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Sarma M, Borkotoky S, Dubey VK. Structure-based drug designing against Leishmania donovani using docking and molecular dynamics simulation studies: exploring glutathione synthetase as a drug target. J Biomol Struct Dyn 2024; 42:7628-7636. [PMID: 37491862 DOI: 10.1080/07391102.2023.2240429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database against Leishmania donovani glutathione synthetase. The three-dimensional structure of Leishmania donovani glutathione synthetase was constructed by homology modeling, using the crystallographic structure of Trypanosoma brucei glutathione synthetase as a template. Subsequently, molecular docking studies were carried out for a large number of compounds using AutoDock Vina. Among the screened compounds, we selected the top five with strong binding affinity to Leishmania donovani glutathione synthetase but having a very low affinity to its human homolog. Further investigations on protein-ligand complexes were done by conducting molecular dynamics (MD) simulation and MM/PBSA analysis. The results revealed that Olysio (Simeprevir) exhibited the lowest binding energy (-89.21 kcal/mol), followed by Telithromycin (-45.34 kcal/mol). These findings showed that these compounds have the potential to act as inhibitors of glutathione synthetase. Hence, our study provides valuable insights for the development of a novel therapeutic strategy against Leishmania donovani by targeting the glutathione synthetase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manash Sarma
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Subhomoi Borkotoky
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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2
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Ahmed G, Jamal F, Tiwari RK, Singh V, Rai SN, Chaturvedi SK, Pandey K, Singh SK, Kumar A, Narayan S, Vamanu E. Arsenic exposure to mouse visceral leishmaniasis model through their drinking water linked to the disease exacerbation via modulation in host protective immunity: a preclinical study. Sci Rep 2023; 13:21461. [PMID: 38052913 PMCID: PMC10698031 DOI: 10.1038/s41598-023-48642-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
A large body of evidence has shown a direct link between arsenic exposure and drug resistance to Leishmania parasites against antimonial preparations in visceral leishmaniasis (VL) hyper-endemic regions, especially in India and its sub-continent. However, the implicated roles of arsenic on the VL host, pathophysiological changes, and immune function have not yet been clarified, particularly at the reported concentration of arsenic in the VL hyper-endemic area of Bihar, India. Herein, we exposed the mouse VL model to arsenic (0.5 mg/L to 2 mg/L) through their drinking water and analyzed its effect on T cells proliferation, Th1/Th2-mediators, MAPK signaling cascade, and parasite load in preclinical models. Coherently, the parasite count in Giemsa stained spleen imprint has been investigated and found significant positive associations with levels of arsenic exposure. The liver and kidney function tests (AST, ALT, ALP, BUN, Creatinine, Urea, etc.) are apparent to hepatonephric toxicity in arsenic exposed VL mice compared to unexposed. This observation appears to be consistent with the up-regulated expression of immune regulatory Th2 mediators (IL-4, IL-10, TGF-β) and down-regulated expression of Th1 mediators (IL-12, IFN-γ, TNF-α) with a suppressed leishmanicidal function of macrophage (ROS, NO, iNOS). We also established that arsenic exposure modulated the host ERK-1/2 and p38 MAPK signaling cascade, limited T lymphocyte proliferation, and a lower IgG2a/IgG1 ratio to favor the Leishmania parasite survival inside the host. This study suggests that the contorted Th1-subtype and exacerbated Th2-subtype immune responses are involved in the increased susceptibility and pathogenesis of Leishmania parasite among subjects/individuals regularly exposed to arsenic.
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Affiliation(s)
- Ghufran Ahmed
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Fauzia Jamal
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Ritesh K Tiwari
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Veer Singh
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Sachchida Nand Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sanjay K Chaturvedi
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Santosh K Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Ashish Kumar
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India
| | - Shyam Narayan
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, 800007, India.
| | - Emanuel Vamanu
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine of Bucharest, 011464, Bucharest, Romania.
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Abd-Alaziz DM, Mansour M, Nasr M, Sammour OA. Spanethosomes as a novel topical carrier for silymarin in contrast to conventional spanlastics: Formulation development, in vitro and ex vivo evaluation for potential treatment of leishmaniasis. J Drug Deliv Sci Technol 2023; 88:104887. [DOI: 10.1016/j.jddst.2023.104887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Vallières C, Golinelli-Cohen MP, Guittet O, Lepoivre M, Huang ME, Vernis L. Redox-Based Strategies against Infections by Eukaryotic Pathogens. Genes (Basel) 2023; 14:genes14040778. [PMID: 37107536 PMCID: PMC10138290 DOI: 10.3390/genes14040778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Redox homeostasis is an equilibrium between reducing and oxidizing reactions within cells. It is an essential, dynamic process, which allows proper cellular reactions and regulates biological responses. Unbalanced redox homeostasis is the hallmark of many diseases, including cancer or inflammatory responses, and can eventually lead to cell death. Specifically, disrupting redox balance, essentially by increasing pro-oxidative molecules and favouring hyperoxidation, is a smart strategy to eliminate cells and has been used for cancer treatment, for example. Selectivity between cancer and normal cells thus appears crucial to avoid toxicity as much as possible. Redox-based approaches are also employed in the case of infectious diseases to tackle the pathogens specifically, with limited impacts on host cells. In this review, we focus on recent advances in redox-based strategies to fight eukaryotic pathogens, especially fungi and eukaryotic parasites. We report molecules recently described for causing or being associated with compromising redox homeostasis in pathogens and discuss therapeutic possibilities.
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Affiliation(s)
- Cindy Vallières
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Marie-Pierre Golinelli-Cohen
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Olivier Guittet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Michel Lepoivre
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Meng-Er Huang
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Laurence Vernis
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
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Regulation of Mitochondrial Energy Metabolism by Glutaredoxin 5 in the Apicomplexan Parasite Neospora caninum. Microbiol Spectr 2023; 11:e0309122. [PMID: 36541793 PMCID: PMC9927405 DOI: 10.1128/spectrum.03091-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Iron-sulfur [Fe-S] clusters are one of the most ancient and functionally versatile natural biosynthetic prosthetic groups required by various proteins involved in important metabolic processes, including the oxidative phosphorylation of proteins, electron transfer, energy metabolism, DNA/RNA metabolism, and protein translation. Apicomplexan parasites harbor two possible [Fe-S] cluster assembly pathways: the iron-sulfur cluster (ISC) pathway in the mitochondria and the sulfur formation (SUF) pathway in the apicoplast. Glutaredoxin 5 (GRX5) is involved in the ISC pathway in many eukaryotes. However, the cellular roles of GRX5 in apicomplexan parasites remain to be explored. Here, we showed that Neospora caninum mitochondrial GRX5 (NcGRX5) deficiency resulted in aberrant mitochondrial ultrastructure and led to a significant reduction in parasite proliferation and virulence in mice, suggesting that NcGRX5 is important for parasite growth in vitro and in vivo. Comparative proteomics and energy metabolomics were used to investigate the effects of NcGRX5 on parasite growth and mitochondrial metabolism. The data showed that disruption of NcGRX5 downregulated the expression of mitochondrial electron transport chain (ETC) and tricarboxylic acid cycle (TCA) cycle proteins and reduced the corresponding metabolic fluxes. Subsequently, we identified 23 proteins that might be adjacent to or interact with NcGRX5 by proximity-based protein labeling techniques and proteomics. The interactions between NcGRX5 and two iron-sulfur cluster synthesis proteins (ISCS and ISCU1) were further confirmed by coimmunoprecipitation assays. In conclusion, NcGRX5 is important for parasite growth and may regulate mitochondrial energy metabolism by mediating the biosynthesis of iron-sulfur clusters. IMPORTANCE Iron-sulfur [Fe-S] clusters are among the oldest and most ubiquitous prosthetic groups, and they are required for a variety of proteins involved in important metabolic processes. The intracellular parasites in the phylum Apicomplexa, including Plasmodium, Toxoplasma gondii, and Neospora caninum, harbor the ISC pathway involved in the biosynthesis of [Fe-S] clusters in mitochondria. These cofactors are required for a variety of important biological processes. However, little is known about the role of oxidoreductase glutaredoxins in these parasites. Our data indicate that NcGRX5 is an essential protein that plays multiple roles in several biological processes of N. caninum. NcGRX5 interacts with the mitochondrial iron-sulfur cluster synthesis proteins ISCS and ISCU1 and also regulates parasite energy metabolism. These data provide an insider's view of the metabolic regulation and iron-sulfur cluster assembly processes in the apicomplexan parasites.
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Genetic Iron Overload Hampers Development of Cutaneous Leishmaniasis in Mice. Int J Mol Sci 2023; 24:ijms24021669. [PMID: 36675185 PMCID: PMC9864902 DOI: 10.3390/ijms24021669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The survival, growth, and virulence of Leishmania spp., a group of protozoan parasites, depends on the proper access and regulation of iron. Macrophages, Leishmania's host cell, may divert iron traffic by reducing uptake or by increasing the efflux of iron via the exporter ferroportin. This parasite has adapted by inhibiting the synthesis and inducing the degradation of ferroportin. To study the role of iron in leishmaniasis, we employed Hjv-/- mice, a model of hemochromatosis. The disruption of hemojuvelin (Hjv) abrogates the expression of the iron hormone hepcidin. This allows unrestricted iron entry into the plasma from ferroportin-expressing intestinal epithelial cells and tissue macrophages, resulting in systemic iron overload. Mice were injected with Leishmania major in hind footpads or intraperitoneally. Compared with wild-type controls, Hjv-/- mice displayed transient delayed growth of L. major in hind footpads, with a significant difference in parasite burden 4 weeks post-infection. Following acute intraperitoneal exposure to L. major, Hjv-/- peritoneal cells manifested increased expression of inflammatory cytokines and chemokines (Il1b, Tnfa, Cxcl2, and Ccl2). In response to infection with L. infantum, the causative agent of visceral leishmaniasis, Hjv-/- and control mice developed similar liver and splenic parasite burden despite vastly different tissue iron content and ferroportin expression. Thus, genetic iron overload due to hemojuvelin deficiency appears to mitigate the early development of only cutaneous leishmaniasis.
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Nasrallah AK, Atia MAM, Abd El-Maksoud RM, Kord MA, Fouad AS. Salt Priming as a Smart Approach to Mitigate Salt Stress in Faba Bean (Vicia faba L.). PLANTS 2022; 11:plants11121610. [PMID: 35736763 PMCID: PMC9228577 DOI: 10.3390/plants11121610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/24/2023]
Abstract
The present investigation aims to highlight the role of salt priming in mitigating salt stress on faba bean. In the absence of priming, the results reflected an increase in H2O2 generation and lipid peroxidation in plants subjected to 200 mM salt shock for one week, accompanied by a decline in growth, photosynthetic pigments, and yield. As a defense, the shocked plants showed enhancements in ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), peroxidase (POX), and superoxide dismutase (SOD) activities. Additionally, the salt shock plants revealed a significant increase in phenolics and proline content, as well as an increase in the expression levels of glutathione (GSH) metabolism-related genes (the L-ascorbate peroxidase (L-APX) gene, the spermidine synthase (SPS) gene, the leucyl aminopeptidase (LAP) gene, the aminopeptidase N (AP-N) gene, and the ribonucleo-side-diphosphate reductase subunit M1 (RDS-M) gene). On the other hand, priming with increasing concentrations of NaCl (50–150 mM) exhibited little significant reduction in some growth- and yield-related traits. However, it maintained a permanent alert of plant defense that enhanced the expression of GSH-related genes, proline accumulation, and antioxidant enzymes, establishing a solid defensive front line ameliorating osmotic and oxidative consequences of salt shock and its injurious effect on growth and yield.
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Affiliation(s)
- Amira K. Nasrallah
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
| | - Mohamed A. M. Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt
- Correspondence: (M.A.M.A.); (A.S.F.); Tel.: +20-1000164922 (M.A.M.A.); +20-1203770992 (A.S.F.)
| | - Reem M. Abd El-Maksoud
- Nucleic Acid & Protein Chemistry Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza 12619, Egypt;
| | - Maimona A. Kord
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
| | - Ahmed S. Fouad
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (A.K.N.); (M.A.K.)
- Correspondence: (M.A.M.A.); (A.S.F.); Tel.: +20-1000164922 (M.A.M.A.); +20-1203770992 (A.S.F.)
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8
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Kumar A, Nimsarkar P, Singh S. Probing the Interactions Responsible for the Structural Stability of Trypanothione Reductase Through Computer Simulation and Biophysical Characterization. Protein J 2022; 41:230-244. [PMID: 35364760 DOI: 10.1007/s10930-022-10052-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 11/26/2022]
Abstract
With the necessity to develop antileishmanial drugs with substrate specificity, trypanothione reductase (TryR) has gained popularity in parasitology. TryR is unique to be present only in trypanosomatids and is functionally similar to glutathione in mammals. It protects against oxidative stress exerted by the host defense mechanism. The TryR enzyme is essential for the survival of Leishmania parasites in the host as it reduces trypanothione and aids in neutralizing hydrogen peroxide produced by the host macrophages during infection. Henceforth, it becomes vital to decipher their functional stability and behaviour in the presence of denaturants. Our study is focused on structural, functional and behavioural stability aspects of TryR with different concentrations of Urea, Guanidinium chloride, alcohol based compounds followed by extensive molecular dynamics simulations in a lipid bilayer system. The results obtained from the study reveal an interesting insight into the possible mechanisms of modulation of the structure, function and stability of the TryR protein.
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Affiliation(s)
- Anurag Kumar
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune, 411007, India
| | - Prajakta Nimsarkar
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune, 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune, 411007, India.
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Grace CA, Forrester S, Silva VC, Carvalho KSS, Kilford H, Chew YP, James S, Costa DL, Mottram JC, Costa CCHN, Jeffares DC. Candidates for Balancing Selection in Leishmania donovani Complex Parasites. Genome Biol Evol 2021; 13:6448231. [PMID: 34865011 PMCID: PMC8717319 DOI: 10.1093/gbe/evab265] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
The Leishmania donovani species complex is the causative agent of visceral leishmaniasis, which cause 20–40,000 fatalities a year. Here, we conduct a screen for balancing selection in this species complex. We used 384 publicly available L. donovani and L. infantum genomes, and sequence 93 isolates of L. infantum from Brazil to describe the global diversity of this species complex. We identify five genetically distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We find that signals of balancing selection are generally not shared between populations, consistent with transient adaptive events, rather than long-term balancing selection. We then apply multiple diversity metrics to identify candidate genes with robust signatures of balancing selection, identifying a curated set of 24 genes with robust signatures. These include zeta toxin, nodulin-like, and flagellum attachment proteins. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides genes for further study.
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Affiliation(s)
- Cooper Alastair Grace
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Sarah Forrester
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Vladimir Costa Silva
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Kátia Silene Sousa Carvalho
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Hannah Kilford
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Yen Peng Chew
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom.,Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sally James
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Dorcas L Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Jeremy C Mottram
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Carlos C H N Costa
- Instituto de Doenças do Sertão, Instituto de Doenças Tropicais Natan Portella, Centro de Ciências da Saúde da Universidade Federal do Piauí, Teresina-PI, Brazil
| | - Daniel C Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
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Salloum T, Moussa R, Rahy R, Al Deek J, Khalifeh I, El Hajj R, Hall N, Hirt RP, Tokajian S. Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex. PLoS Negl Trop Dis 2020; 14:e0008684. [PMID: 32946436 PMCID: PMC7526921 DOI: 10.1371/journal.pntd.0008684] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 09/30/2020] [Accepted: 08/06/2020] [Indexed: 12/18/2022] Open
Abstract
Leishmania tropica is one of the main causative agents of cutaneous leishmaniasis (CL). Population structures of L. tropica appear to be genetically highly diverse. However, the relationship between L. tropica strains genomic diversity, protein coding gene evolution and biogeography are still poorly understood. In this study, we sequenced the genomes of three new clinical L. tropica isolates, two derived from a recent outbreak of CL in camps hosting Syrian refugees in Lebanon and one historical isolate from Azerbaijan to further refine comparative genome analyses. In silico multilocus microsatellite typing (MLMT) was performed to integrate the current diversity of genome sequence data in the wider available MLMT genetic population framework. Single nucleotide polymorphism (SNPs), gene copy number variations (CNVs) and chromosome ploidy were investigated across the available 18 L. tropica genomes with a main focus on protein coding genes. MLMT divided the strains in three populations that broadly correlated with their geographical distribution but not populations defined by SNPs. Unique SNPs profiles divided the 18 strains into five populations based on principal component analysis. Gene ontology enrichment analysis of the protein coding genes with population specific SNPs profiles revealed various biological processes, including iron acquisition, sterols synthesis and drug resistance. This study further highlights the complex links between L. tropica important genomic heterogeneity and the parasite broad geographic distribution. Unique sequence features in protein coding genes identified in distinct populations reveal potential novel markers that could be exploited for the development of more accurate typing schemes to further improve our knowledge of the evolution and epidemiology of the parasite as well as highlighting protein variants of potential functional importance underlying L. tropica specific biology.
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Rim Moussa
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Ryan Rahy
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Jospin Al Deek
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Ibrahim Khalifeh
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - Rana El Hajj
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - Neil Hall
- Earlham Institute, Norwich research Park, University of East Anglia, Norwich, United Kingdom
| | - Robert P. Hirt
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail: (RPH); (ST)
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
- * E-mail: (RPH); (ST)
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Chauhan N, Singh S. Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania. Front Bioeng Biotechnol 2019; 7:336. [PMID: 31803732 PMCID: PMC6877600 DOI: 10.3389/fbioe.2019.00336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 01/10/2023] Open
Abstract
Background: The integration of computational and mathematical approaches is used to provide a key insight into the biological systems. Through systems biology approaches we seek to find detailed and more robust information on Leishmanial metabolic network. Forman/Forman-Ricci curvature measures were applied to identify important nodes in the network(s). This was followed by flux balance analysis (FBA) to decipher important drug targets. Results: Our results revealed several key high curvature nodes (metabolites) belonging to common yet crucial metabolic networks, thus, maintaining the integrity of the network which signifies its robustness. Further analysis revealed the presence of some of these metabolites, MGO, in redox metabolism of the parasite. Being a component in the glyoxalase pathway and highly cytotoxic, we further attempted to study the outcome of the deletion of the key enzyme (GLOI) mainly involved in the neutralization of MGO by utilizing FBA. The model and the objective function kept as simple as possible demonstrated an interesting emergent behavior. The non-functional GLOI in the model contributed to "zero" flux which signifies the key role of GLOI as a rate limiting enzyme. This has led to several fold increase production of MGO, thereby, causing an increased level of MGO•- generation. Conclusions: The integrated computational approaches have deciphered GLOI as a potential target both from curvature measures as well as FBA which could further be explored for kinetic modeling by implying various redox-dependent constraints on the model. Furthermore, a constraint-based FBA on a larger model could further be explored to get broader picture to understand the exact underlying mechanisms. Designing various in vitro experimental perspectives could churn the therapeutic importance of GLOI.
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