Target-Based Molecular Modeling Strategies for Schistosomiasis Drug Discovery

References

• World Health Organization . First WHO report on neglected tropical diseases: working to overcome the global impact of neglected tropical diseases. http://whqlibdoc.who.int.
   Google Scholar
• Fenwick A . The global burden of neglected tropical diseases. Public Health126 (3), 233–236 (2012).
   PubMed Web of Science ®Google Scholar
• Hotez PJ , DumonteilE, CraviotoMBet al. An unfolding tragedy of Chagas disease in North America. PLoS Negl. Trop. Dis.7 (10), e2300 (2013).
   PubMed Web of Science ®Google Scholar
• Nwaka S , HudsonA. Innovative lead discovery strategies for tropical diseases. Nat. Rev. Drug Discov.5 (11), 941–955 (2006).
   PubMed Web of Science ®Google Scholar
• Jakobsen PH , WangM, NwakaS. Innovative partnerships for drug discovery against neglected diseases. PLoS Negl. Trop. Dis.5 (9), e1221 (2011).
   PubMed Web of Science ®Google Scholar
• Linehan M , HansonC, WeaverAet al. Integrated implementation of programs targeting neglected tropical diseases through preventive chemotherapy: proving the feasibility at national scale. Am. J. Trop. Med. Hyg.84 (1), 5–14 (2011).
   PubMed Web of Science ®Google Scholar
• Bush S , HopkinsAD. Public–private partnerships in neglected tropical disease control: the role of nongovernmental organizations. Acta Trop.120 (Suppl. 1), S169–S172 (2011).
   PubMedGoogle Scholar
• Colley DG , BustinduyAL, SecorWE, KingCH. Human schistosomiasis. Lancet383 (9936), 2253–2264 (2014).
   PubMed Web of Science ®Google Scholar
• Gray DJ , RossAG, LiYS, McManusDP. Diagnosis and management of schistosomiasis. BMJ342, d2651 (2011).
   PubMed Web of Science ®Google Scholar
• World Health Organization . Sustaining the drive to overcome the global impact of neglected tropical diseases: second WHO report on neglected tropical diseases. www.who.int.
   Google Scholar
• Ezeamama AE , McGarveyST, HoganJet al. Treatment for Schistosoma japonicum reduction of intestinal parasite load, and cognitive test score improvements in school-aged children. PLoS Negl. Trop. Dis.6 (5), e1634 (2012).
   PubMed Web of Science ®Google Scholar
• Thétiot-Laurent SAL , BoissierJ, RobertA, MeunierB. Schistosomiasis chemotherapy. Angew. Chem. Int. Ed. Engl.52 (31), 7936–7956 (2013).
   PubMed Web of Science ®Google Scholar
• Taman A , AzabM. Present-day anthelmintics and perspectives on future new targets. Parasitol. Res.113 (7), 2425–2433 (2014).
   PubMed Web of Science ®Google Scholar
• Caffrey CR , SecorWE. Schistosomiasis: from drug deployment to drug development. Curr. Opin. Infect. Dis.24 (5), 410–417 (2011).
   PubMed Web of Science ®Google Scholar
• Pammolli F , MagazziniL, RiccaboniM. The productivity crisis in pharmaceutical R&D. Nat. Rev. Drug Discov.10 (6), 428–438 (2011).
   PubMed Web of Science ®Google Scholar
• Juliano RL . Pharmaceutical innovation and public policy: the case for a new strategy for drug discovery and development. Sci. Publ. Policy40 (3), 393–405 (2013).
   Web of Science ®Google Scholar
• Ferreira LG , AndricopuloAD. Medicinal chemistry approaches to neglected diseases drug discovery. J. Mod. Med. Chem.2 (1), 20–31 (2014).
   Google Scholar
• Taboureau O , BaellJB, Fernández-RecioJ, VilloutreixBO. Established and emerging trends in computational drug discovery in the structural genomics era. Chem. Biol.19 (1), 29–41 (2012).
   PubMed Web of Science ®Google Scholar
• Weigelt J . Structural genomics – impact on biomedicine and drug discovery. Exp. Cell Res.316 (8), 1332–1338 (2010).
   PubMed Web of Science ®Google Scholar
• Takeda JI , SuzukiY, SakateRet al. H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic Acids Res.38 (Suppl. 1), D86–D90 (2010).
   PubMedGoogle Scholar
• Kumar S , JenaL, DafS, MohodK, GoyalP, VarmaAK. hpvPDB: an online proteome reserve for human papillomavirus. Genomics Inform.11 (4), 289–291 (2013).
   PubMedGoogle Scholar
• Wishart DS , JewisonT, GuoACet al. HMDB 3.0 – the human metabolome database in 2013. Nucleic Acids Res.41, D801–D807 (2013).
   PubMed Web of Science ®Google Scholar
• Gaulton A , BellisLJ, BentoAPet al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res.40 (D1), D1100–D1107 (2012).
   PubMed Web of Science ®Google Scholar
• Benson DA , CavanaughM, ClarkKet al. GenBank. Nucleic Acids Res.41, D36–D42 (2013).
   PubMed Web of Science ®Google Scholar
• Wilson GL , LillMA. Integrating structure-based and ligand-based approaches for computational drug design. Future Med. Chem.3 (6), 735–750 (2011).
   PubMed Web of Science ®Google Scholar
• Blaney J . A very short history of structure-based design: how did we get here and where do we need to go?J. Comput. Aided Mol. Des.26 (1), 13–14 (2012).
   PubMed Web of Science ®Google Scholar
• Lionta E , SpyrouG, VassilatisDK, CourniaZ. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr. Top. Med. Chem.14 (16), 1923–1938 (2014).
   PubMed Web of Science ®Google Scholar
• Vidler LR , FilippakopoulosP, FedorovOet al. Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J. Med. Chem.56 (20), 8073–8088 (2013).
   PubMed Web of Science ®Google Scholar
• Valasani KR , VangavaraguJR, DayVW, YanSS. Structure based design, synthesis, pharmacophore modeling, virtual screening, and molecular docking studies for identification of novel cyclophilin D inhibitors. J. Chem. Inf. Model.54 (3), 902–912 (2014).
   PubMed Web of Science ®Google Scholar
• Berman HM , WestbrookJ, FengZet al. The protein data bank. Nucleic Acids Res.28 (1), 235–242 (2000).
   PubMed Web of Science ®Google Scholar
• Leach AR , GilletVJ, LewisRA, TaylorR. Three-dimensional pharmacophore methods in drug discovery. J. Med. Chem.53 (2), 539–558 (2010).
   PubMed Web of Science ®Google Scholar
• Mittal A , PaliwalS, SharmaM, SinghA, SharmaS, YadavD. Pharmacophore based virtual screening, molecular docking and biological evaluation to identify novel PDE5 inhibitors with vasodilatory activity. Bioorg. Med. Chem. Lett.24 (14), 3137–3141 (2014).
   PubMed Web of Science ®Google Scholar
• Verma J , KhedkarVM, CoutinhoEC. 3D-QSAR in drug design – a review. Curr. Top. Med. Chem.10 (1), 95–115 (2010).
   PubMed Web of Science ®Google Scholar
• Mavromoustakos T , DurdagiS, KoukoulitsaCet al. Strategies in the rational drug design. Curr. Med. Chem.18 (17), 2517–2530 (2011).
   PubMed Web of Science ®Google Scholar
• Irwin JJ , SterlingT, MysingerMM, BolstadES, ColemanRG. ZINC: a free tool to discover chemistry for biology. J. Chem. Inf. Model.52 (7), 1757–1768 (2012).
   PubMed Web of Science ®Google Scholar
• Wang Y , XiaoJ, SuzekTO, ZhangJ, WangJ, BryantSH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res.37 (Suppl. 2), W623–W633 (2009).
   PubMed Web of Science ®Google Scholar
• Caffrey CR . Chemotherapy of schistosomiasis: present and future. Curr. Opin. Chem. Biol.11 (4), 433–439 (2007).
   PubMed Web of Science ®Google Scholar
• Gilbert IH . Drug discovery for neglected diseases: molecular target-based and phenotypic approaches: miniperspectives series on phenotypic screening for antiinfective targets. J. Med. Chem.56 (20), 7719–7726 (2013).
   PubMed Web of Science ®Google Scholar
• Berriman M , HaasBJ, LoVerdePTet al. The genome of the blood fluke Schistosoma mansoni. Nature460 (7253), 352–358 (2009).
   PubMed Web of Science ®Google Scholar
• Zhou Y , ZhengH, ChenYet al. The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature460 (7253), 345–351 (2009).
   PubMed Web of Science ®Google Scholar
• Young ND , JexAR, LiBet al. Whole-genome sequence of Schistosoma haematobium. Nat. Genet.44 (2), 221–225 (2012).
   PubMed Web of Science ®Google Scholar
• Caffrey CR , RohwerA, OellienFet al. A comparative chemogenomics strategy to predict potential drug targets in the metazoan pathogen, Schistosoma mansoni. PLoS ONE4 (2), e4413 (2009).
   PubMed Web of Science ®Google Scholar
• Zerlotini A , HeigesM, WangHet al. SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res.37 (Suppl. 1), D579–D582 (2009).
   PubMedGoogle Scholar
• Logan-Klumpler FJ , De SilvaN, BoehmeUet al. GeneDB – an annotation database for pathogens. Nucleic Acids Res.40 (D1), D98–D108 (2012).
   PubMed Web of Science ®Google Scholar
• De Sousa TN , De Menezes NetoA, De BritoCFA. “Omics” in the study of the major parasitic diseases malaria and schistosomiasis. Infect. Genet. Evol.19, 258–273 (2013).
   PubMed Web of Science ®Google Scholar
• Rana AK , Misra-BhattacharyaS. Current drug targets for helminthic diseases. Parasitol. Res.112 (5), 1819–1831 (2013).
   PubMed Web of Science ®Google Scholar
• Njoroge M , NjugunaNM, MutaiP, OngaroraDS, SmithPW, ChibaleK. Recent approaches to chemical discovery and development against malaria and the neglected tropical diseases human African trypanosomiasis and schistosomiasis. Chem. Rev.114 (22), 11138–11163 (2014).
   PubMed Web of Science ®Google Scholar
• Schiedel M , MarekM, LancelotJet al. Fluorescence-based screening assays for the NAD+-dependent histone deacetylase smSirt2 from Schistosoma mansoni. J. Biomol. Screen.20 (1), 112–121 (2015).
   PubMedGoogle Scholar
• Pitkänen E , RousuJ, UkkonenE. Computational methods for metabolic reconstruction. Curr. Opin. Biotechnol.21 (1), 70–77 (2010).
   PubMed Web of Science ®Google Scholar
• Shinde S , MolM, SinghS. Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: a systems biology view for pharmacological intervention. Gene550 (2), 214–222 (2014).
   PubMed Web of Science ®Google Scholar
• Rojo-Arreola L , LongT, AsarnowD, SuzukiBM, SinghR, CaffreyCR. Chemical and genetic validation of the statin drug target to treat the helminth disease, schistosomiasis. PLoS ONE9 (1), e87594 (2014).
   PubMed Web of Science ®Google Scholar
• Buro C , BeckmannS, OliveiraKCet al. Imatinib treatment causes substantial transcriptional changes in adult Schistosoma mansoni in vitro exhibiting pleiotropic effects PLoS Negl. Trop. Dis. 8 (6), e2923 (2014).
   PubMed Web of Science ®Google Scholar
• Greuber EK , Smith-PearsonP, WangJ, PendergastAM. Role of ABL family kinases in cancer: from leukaemia to solid tumours. Nat. Rev. Cancer13 (8), 559–571 (2013).
   PubMed Web of Science ®Google Scholar
• Hantschel O , GrebienF, Superti-FurgaG. The growing arsenal of ATP-competitive and allosteric inhibitors of BCR-ABL. Cancer Res.72 (19), 4890–4895 (2012).
   PubMed Web of Science ®Google Scholar
• Beckmann S , QuackT, BurmeisterCet al. Schistosoma mansoni: signal transduction processes during the development of the reproductive organs. Parasitology137 (3), 497–520 (2010).
   PubMed Web of Science ®Google Scholar
• Beckmann S , HahnelS, CailliauKet al. Characterization of the Src/Abl hybrid kinase SmTK6 of Schistosoma mansoni. J. Biol. Chem.286 (49), 42325–42336 (2011).
   PubMed Web of Science ®Google Scholar
• Nagar B , BornmannWG, PellicenaPet al. Crystal structures of the kinase domain of c-Abl in complex with the small molecule inhibitors PD173955 and imatinib (STI-571). Cancer Res.62 (15), 4236–43 (2002).
   PubMed Web of Science ®Google Scholar
• Pereira HM , CleasbyA, PenaSED, FrancoGOR, GarrattRC. Cloning, expression and preliminary crystallographic studies of the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni. Acta Crystallogr. D Biol. Crystallogr.59 (6), 1096–1099 (2003).
   PubMedGoogle Scholar
• Postigo MP , KroghR, TerniMFet al. Enzyme kinetics, structural analysis and molecular modeling studies on a series of Schistosoma mansoni PNP inhibitors. J. Braz. Chem. Soc.22 (3), 583–591 (2011).
   Web of Science ®Google Scholar
• Castilho MS , PostigoMP, PereiraHM, OlivaG, AndricopuloAD. Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: Kinetic and structural studies. Bioorg. Med. Chem.18 (4), 1421–1427 (2010).
   PubMed Web of Science ®Google Scholar
• Postigo MP , GuidoRV, OlivaGet al. Discovery of new inhibitors of Schistosoma mansoni PNP by pharmacophore-based virtual screening. J. Chem. Inf. Model.50 (9), 1693–1705 (2010).
   PubMed Web of Science ®Google Scholar
• Payne DJ , WarrenPV, HolmesDJ, JiY, LonsdaleJT. Bacterial fatty-acid biosynthesis: a genomics-driven target for antibacterial drug discovery. Drug Discov. Today6 (10), 537–544 (2001).
   PubMed Web of Science ®Google Scholar
• Liu J , DyerD, WangJet al. 3-oxoacyl-ACP reductase from Schistosoma japonicum: integrated in silico-in vitro strategy for discovering antischistosomal lead compounds. PloS ONE8 (6), e64984 (2013).
   PubMed Web of Science ®Google Scholar
• Brouwers JF , VersluisC, van GoldeLM, TielensAG. 5-Octadecenoic acid: evidence for a novel type of fatty acid modification in schistosomes. Biochem. J.334 (Pt 2), 315–319 (1998).
   PubMedGoogle Scholar
• Bannister AJ , KouzaridesT. Regulation of chromatin by histone modifications. Cell Res.21 (3), 381–395 (2011).
   PubMed Web of Science ®Google Scholar
• Dawson MA , KouzaridesT. Cancer epigenetics: from mechanism to therapy. Cell150 (1), 12–27 (2012).
   PubMed Web of Science ®Google Scholar
• Marek M , KannanS, HauserATet al. Structural basis for the inhibition of histone deacetylase 8 (HDAC8), a key epigenetic player in the blood fluke Schistosoma mansoni. PLoS Pathog.9 (9), e1003645 (2013).
   PubMed Web of Science ®Google Scholar
• Kannan S , MelesinaJ, HauserATet al. Discovery of inhibitors of Schistosoma mansoni HDAC8 by combining homology modeling, virtual screening, and in vitro validation. J. Chem. Inf. Model.54 (10), 3005–3019 (2014).
   PubMed Web of Science ®Google Scholar
• Singh J , PetterRC, BaillieTA, WhittyA. The resurgence of covalent drugs. Nat. Rev. Drug Discov.10 (4), 307–317 (2011).
   PubMed Web of Science ®Google Scholar
• Ouyang X , ZhouS, SuCTT, GeZ, LiR, KwohCK. CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints. J. Comput. Chem.34 (4), 326–336 (2013).
   PubMed Web of Science ®Google Scholar
• Xu M , LillMA. Induced fit docking, and the use of QM/MM methods in docking. Drug Discov. Today Technol.10 (3), e411–e418 (2013).
   PubMedGoogle Scholar
• Menikarachchi LC , GascónJA. QM/MM approaches in medicinal chemistry research. Curr. Top. Med. Chem.10 (1), 46–54 (2010).
   PubMed Web of Science ®Google Scholar
• Fanfrlik J , BrahmkshatriyaPS, RězáčJet al. Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors. J. Phys. Chem. B.117 (48), 14973–14982 (2013).
   PubMed Web of Science ®Google Scholar