1
|
OUP accepted manuscript. Brief Funct Genomics 2022; 21:243-269. [DOI: 10.1093/bfgp/elac007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
|
2
|
Proteomic Analysis of Leishmania donovani Membrane Components Reveals the Role of Activated Protein C Kinase in Host-Parasite Interaction. Pathogens 2021; 10:pathogens10091194. [PMID: 34578226 PMCID: PMC8465321 DOI: 10.3390/pathogens10091194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/05/2022] Open
Abstract
Visceral leishmaniasis (VL), mainly caused by the Leishmania donovani parasitic infection, constitutes a potentially fatal disease, for which treatment is primarily dependent on chemotherapy. The emergence of a resistant parasite towards current antileishmanial agents and increasing reports of relapses are the major concerns. Detailed research on the molecular interaction at the host-parasite interface may provide the identification of the parasite and the host-related factors operating during disease development. Genomic and proteomic studies highlighted several essential secretory and cytosolic proteins that play vital roles during Leishmania pathogenesis. The aim of this study was to identify membrane proteins from the Leishmania donovani parasite and the host macrophage that interact with each other using 2-DE/MALDI-TOF/MS. We identified membrane proteins including activated protein C kinase, peroxidoxin, small myristoylated protein 1 (SMP-1), and cytochrome C oxidase from the parasite, while identifying filamin A interacting protein 1(FILIP1) and β-actin from macrophages. We further investigated parasite replication and persistence within macrophages following the macrophage-amastigote model in the presence or absence of withaferin (WA), an inhibitor of activated C kinase. WA significantly reduced Leishmania donovani replication within host macrophages. This study sheds light on the important interacting proteins for parasite proliferation and virulence, and the establishment of infection within host cells, which can be targeted further to develop a strategy for chemotherapeutic intervention.
Collapse
|
3
|
Atkinson LE, McCoy CJ, Crooks BA, McKay FM, McVeigh P, McKenzie D, Irvine A, Harrington J, Rosa BA, Mitreva M, Marks NJ, Maule AG, Mousley A. Phylum-Spanning Neuropeptide GPCR Identification and Prioritization: Shaping Drug Target Discovery Pipelines for Nematode Parasite Control. Front Endocrinol (Lausanne) 2021; 12:718363. [PMID: 34659113 PMCID: PMC8515059 DOI: 10.3389/fendo.2021.718363] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
Nematode parasites undermine human health and global food security. The frontline anthelmintic portfolio used to treat parasitic nematodes is threatened by the escalation of anthelmintic resistance, resulting in a demand for new drug targets for parasite control. Nematode neuropeptide signalling pathways represent an attractive source of novel drug targets which currently remain unexploited. The complexity of the nematode neuropeptidergic system challenges the discovery of new targets for parasite control, however recent advances in parasite 'omics' offers an opportunity for the in silico identification and prioritization of targets to seed anthelmintic discovery pipelines. In this study we employed Hidden Markov Model-based searches to identify ~1059 Caenorhabditis elegans neuropeptide G-protein coupled receptor (Ce-NP-GPCR) encoding gene homologs in the predicted protein datasets of 10 key parasitic nematodes that span several phylogenetic clades and lifestyles. We show that, whilst parasitic nematodes possess a reduced complement of Ce-NP-GPCRs, several receptors are broadly conserved across nematode species. To prioritize the most appealing parasitic nematode NP-GPCR anthelmintic targets, we developed a novel in silico nematode parasite drug target prioritization pipeline that incorporates pan-phylum NP-GPCR conservation, C. elegans-derived reverse genetics phenotype, and parasite life-stage specific expression datasets. Several NP-GPCRs emerge as the most attractive anthelmintic targets for broad spectrum nematode parasite control. Our analyses have also identified the most appropriate targets for species- and life stage- directed chemotherapies; in this context we have identified several NP-GPCRs with macrofilaricidal potential. These data focus functional validation efforts towards the most appealing NP-GPCR targets and, in addition, the prioritization strategy employed here provides a blueprint for parasitic nematode target selection beyond NP-GPCRs.
Collapse
Affiliation(s)
- Louise E. Atkinson
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Ciaran J. McCoy
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Bethany A. Crooks
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Fiona M. McKay
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paul McVeigh
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Darrin McKenzie
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Allister Irvine
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - John Harrington
- Boehringer Ingelheim Animal Health, Athens, GA, United States
| | - Bruce A. Rosa
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Nikki J. Marks
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Aaron G. Maule
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Angela Mousley
- Microbes and Pathogen Biology, The Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- *Correspondence: Angela Mousley,
| |
Collapse
|
4
|
Cuesta-Astroz Y, Santos A, Oliveira G, Jensen LJ. Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. Front Immunol 2019; 10:212. [PMID: 30815000 PMCID: PMC6381214 DOI: 10.3389/fimmu.2019.00212] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/24/2019] [Indexed: 01/03/2023] Open
Abstract
The study of molecular host–parasite interactions is essential to understand parasitic infection and adaptation within the host system. As well, prevention and treatment of infectious diseases require a clear understanding of the molecular crosstalk between parasites and their hosts. Yet, large-scale experimental identification of host–parasite molecular interactions remains challenging, and the use of computational predictions becomes then necessary. Here, we propose a computational integrative approach to predict host—parasite protein—protein interaction (PPI) networks resulting from the human infection by 15 different eukaryotic parasites. We used an orthology-based approach to transfer high-confidence intraspecies interactions obtained from the STRING database to the corresponding interspecies homolog protein pairs in the host–parasite system. Our approach uses either the parasites predicted secretome and membrane proteins, or only the secretome, depending on whether they are uni- or multi-cellular, respectively, to reduce the number of false predictions. Moreover, the host proteome is filtered for proteins expressed in selected cellular localizations and tissues supporting the parasite growth. We evaluated the inferred interactions by analyzing the enriched biological processes and pathways in the predicted networks and their association with known parasitic invasion and evasion mechanisms. The resulting PPI networks were compared across parasites to identify common mechanisms that may define a global pathogenic hallmark. We also provided a study case focusing on a closer examination of the human–S. mansoni predicted interactome, detecting central proteins that have relevant roles in the human–S. mansoni network, and identifying tissue-specific interactions with key roles in the life cycle of the parasite. The predicted PPI networks can be visualized and downloaded at http://orthohpi.jensenlab.org.
Collapse
Affiliation(s)
- Yesid Cuesta-Astroz
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ, Belo Horizonte, Brazil
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Dos Santos Vasconcelos CR, de Lima Campos T, Rezende AM. Building protein-protein interaction networks for Leishmania species through protein structural information. BMC Bioinformatics 2018; 19:85. [PMID: 29510668 PMCID: PMC5840830 DOI: 10.1186/s12859-018-2105-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Background Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum. These parasites cause Leishmaniasis, a worldwide distributed and neglected disease, with limited treatment options using currently available drugs. Results The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. Our final model obtained an AUC = 0.88, with recall = 0.69, specificity = 0.88 and precision = 0.83. Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis, and 708 protein structures and 7391 protein interactions for L. infantum. The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. Conclusions The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. Electronic supplementary material The online version of this article (10.1186/s12859-018-2105-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Crhisllane Rafaele Dos Santos Vasconcelos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
| | - Túlio de Lima Campos
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil.,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil
| | - Antonio Mauro Rezende
- Microbiology Department of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Bioinformatics Plataform of Instituto Aggeu Magalhães - FIOCRUZ, Recife, PE, Brazil. .,Genetics Department of Universidade Federal de Pernambuco, Recife, PE, Brazil.
| |
Collapse
|
6
|
Sotillo J, Toledo R, Mulvenna J, Loukas A. Exploiting Helminth-Host Interactomes through Big Data. Trends Parasitol 2017; 33:875-888. [PMID: 28734897 DOI: 10.1016/j.pt.2017.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022]
Abstract
Helminths facilitate their parasitic existence through the production and secretion of different molecules, including proteins. Some helminth proteins can manipulate the host's immune system, a phenomenon that is now being exploited with a view to developing therapeutics for inflammatory diseases. In recent years, hundreds of helminth genomes have been sequenced, but as a community we are still taking baby steps when it comes to identifying proteins that govern host-helminth interactions. The information generated from genomic, immunomic, and proteomic studies, as well as from cutting-edge approaches such as proteogenomics, is leading to a substantial volume of big data that can be utilised to shed light on fundamental biology and provide solutions for the development of bioactive-molecule-based therapeutics.
Collapse
Affiliation(s)
- Javier Sotillo
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.
| | - Rafael Toledo
- Departament de Farmacia, Tecnologia Farmacéutica y Parasitologia, Facultat de Farmacia, Universitat de Valencia, Spain
| | - Jason Mulvenna
- QIMR-Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alex Loukas
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.
| |
Collapse
|
7
|
Mondal SI, Mahmud Z, Elahi M, Akter A, Jewel NA, Muzahidul Islam M, Ferdous S, Kikuchi T. Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. In Silico Pharmacol 2017; 5:1. [PMID: 28401513 DOI: 10.1007/s40203-017-0021-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 03/20/2017] [Indexed: 11/29/2022] Open
Abstract
Protein-protein interaction (PPI) and host-pathogen interactions (HPI) proteomic analysis has been successfully practiced for potential drug target identification in pathogenic infections. In this research, we attempted to identify new drug target based on PPI and HPI computation approaches and subsequently design new drug against devastating enterohemorrhagic Escherichia coli O104:H4 C277-11 (Broad), which causes life-threatening food borne disease outbreak in Germany and other countries in Europe in 2011. Our systematic in silico analysis on PPI and HPI of E. coli O104:H4 was able to identify bacterial D-galactose-binding periplasmic and UDP-N-acetylglucosamine 1-carboxyvinyltransferase as attractive candidates for new drug targets. Furthermore, computational three-dimensional structure modeling and subsequent molecular docking finally proposed [3-(5-Amino-7-Hydroxy-[1,2,3]Triazolo[4,5-D]Pyrimidin-2-Yl)-N-(3,5-Dichlorobenzyl)-Benzamide)] and (6-amino-2-[(1-naphthylmethyl)amino]-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one) as promising candidate drugs for further evaluation and development for E. coli O104:H4 mediated diseases. Identification of new drug target would be of great utility for humanity as the demand for designing new drugs to fight infections is increasing due to the developing resistance and side effects of current treatments. This research provided the basis for computer aided drug design which might be useful for new drug target identification and subsequent drug design for other infectious organisms.
Collapse
Affiliation(s)
- Shakhinur Islam Mondal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh. .,Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Zabed Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Montasir Elahi
- Department of Diagnosis, Prevention and Treatment of Dementia, Juntendo University Graduate School of Medicine, Bunkyō, Tokyo, Japan
| | - Arzuba Akter
- Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.,Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Nurnabi Azad Jewel
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Sabiha Ferdous
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| |
Collapse
|
8
|
Rosa BA, McNulty SN, Mitreva M, Jasmer DP. Direct experimental manipulation of intestinal cells in Ascaris suum, with minor influences on the global transcriptome. Int J Parasitol 2017; 47:271-279. [PMID: 28223178 DOI: 10.1016/j.ijpara.2016.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/24/2022]
Abstract
Ascaris suum provides a powerful model for studying parasitic nematodes, including individual tissues such as the intestine, an established target for anthelmintic treatments. Here, we add a valuable experimental component to our existing functional, proteomic, transcriptomic and phylogenomic studies of the Ascaris suum intestine, by developing a method to manipulate intestinal cell functions via direct delivery of experimental treatments (in this case, double-stranded (ds)RNA) to the apical intestinal membrane. We developed an intestinal perfusion method for direct, controlled delivery of dsRNA/heterogeneous small interfering (hsi) RNA into the intestinal lumen for experimentation. RNA-Seq (22 samples) was used to assess influences of the method on global intestinal gene expression. Successful mRNA-specific knockdown in intestinal cells of adult A. suum was accomplished with this new experimental method. Global transcriptional profiling confirmed that targeted transcripts were knocked down more significantly than any others, with only 12 (0.07% of all genes) or 238 (1.3%) off-target gene transcripts consistently differentially regulated by dsRNA treatment or the perfusion experimental design, respectively (after 24h). The system supports controlled, effective delivery of treatments (dsRNA/hsiRNA) to the apical intestinal membrane with relatively minor off-target effects, and builds on our experimental model to dissect A. suum intestinal cell functions with broad relevance to parasitic nematodes.
Collapse
Affiliation(s)
- Bruce A Rosa
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Samantha N McNulty
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Makedonka Mitreva
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Douglas P Jasmer
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA.
| |
Collapse
|
9
|
Wei ZS, Yang JY, Shen HB, Yu DJ. A Cascade Random Forests Algorithm for Predicting Protein-Protein Interaction Sites. IEEE Trans Nanobioscience 2015; 14:746-60. [DOI: 10.1109/tnb.2015.2475359] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
10
|
Genome mining offers a new starting point for parasitology research. Parasitol Res 2015; 114:399-409. [PMID: 25563615 DOI: 10.1007/s00436-014-4299-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
Abstract
Parasites including helminthes, protozoa, and medical arthropod vectors are a major cause of global infectious diseases, affecting one-sixth of the world's population, which are responsible for enormous levels of morbidity and mortality important and remain impediments to economic development especially in tropical countries. Prevalent drug resistance, lack of highly effective and practical vaccines, as well as specific and sensitive diagnostic markers are proving to be challenging problems in parasitic disease control in most parts of the world. The impressive progress recently made in genome-wide analysis of parasites of medical importance, including trematodes of Clonorchis sinensis, Opisthorchis viverrini, Schistosoma haematobium, S. japonicum, and S. mansoni; nematodes of Brugia malayi, Loa loa, Necator americanus, Trichinella spiralis, and Trichuris suis; cestodes of Echinococcus granulosus, E. multilocularis, and Taenia solium; protozoa of Babesia bovis, B. microti, Cryptosporidium hominis, Eimeria falciformis, E. histolytica, Giardia intestinalis, Leishmania braziliensis, L. donovani, L. major, Plasmodium falciparum, P. vivax, Trichomonas vaginalis, Trypanosoma brucei and T. cruzi; and medical arthropod vectors of Aedes aegypti, Anopheles darlingi, A. sinensis, and Culex quinquefasciatus, have been systematically covered in this review for a comprehensive understanding of the genetic information contained in nuclear, mitochondrial, kinetoplast, plastid, or endosymbiotic bacterial genomes of parasites, further valuable insight into parasite-host interactions and development of promising novel drug and vaccine candidates and preferable diagnostic tools, thereby underpinning the prevention and control of parasitic diseases.
Collapse
|
11
|
Protein arrays as tool for studies at the host-pathogen interface. J Proteomics 2013; 94:387-400. [PMID: 24140974 DOI: 10.1016/j.jprot.2013.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 01/10/2023]
Abstract
Pathogens and parasites encode a wide spectrum of multifunctional proteins interacting to and modifying proteins in host cells. However, the current lack of a reliable method to unveil the protein-protein interactions (PPI) at the host-pathogen interface is retarding our understanding of many important pathogenic processes. Thus, the identification of proteins involved in host-pathogen interactions is important for the elucidation of virulence determinants, mechanisms of infection, host susceptibility and/or disease resistance. In this sense, proteomic technologies have experienced major improvements in recent years and protein arrays are a powerful and modern method for studying PPI in a high-throughput format. This review focuses on these techniques analyzing the state-of-the-art of proteomic technologies and their possibilities to diagnose and explore host-pathogen interactions. Major technical advancements, applications and protocol concerns are presented, so readers can appreciate the immense progress achieved and the current technical options available for studying the host-pathogen interface. Finally, future uses of this kind of array-based proteomic tools in the fight against infectious and parasitic diseases are discussed.
Collapse
|
12
|
Zoraghi R, Reiner NE. Protein interaction networks as starting points to identify novel antimicrobial drug targets. Curr Opin Microbiol 2013; 16:566-72. [PMID: 23938265 DOI: 10.1016/j.mib.2013.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 01/17/2023]
Abstract
Novel classes of antimicrobials are needed to address the challenge of multidrug-resistant bacteria. Current bacterial drug targets mainly consist of specific proteins or subsets of proteins without regard for either how these targets are integrated in cellular networks or how they may interact with host proteins. However, proteins rarely act in isolation, and the majority of biological processes are dependent on interactions with other proteins. Consequently, protein-protein interaction (PPI) networks offer a realm of unexplored potential for next-generation drug targets. In this review, we argue that the architecture of bacterial or host-pathogen protein interactomes can provide invaluable insights for the identification of novel antibacterial drug targets.
Collapse
Affiliation(s)
- Roya Zoraghi
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
13
|
Current drug targets for helminthic diseases. Parasitol Res 2013; 112:1819-31. [PMID: 23529336 DOI: 10.1007/s00436-013-3383-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/05/2013] [Indexed: 01/08/2023]
Abstract
More than 2 billion people are infected with helminth parasites across the globe. The burgeoning drug resistance against current anthelmintics in parasitic worms of humans and livestock requires urgent attention to tackle these recalcitrant worms. This review focuses on the advancements made in the area of helminth drug target discovery especially from the last few couple of decades. It highlights various approaches made in this field and enlists the potential drug targets currently being pursued to target economically important helminth species both from human as well as livestock to combat disease pathology of schistosomiasis, onchocerciasis, lymphatic filariasis, and other important macroparasitic diseases. Research in the helminths study is trending to identify potential and druggable targets through genomic, proteomic, biochemical, biophysical, in vitro experiments, and in vivo experiments in animal models. The availability of major helminths genome sequences and the subsequent availability of genome-scale functional datasets through in silico search and prioritization are expected to guide the experimental work necessary for target-based drug discovery. Organized and documented list of drug targets from various helminths of economic importance have been systematically covered in this review for further exploring their use and applications, which can give physicians and veterinarians effective drugs in hand to enable them control worm infections.
Collapse
|
14
|
Using existing drugs as leads for broad spectrum anthelmintics targeting protein kinases. PLoS Pathog 2013; 9:e1003149. [PMID: 23459584 PMCID: PMC3573124 DOI: 10.1371/journal.ppat.1003149] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 11/29/2012] [Indexed: 01/22/2023] Open
Abstract
As one of the largest protein families, protein kinases (PKs) regulate nearly all processes within the cell and are considered important drug targets. Much research has been conducted on inhibitors for PKs, leading to a wealth of compounds that target PKs that have potential to be lead anthelmintic drugs. Identifying compounds that have already been developed to treat neglected tropical diseases is an attractive way to obtain lead compounds inexpensively that can be developed into much needed drugs, especially for use in developing countries. In this study, PKs from nematodes, hosts, and DrugBank were identified and classified into kinase families and subfamilies. Nematode proteins were placed into orthologous groups that span the phylum Nematoda. A minimal kinome for the phylum Nematoda was identified, and properties of the minimal kinome were explored. Orthologous groups from the minimal kinome were prioritized for experimental testing based on RNAi phenotype of the Caenorhabditis elegans ortholog, transcript expression over the life-cycle and anatomic expression patterns. Compounds linked to targets in DrugBank belonging to the same kinase families and subfamilies in the minimal nematode kinome were extracted. Thirty-five compounds were tested in the non-parasitic C. elegans and active compounds progressed to testing against nematode species with different modes of parasitism, the blood-feeding Haemonchus contortus and the filarial Brugia malayi. Eighteen compounds showed efficacy in C. elegans, and six compounds also showed efficacy in at least one of the parasitic species. Hypotheses regarding the pathway the compounds may target and their molecular mechanism for activity are discussed. Parasitic nematode infection is a large global health and economic problem, infecting around 2 billion people and costing $100 billion in crops and livestock. People in developing countries often live on one dollar per day, so treatments cannot be expensive, therefore using pre-existing drugs as lead compounds provides an economical way to begin to develop affordable treatments. Protein kinases were chosen as the focus of this work due to the large number of pre-existing drugs that target them and their important role in regulating almost all activities in the cell. Herein we describe a set of protein kinases conserved in diverse nematode species and experimental screening results of pre-existing drugs that target these kinases. The compounds that show in vitro efficacy in both C. elegans and parasitic nematodes, H. contortus or B. malayi have potential to be optimized further. These compounds have potential to provide accessible treatment to people in developing countries, as well as improving the health of livestock and boosting food production globally.
Collapse
|
15
|
McVeigh P, Atkinson L, Marks NJ, Mousley A, Dalzell JJ, Sluder A, Hammerland L, Maule AG. Parasite neuropeptide biology: Seeding rational drug target selection? Int J Parasitol Drugs Drug Resist 2012; 2:76-91. [PMID: 24533265 PMCID: PMC3862435 DOI: 10.1016/j.ijpddr.2011.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 01/16/2023]
Abstract
The rationale for identifying drug targets within helminth neuromuscular signalling systems is based on the premise that adequate nerve and muscle function is essential for many of the key behavioural determinants of helminth parasitism, including sensory perception/host location, invasion, locomotion/orientation, attachment, feeding and reproduction. This premise is validated by the tendency of current anthelmintics to act on classical neurotransmitter-gated ion channels present on helminth nerve and/or muscle, yielding therapeutic endpoints associated with paralysis and/or death. Supplementary to classical neurotransmitters, helminth nervous systems are peptide-rich and encompass associated biosynthetic and signal transduction components - putative drug targets that remain to be exploited by anthelmintic chemotherapy. At this time, no neuropeptide system-targeting lead compounds have been reported, and given that our basic knowledge of neuropeptide biology in parasitic helminths remains inadequate, the short-term prospects for such drugs remain poor. Here, we review current knowledge of neuropeptide signalling in Nematoda and Platyhelminthes, and highlight a suite of 19 protein families that yield deleterious phenotypes in helminth reverse genetics screens. We suggest that orthologues of some of these peptidergic signalling components represent appealing therapeutic targets in parasitic helminths.
Collapse
Affiliation(s)
- Paul McVeigh
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Louise Atkinson
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Nikki J. Marks
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Angela Mousley
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Johnathan J. Dalzell
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Ann Sluder
- Scynexis Inc., P.O. Box 12878, Research Triangle Park, NC 27709-2878, USA
| | | | - Aaron G. Maule
- Molecular Biosciences–Parasitology, Institute of Agri-Food and Land Use, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| |
Collapse
|
16
|
Manzano-Román R, Díaz-Martín V, González-González M, Matarraz S, Álvarez-Prado AF, LaBaer J, Orfao A, Pérez-Sánchez R, Fuentes M. Self-assembled Protein Arrays from an Ornithodoros moubata Salivary Gland Expression Library. J Proteome Res 2012; 11:5972-82. [DOI: 10.1021/pr300696h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Raul Manzano-Román
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Veronica Díaz-Martín
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Maria González-González
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Sergio Matarraz
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Angel Francisco Álvarez-Prado
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized
Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-6401, United States
| | - Alberto Orfao
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Ricardo Pérez-Sánchez
- Parasitología Animal, Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA, CSIC), Cordel de Merinas, 40-52, 37008 Salamanca, Spain
| | - Manuel Fuentes
- Centro de Investigación
del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina
y Servicio General de Citometría, Universidad de Salamanca, 37007 Salamanca, Spain
| |
Collapse
|
17
|
Hain AUP, Weltzer RR, Hammond H, Jayabalasingham B, Dinglasan RR, Graham DRM, Colquhoun DR, Coppens I, Bosch J. Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction. J Struct Biol 2012; 180:551-62. [PMID: 22982544 DOI: 10.1016/j.jsb.2012.09.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/26/2012] [Accepted: 09/03/2012] [Indexed: 12/22/2022]
Abstract
The autophagy-related proteins are thought to serve multiple functions in Plasmodium and are considered essential to parasite survival and development. We have studied two key interacting proteins, Atg8 and Atg3, of the autophagy pathway in Plasmodium falciparum. These proteins are vital for the formation and elongation of the autophagosome and essential to the process of macroautophagy. Autophagy may be required for conversion of the sporozoite into erythrocytic-infective merozoites and may be crucial for other functions during asexual blood stages. Here we describe the identification of an Atg8 family interacting motif (AIM) in Plasmodium Atg3, which binds Plasmodium Atg8. We determined the co-crystal structure of PfAtg8 with a short Atg3¹⁰³⁻¹¹⁰ peptide, corresponding to this motif, to 2.2 Å resolution. Our in vitro interaction studies are in agreement with our X-ray crystal structure. Furthermore they suggest an important role for a unique Apicomplexan loop absent from human Atg8 homologues. Prevention of the protein-protein interaction of full length PfAtg8 with PfAtg3 was achieved at low micromolar concentrations with a small molecule, 1,2,3-trihydroxybenzene. Together our structural and interaction studies represent a starting point for future antimalarial drug discovery and design for this novel protein-protein interaction.
Collapse
Affiliation(s)
- Adelaide U P Hain
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Murfin KE, Dillman AR, Foster JM, Bulgheresi S, Slatko BE, Sternberg PW, Goodrich-Blair H. Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age. THE BIOLOGICAL BULLETIN 2012; 223:85-102. [PMID: 22983035 PMCID: PMC3508788 DOI: 10.1086/bblv223n1p85] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nematodes are ubiquitous organisms that have a significant global impact on ecosystems, economies, agriculture, and human health. The applied importance of nematodes and the experimental tractability of many species have promoted their use as models in various research areas, including developmental biology, evolutionary biology, ecology, and animal-bacterium interactions. Nematodes are particularly well suited for the investigation of host associations with bacteria because all nematodes have interacted with bacteria during their evolutionary history and engage in a variety of association types. Interactions between nematodes and bacteria can be positive (mutualistic) or negative (pathogenic/parasitic) and may be transient or stably maintained (symbiotic). Furthermore, since many mechanistic aspects of nematode-bacterium interactions are conserved, their study can provide broader insights into other types of associations, including those relevant to human diseases. Recently, genome-scale studies have been applied to diverse nematode-bacterial interactions and have helped reveal mechanisms of communication and exchange between the associated partners. In addition to providing specific information about the system under investigation, these studies also have helped inform our understanding of genome evolution, mutualism, and innate immunity. In this review we discuss the importance and diversity of nematodes, "omics"' studies in nematode-bacterial systems, and the wider implications of the findings.
Collapse
Affiliation(s)
- Kristen E. Murfin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Adler R. Dillman
- HHMI and Division of Biology, California Institute of Technology, 156-29, Pasadena, CA 91125, USA
| | - Jeremy M. Foster
- Parasitology Division, New England Biolabs, Inc., 240 County Rd, Ipswich, MA 01938, USA
| | - Silvia Bulgheresi
- Department of Genetics in Ecology, University of Vienna, Vienna, Austria
| | - Barton E. Slatko
- Parasitology Division, New England Biolabs, Inc., 240 County Rd, Ipswich, MA 01938, USA
| | - Paul W. Sternberg
- HHMI and Division of Biology, California Institute of Technology, 156-29, Pasadena, CA 91125, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Corresponding author Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, , phone: 608-265-4537, fax: 608-262-9865
| |
Collapse
|
19
|
Choi YJ, Ghedin E, Berriman M, McQuillan J, Holroyd N, Mayhew GF, Christensen BM, Michalski ML. A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis 2011; 5:e1409. [PMID: 22180794 PMCID: PMC3236722 DOI: 10.1371/journal.pntd.0001409] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 10/19/2011] [Indexed: 11/19/2022] Open
Abstract
Background Developing intervention strategies for the control of parasitic nematodes continues to be a significant challenge. Genomic and post-genomic approaches play an increasingly important role for providing fundamental molecular information about these parasites, thus enhancing basic as well as translational research. Here we report a comprehensive genome-wide survey of the developmental transcriptome of the human filarial parasite Brugia malayi. Methodology/Principal Findings Using deep sequencing, we profiled the transcriptome of eggs and embryos, immature (≤3 days of age) and mature microfilariae (MF), third- and fourth-stage larvae (L3 and L4), and adult male and female worms. Comparative analysis across these stages provided a detailed overview of the molecular repertoires that define and differentiate distinct lifecycle stages of the parasite. Genome-wide assessment of the overall transcriptional variability indicated that the cuticle collagen family and those implicated in molting exhibit noticeably dynamic stage-dependent patterns. Of particular interest was the identification of genes displaying sex-biased or germline-enriched profiles due to their potential involvement in reproductive processes. The study also revealed discrete transcriptional changes during larval development, namely those accompanying the maturation of MF and the L3 to L4 transition that are vital in establishing successful infection in mosquito vectors and vertebrate hosts, respectively. Conclusions/Significance Characterization of the transcriptional program of the parasite's lifecycle is an important step toward understanding the developmental processes required for the infectious cycle. We find that the transcriptional program has a number of stage-specific pathways activated during worm development. In addition to advancing our understanding of transcriptome dynamics, these data will aid in the study of genome structure and organization by facilitating the identification of novel transcribed elements and splice variants. Lymphatic filariasis, also known as elephantiasis, is a tropical disease affecting over 120 million people worldwide. More than 40 million people live with painful, disfiguring symptoms that can cause severe debilitation and social stigma. The disease is caused by infection with thread-like filarial nematodes (roundworms) that have a complex parasitic lifecycle involving both human and mosquito hosts. In the study, the authors profiled the transcriptome (the set of genes transcribed into messenger RNA rather than all of those in the genome) of the human filarial worm Brugia malayi in different lifecyle stages using deep sequencing technology. The analysis revealed major transitions in RNA expression from eggs through larval stages to adults. Using statistical approaches, the authors identified groups of genes with distinct life stage dependent transcriptional patterns, with particular emphasis on genes displaying sex-biased or germline-enriched patterns and those displaying significant changes during larval development. This study presents a first comprehensive analysis of the lifecycle transcriptome of B. malayi, providing fundamental molecular information that should help researchers better understand parasite biology and could provide clues for the development of more effective interventions.
Collapse
Affiliation(s)
- Young-Jun Choi
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Elodie Ghedin
- Department of Computational and Systems Biology, Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Matthew Berriman
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jacqueline McQuillan
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nancy Holroyd
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - George F. Mayhew
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bruce M. Christensen
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michelle L. Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|