholar
- Singh R, Pandey PN (2015) Molecular docking and molecular dynamics study on SmHDAC1 to identify potential lead compounds against Schistosomiasis. Mol Biol Rep 42(3):689–698View ArticleGoogle Scholar
- Singh R, Singh S, Pandey PN (2015) In-silico analysis of sirt2 from Schistosoma mansoni: structures, conformations, and interactions with inhibitors. J Biomol Struct Dyn. doi:10.1080/07391102.2015.1065205
- Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739View ArticleGoogle Scholar
- Vergnes B, Sereno D, Madjidian-Sereno N, Lemesre J-L, Ouaissi A (2002) Cytoplasmic SIR2 homologue overexpression promotes survival of Leishmania parasites by preventing programmed cell death. Gene 296(1):139–150View ArticleGoogle Scholar
- Volkamer A, Kuhn D, Rippmann F, Rarey M (2012) DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics 28(15):2074–2075View ArticleGoogle Scholar
- Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(suppl 2):W407–W410View ArticleGoogle Scholar