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Zarin S, Shariq M, Rastogi N, Ahuja Y, Manjunath P, Alam A, Hasnain SE, Ehtesham NZ. Rv2231c, a unique histidinol phosphate aminotransferase from Mycobacterium tuberculosis, supports virulence by inhibiting host-directed defense. Cell Mol Life Sci 2024; 81:203. [PMID: 38698289 PMCID: PMC11065945 DOI: 10.1007/s00018-024-05200-8] [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: 06/23/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
Abstract
Nitrogen metabolism of M. tuberculosis is critical for its survival in infected host cells. M. tuberculosis has evolved sophisticated strategies to switch between de novo synthesis and uptake of various amino acids from host cells for metabolic demands. Pyridoxal phosphate-dependent histidinol phosphate aminotransferase-HspAT enzyme is critically required for histidine biosynthesis. HspAT is involved in metabolic synthesis of histidine, phenylalanine, tyrosine, tryptophan, and novobiocin. We showed that M. tuberculosis Rv2231c is a conserved enzyme with HspAT activity. Rv2231c is a monomeric globular protein that contains α-helices and β-sheets. It is a secretory and cell wall-localized protein that regulates critical pathogenic attributes. Rv2231c enhances the survival and virulence of recombinant M. smegmatis in infected RAW264.7 macrophage cells. Rv2231c is recognized by the TLR4 innate immune receptor and modulates the host immune response by suppressing the secretion of the antibacterial pro-inflammatory cytokines TNF, IL-12, and IL-6. It also inhibits the expression of co-stimulatory molecules CD80 and CD86 along with antigen presenting molecule MHC-I on macrophage and suppresses reactive nitrogen species formation, thereby promoting M2 macrophage polarization. Recombinant M. smegmatis expressing Rv2231c inhibited apoptosis in macrophages, promoting efficient bacterial survival and proliferation, thereby increasing virulence. Our results indicate that Rv2231c is a moonlighting protein that regulates multiple functions of M. tuberculosis pathophysiology to increase its virulence. These mechanistic insights can be used to better understand the pathogenesis of M. tuberculosis and to design strategies for tuberculosis mitigation.
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Affiliation(s)
- Sheeba Zarin
- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Mohd Shariq
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Nilisha Rastogi
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Yashika Ahuja
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - P Manjunath
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Anwar Alam
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, 201310, India
| | - Seyed Ehtesham Hasnain
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India.
| | - Nasreen Zafar Ehtesham
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
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Sasidharan S, Saudagar P. An anti-leishmanial compound 4',7-dihydroxyflavone elicits ROS-mediated apoptosis-like death in Leishmania parasite. FEBS J 2023. [PMID: 36871140 DOI: 10.1111/febs.16770] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/12/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
The treatment for leishmaniasis is currently plagued by side effects such as toxicity and the emergence of drug resistance to the available repertoire of drugs, as well as the expense of these drugs. Considering such rising concerns, we report the anti-leishmanial activity and mechanism of a flavone compound 4',7-dihydroxyflavone (TI 4). Four flavanoids were initially screened for anti-leishmanial activity and cytotoxicity. The results showed that the compound TI 4 exhibited higher activity and selectivity index at the same time as maintaining low cytotoxicity. Preliminary microscopic studies and fluorescence-activated cell sorting analysis reported that the parasite underwent apoptosis on TI 4 treatment. Further in-depth studies revealed high reactive oxygen species (ROS) production and thiol levels in the parasites, suggesting ROS-mediated apoptosis in the parasites upon TI 4 treatment. Other apoptotic indicators such as intracellular Ca2+ and mitochondrial membrane potential also indicated the onset of apoptosis in the treated parasites. The mRNA expression levels signified that the redox metabolism genes were upregulated by two-fold along with the apoptotic genes. In summary, the use of TI 4 on Leishmania parasites induces ROS-mediated apoptosis; therefore, the compound has immense potential to be an anti-leishmanial drug. However, in vivo studies would be required to ascertain its safety and efficacy before we can exploit the compound against the growing leishmaniasis crisis.
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Affiliation(s)
- Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, India
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Sasidharan S, Saudagar P. Knockout of Tyrosine Aminotransferase Gene by Homologous Recombination Arrests Growth and Disrupts Redox Homeostasis in Leishmania Parasite. Parasitol Res 2022; 121:3229-3241. [PMID: 36056961 DOI: 10.1007/s00436-022-07642-0] [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: 05/17/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022]
Abstract
Tyrosine aminotransferase is a well-characterized enzyme in the Leishmania parasite, but the role of TAT in the parasite functioning remains largely unknown. In this study, we attempt to gain a better understanding of the enzyme's role in the parasite by gene knockout and overexpression of the TAT gene. The overexpression of TAT protein was well tolerated by the parasites in two independent repeats. Single knockout of TAT gene by homologous recombination, LdTAT+/- displayed distinct retardation in the proliferation rates and entered the death phase immediately. Morphology of LdTAT+/- parasites had important structural defects as they rounded up with elongated flagella. Gene regulation studies suggested the upregulation of key apoptotic and redox metabolism genes in LdTAT+/-. Moreover, LdTAT+/- cells accumulated higher ROS, thiols, intracellular Ca2+ concentrations, and mitochondrial membrane depolarization signifying the onset of apoptosis. Tocopherol levels were reduced by 50% in LdTAT+/- suggesting the involvement of TAT in tocopherol biosynthesis in the parasite. Overall, our results provide the first evidence that gene knockout of TAT results in apoptosis and that TAT is required for the survival and viability of Leishmania donovani.
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Affiliation(s)
- Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, 506004, India.
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4
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Sasidharan S, Tripathi T, Saudagar P. Critical Insight into Plausible Acquired Tocopherol Pathway in Neglected Human Trypanosomatids. ACS OMEGA 2021; 6:31396-31403. [PMID: 34869966 PMCID: PMC8637591 DOI: 10.1021/acsomega.1c05046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/27/2021] [Indexed: 06/02/2023]
Abstract
Despite global therapeutic advancements, tropical parasitic infections like trypanosomiasis and leishmaniasis continue to be a major health concern in developing countries. These two tropical infectious diseases lead to enormous economic loss, significant disability, and morbidity, accounting for over one million deaths per year worldwide. The causative parasites, which shuttle between an insect vector and a mammalian host, thrive either in the bloodstream or in the intramacrophage environments. Essentially, the parasites live in an environment of oxidative stress and therefore require metabolic pathways to counterbalance the host immune response and survive the adverse conditions. Apart from the trypanothione pathway elucidated in the parasites, there exists a tocopherol pathway that functions to scavenge the reactive chemical species. This pathway, unique to photosynthetic organisms, is essential for the parasite's survival, though the enzymes involved remain largely uncharacterized. Consequently, an understanding of the origin of the pathway and where and how the interconnected tocopherol pathway functions may result in the identification of promising and potential therapeutic interventions to combat these deadly diseases. Recent works underline the presence of the tocopherol pathway in trypanosomatids and hypothesize that trypanosomatids may be tocopherol prototrophs. This review focuses on the biosynthesis of tocopherols in Trypanosoma and Leishmania in light of the current evidence.
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Affiliation(s)
- Santanu Sasidharan
- Department
of Biotechnology, National Institute of
Technology Warangal, Warangal 506004, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Prakash Saudagar
- Department
of Biotechnology, National Institute of
Technology Warangal, Warangal 506004, India
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Gontijo VS, Colombo FA, Ferreira Espuri P, Freitas PGD, Nunes JB, Alves LB, Veloso MP, Alves RB, Freitas RP, Marques MJ. In vivo evaluation of anti-Leishmania activity of alkyltriazoles and alkylphosphocholines by oral route. Exp Parasitol 2021; 226-227:108123. [PMID: 34144040 DOI: 10.1016/j.exppara.2021.108123] [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: 06/02/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
The failures in the treatment of leishmaniasis is an increasing problem around the world, especially related to resistance. Thus, we describe the synthesis and in vivo anti-Leishmania activity of alkylphosphocholine and alkyltriazoles; besides, their likely action mechanisms stem from some eventual inhibition of parasite enzymes using computational tools. These compounds were tested in an in vivo hamster model infected with Leishmania Leishmania infantum chagasi. Fifty days after parasite inoculation, the two compounds 12-azidedodecylphosphocholine (3) and 3-(1-(12-fluorododecyl)-1H-1,2,3-triazol-1-yl)propano-1-ol (9), were separately administered once a day as oral suspensions (25 and 12.5 mg/kg/day, respectively) during ten days, and their efficacy was compared to the reference compound pentavalent antimonial Glucantime (GLU). Compound 3 significantly reduced the number of parasites in the spleen (4.93 × 102 amastigotes/g) and liver (4.52 × 103 amastigotes/g). Compound 9 reduced the number of amastigotes in the spleen to 1.30 × 104 and 1.36 × 103 amastigotes/g in the liver. GLU was the most effective overall treatment (7.50 × 101 and 2.28 × 102 amastigotes/g in the spleen and liver, respectively). The high activity levels of these compounds in vivo may stem from their high in vitro leishmanicidal activity and lipophilicity. The in silico absorption, distribution, metabolism, and excretion studies also showed some anti-Leishmania potential. Compound 9 had more lipophilic characteristics than those of compound 3. In silico studies of the nine enzymes of compounds 3 and 9 showed significant evidence of interactions with nicotimidase and tyrosine aminotransferase, demonstrating possible inhibition enzymes present in L. (L.) infantum chagasi. These compounds could be a promising template for developing a new class of leishmanicidal agents, by oral route, and deserve further investigation to explore different therapeutic regimens.
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Affiliation(s)
- Vanessa Silva Gontijo
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil.
| | - Fabio Antônio Colombo
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Patrícia Ferreira Espuri
- Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Poliany Graziella de Freitas
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Juliana Barbosa Nunes
- Laboratório de Patologia de Moléstias Infecciosas, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, Av. Dr. Arnaldo, 455. Cerqueira César, São Paulo, 01246-903, São Paulo, SP, Brazil
| | - Levy Bueno Alves
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Márcia Paranho Veloso
- Laboratório de Modelagem Molecular e Simulação Computacional, MolMod-CS, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil
| | - Rosemeire Brondi Alves
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Rossimiriam Pereira Freitas
- Departamento de Química, ICEx, UFMG, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcos José Marques
- Departamento de Patologia e Parasitologia, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700- Centro, 37130-001, Alfenas, MG, Brazil.
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Identification of 3-Methoxycarpachromene and Masticadienonic Acid as New Target Inhibitors against Trypanothione Reductase from Leishmania Infantum Using Molecular Docking and ADMET Prediction. Molecules 2021; 26:molecules26113335. [PMID: 34206087 PMCID: PMC8199445 DOI: 10.3390/molecules26113335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/17/2022] Open
Abstract
Polyphenolic and Terpenoids are potent natural antiparasitic compounds. This study aimed to identify new drug against Leishmania parasites, leishmaniasis’s causal agent. A new in silico analysis was accomplished using molecular docking, with the Autodock vina program, to find the binding affinity of two important phytochemical compounds, Masticadienonic acid and the 3-Methoxycarpachromene, towards the trypanothione reductase as target drugs, responsible for the defense mechanism against oxidative stress and virulence of these parasites. There were exciting and new positive results: the molecular docking results show as elective binding profile for ligands inside the active site of this crucial enzyme. The ADMET study suggests that the 3-Methoxycarpachromene has the highest probability of human intestinal absorption. Through this work, 3-Methoxycarpachromene and Masticadienonic acid are shown to be potentially significant in drug discovery, especially in treating leishmaniasis. Hence, drug development should be completed with promising results.
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Sasidharan S, Saudagar P. Flavones reversibly inhibit Leishmania donovani tyrosine aminotransferase by binding to the catalytic pocket: An integrated in silico-in vitro approach. Int J Biol Macromol 2020; 164:2987-3004. [PMID: 32798546 DOI: 10.1016/j.ijbiomac.2020.08.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
The current drugs for treating Leishmaniasis are toxic, non-economical and with the emergence of drug resistance makes the need for novel therapeutics urgent and necessary. In the current study, we report the identification of compounds TI 1-5 against tyrosine aminotransferase of L. donovani from a curated ZINC15 database containing 183,659 compounds. These flavonoid compounds had binding energies < -8 kcal/mol and interacted with the active site residues S151, K286, C290, and P291. Assessment of physicochemical descriptors and ADMET properties established the drug likeliness of these compounds. The all-atom molecular dynamic simulations of the TAT-TI complexes exhibited stable geometrical properties and further trajectory analysis revealed the high-affinity interactions of TI 1, 3, 4, and 5 with the active site residues. DFT calculations reported the high electrophilic nature of TI 2 while other TI compounds demonstrated good kinetic stability and reactivity. From in vitro studies, TI 3 and TI 4 had the highest inhibition with Ki values of 0.9 ± 0.2 μM and 0.30 ± 0.1 μM, respectively. Taken together, the results from this study indicate the potentiality of TI 1, 3, 4, and 5 as anti-leishmanial leads, and these compounds can be exploited to manage the growing Leishmaniasis crisis in the world.
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Affiliation(s)
- Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal, 506004, Telangana, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, 506004, Telangana, India.
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8
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de Souza ML, Gonzaga da Costa LA, Silva EDO, de Sousa ALMD, Dos Santos WM, Rolim Neto PJ. Recent strategies for the development of oral medicines for the treatment of visceral leishmaniasis. Drug Dev Res 2020; 81:803-814. [PMID: 32394440 DOI: 10.1002/ddr.21684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 01/02/2023]
Abstract
Considered prevalent in many countries on five continents, especially in low-income regions, leishmaniasis is a neglected tropical disease classified by World Health Organization as one of the diseases for which the development of new treatments is a priority. It is an infectious disease caused by protozoa of the genus Leishmania, whose species may cause different clinical manifestations, such as cutaneous and visceral leishmaniasis (VL). Treatment is exclusively by drug therapy, as it has not been possible to develop vaccines yet. Currently available drugs are not fully effective in all cases; they have parenteral administration and exhibit a number of serious and very common adverse effects. The only oral drug available is expensive and it is not available in many endemic countries. Injectable administration is the main problem of treatments, since it requires patients to go to health centers, hospitalization and professional administration, which are conditions that are not adapted to the reality of the poverty conditions of patients with the disease. In this context, the development of an oral medicine has become a focus as it may solve many of these issues. Based on this scenario, this review aimed to investigate which therapeutic alternatives have been studied for the development of oral drugs directed to the treatment of human VL.
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Affiliation(s)
- Myla Lôbo de Souza
- Laboratory of Technology of Medicines, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Emerson de Oliveira Silva
- Laboratory of Technology of Medicines, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | | | - Widson Michael Dos Santos
- Laboratory of Technology of Medicines, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
| | - Pedro José Rolim Neto
- Laboratory of Technology of Medicines, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil
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9
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Costa CHSD, Bichara TW, Gomes GC, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana. J Biomol Struct Dyn 2020; 39:2044-2055. [PMID: 32174264 DOI: 10.1080/07391102.2020.1742206] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Allosteric changes modulate the enzymatic activity, leading to activation or inhibition of the molecular target. Understanding the induced fit accommodation mechanism of a ligand in its lowest-free energy state and the subsequent conformational changes induced in the protein are important questions for drug design. In the present study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were applied to analyze the glycerol-3-phosphate dehydrogenase of Leishmania mexicana (LmGPDH) conformational changes induced by its cofactor and substrate binding. GPDH is a nicotinamide adenine dinucleotide (NAD)-dependent enzyme, which has been reported as an interesting target for drug discovery and development against leishmaniasis. Despite its relevance for glycolysis and pentose phosphate pathways, the structural flexibility and conformational motions of LmGPDH in complex with NADH and dihydroxyacetone phosphate (DHAP) remain unexplored. Here, we analyzed the conformational dynamics of the enzyme-NADH complex (cofactor), and the enzyme-NADH-DHAP complex (adduct), mapped the hydrogen-bond interactions for the complexes and pointed some structural determinants of the enzyme that emerge from these contacts to NADH and DHAP. Finally, we proposed a consistent mechanism for the conformational changes on the first step of the reversible redox conversion of dihydroxyacetone phosphate to glycerol 3-phosphate, indicating key residues and interactions that could be further explored in drug discovery.
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Affiliation(s)
| | | | | | | | | | | | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Belém, PA, Brazil
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10
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Halder AK, Dias Soeiro Cordeiro MN. Advanced in Silico Methods for the Development of Anti- Leishmaniasis and Anti-Trypanosomiasis Agents. Curr Med Chem 2020; 27:697-718. [DOI: 10.2174/0929867325666181031093702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/24/2018] [Accepted: 09/19/2018] [Indexed: 11/22/2022]
Abstract
Leishmaniasis and trypanosomiasis occur primarily in undeveloped countries and account
for millions of deaths and disability-adjusted life years. Limited therapeutic options, high toxicity of
chemotherapeutic drugs and the emergence of drug resistance associated with these diseases demand
urgent development of novel therapeutic agents for the treatment of these dreadful diseases. In the last
decades, different in silico methods have been successfully implemented for supporting the lengthy and
expensive drug discovery process. In the current review, we discuss recent advances pertaining to in
silico analyses towards lead identification, lead modification and target identification of antileishmaniasis
and anti-trypanosomiasis agents. We describe recent applications of some important in
silico approaches, such as 2D-QSAR, 3D-QSAR, pharmacophore mapping, molecular docking, and so
forth, with the aim of understanding the utility of these techniques for the design of novel therapeutic
anti-parasitic agents. This review focuses on: (a) advanced computational drug design options; (b) diverse
methodologies - e.g.: use of machine learning tools, software solutions, and web-platforms; (c)
recent applications and advances in the last five years; (d) experimental validations of in silico predictions;
(e) virtual screening tools; and (f) rationale or justification for the selection of these in silico
methods.
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Affiliation(s)
- Amit Kumar Halder
- LAQV@ REQUIMTE/Department of Chemistry and Biochemistry, University of Porto, Porto 4169-007, Portugal
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11
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Balanco JMF, Sussmann RAC, Verdaguer IB, Gabriel HB, Kimura EA, Katzin AM. Tocopherol biosynthesis in Leishmania ( L.) amazonensis promastigotes. FEBS Open Bio 2019; 9:743-754. [PMID: 30984548 PMCID: PMC6443866 DOI: 10.1002/2211-5463.12613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 01/25/2023] Open
Abstract
Leishmaniasis is a neglected disease caused by a trypanosomatid protozoan of the genus Leishmania. Most drugs used to treat leishmaniasis are highly toxic, and the emergence of drug‐resistant strains has been observed. Therefore, new therapeutic targets against leishmaniasis are required. Several isoprenoid compounds, including dolichols or ubiquinones, have been shown to be important for cell viability and proliferation in various trypanosomatid species. Here, we detected the biosynthesis of tocopherol in Leishmania (L.) amazonensis promastigotes in vitro through metabolic labelling with [1‐(n)‐3H]‐phytol. Subsequently, we confirmed the presence of vitamin E in the parasite by gas chromatography–mass spectrometry. Treatment with usnic acid or nitisinone, inhibitors of precursors of vitamin E synthesis, inhibited growth of the parasite in a concentration‐dependent manner. This study provides the first evidence of tocopherol biosynthesis in a trypanosomatid and suggests that inhibitors of the enzyme 4‐hydroxyphenylpyruvate dioxygenase may be suitable for use as antileishmanial compounds. Database The amino acid sequence of a conserved hypothetical protein [Leishmania mexicana MHOM/GT/2001/U1103] has been deposited in GenBank (CBZ28005.1)
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Affiliation(s)
- José Mário F Balanco
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
| | - Rodrigo A C Sussmann
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
| | - Ignasi B Verdaguer
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
| | - Heloisa B Gabriel
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
| | - Emilia A Kimura
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
| | - Alejandro M Katzin
- Department of Parasitology Institute of Biomedical Sciences University of São Paulo Brazil
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12
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Maggi M, Scotti C. Enzymes in Metabolic Anticancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:173-199. [PMID: 31482500 DOI: 10.1007/978-981-13-7709-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cancer treatment has greatly improved over the last 50 years, but it remains challenging in several cases. Useful therapeutic targets are normally unique peculiarities of cancer cells that distinguish them from normal cells and that can be tackled with appropriate drugs. It is now known that cell metabolism is rewired during tumorigenesis and metastasis as a consequence of oncogene activation and oncosuppressors inactivation, leading to a new cellular homeostasis typically directed towards anabolism. Because of these modifications, cells can become strongly or absolutely dependent on specific substrates, like sugars, lipids or amino acids. Cancer addictions are a relevant target for therapy, as removal of an essential substrate can lead to their selective cell-cycle arrest or even to cell death, leaving normal cells untouched. Enzymes can act as powerful agents in this respect, as demonstrated by asparaginase, which has been included in the treatment of Acute Lymphoblastic Leukemia for half a century. In this review, a short outline of cancer addictions will be provided, focusing on the main cancer amino acid dependencies described so far. Therapeutic enzymes which have been already experimented at the clinical level will be discussed, along with novel potential candidates that we propose as new promising molecules. The intrinsic limitations of their present molecular forms, along with molecular engineering solutions to explore, will also be presented.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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13
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Alonso A, Larraga V, Alcolea PJ. The contribution of DNA microarray technology to gene expression profiling in Leishmania spp.: A retrospective view. Acta Trop 2018; 187:129-139. [PMID: 29746872 DOI: 10.1016/j.actatropica.2018.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/04/2018] [Accepted: 05/06/2018] [Indexed: 01/15/2023]
Abstract
The first completed genome project of any living organism, excluding viruses, was of the gammaproteobacteria Haemophilus influenzae in 1995. Until the last decade, genome sequencing was very tedious because genome survey sequences (GSS) and/or expressed sequence tags (ESTs) belonging to plasmid, cosmid, and artificial chromosome genome libraries had to be sequenced and assembled in silico. No genome is completely assembled because gaps and unassembled contigs are always remaining. However, most represent an organism's whole genome from a practical point of view. The first genome sequencing projects of trypanosomatid parasites Leishmania major, Trypanosoma cruzi, and T. brucei were completed in 2005 following those strategies. The functional genomics era developed on the basis of microarray technology and has been continuously evolving. In the case of the genus Leishmania, substantial information about differentiation in the digenetic life cycle of the parasite has been obtained. More recently, next generation sequencing has revolutionized genome sequencing and functional genomics, leading to more sensitive and accurate results by using much fewer resources. Though this new technology is more advantageous, it does not invalidate microarray results. In fact, promising vaccine candidates and drug targets have been found by means of microarray-based screening and preliminary proof-of-concept tests.
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Structure-Based Discovery and Synthesis of Potential Transketolase Inhibitors. Molecules 2018; 23:molecules23092116. [PMID: 30142874 PMCID: PMC6225308 DOI: 10.3390/molecules23092116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 01/09/2023] Open
Abstract
Transketolase (TKL) plays a key role in plant photosynthesis and has been predicted to be a potent herbicide target. Homology modeling and molecular dynamics simulation were used to construct a target protein model. A target-based virtual screening was developed to discover novel potential transketolase inhibitors. Based on the receptor transketolase 1 and a target-based virtual screening combined with structural similarity, six new compounds were selected from the ZINC database. Among the structural leads, a new compound ZINC12007063 was identified as a novel inhibitor of weeds. Two novel series of carboxylic amide derivatives were synthesized, and their structures were rationally identified by NMR and HRMS. Biological evaluation of the herbicidal and antifungal activities indicated that the compounds 4u and 8h were the most potent herbicidal agents, and they also showed potent fungicidal activity with a relatively broad-spectrum. ZINC12007063 was identified as a lead compound of potential transketolase inhibitors, 4u and 8h which has the herbicidal and antifungal activities were synthesized based on ZINC12007063. This study lays a foundation for the discovery of new pesticides.
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15
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Evolutionary Perspectives of Genotype-Phenotype Factors in Leishmania Metabolism. J Mol Evol 2018; 86:443-456. [PMID: 30022295 DOI: 10.1007/s00239-018-9857-5] [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: 02/13/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
The sandfly midgut and the human macrophage phagolysosome provide antagonistic metabolic niches for the endoparasite Leishmania to survive and populate. Although these environments fluctuate across developmental stages, the relative changes in both these environments across parasite generations might remain gradual. Such environmental restrictions might endow parasite metabolism with a choice of specific genotypic and phenotypic factors that can constrain enzyme evolution for successful adaptation to the host. With respect to the available cellular information for Leishmania species, for the first time, we measure the relative contribution of eight inter-correlated predictors related to codon usage, GC content, gene expression, gene length, multi-functionality, and flux-coupling potential of an enzyme on the evolutionary rates of singleton metabolic genes and further compare their effects across three Leishmania species. Our analysis reveals that codon adaptation, multi-functionality, and flux-coupling potential of an enzyme are independent contributors of enzyme evolutionary rates, which can together explain a large variation in enzyme evolutionary rates across species. We also hypothesize that a species-specific occurrence of duplicated genes in novel subcellular locations can create new flux routes through certain singleton flux-coupled enzymes, thereby constraining their evolution. A cross-species comparison revealed both common and species-specific genes whose evolutionary divergence was constrained by multiple independent factors. Out of these, previously known pharmacological targets and virulence factors in Leishmania were identified, suggesting their evolutionary reasons for being important survival factors to the parasite. All these results provide a fundamental understanding of the factors underlying adaptive strategies of the parasite, which can be further targeted.
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Sinha R, C MM, Raghwan, Das S, Das S, Shadab M, Chowdhury R, Tripathy S, Ali N. Genome Plasticity in Cultured Leishmania donovani: Comparison of Early and Late Passages. Front Microbiol 2018; 9:1279. [PMID: 30018594 PMCID: PMC6037818 DOI: 10.3389/fmicb.2018.01279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
Leishmania donovani possesses a complex heteroxenic life cycle where infective metacyclic promastigotes are pre-adapted to infect their host and cope up with intracellular stress. Exploiting the similarities between cultured and sandfly derived promastigotes, we used early and late passage cultured promastigotes to show specific changes at genome level which compromise pathogen fitness reflected in gene expression and infection studies. The pathogen loses virulence mostly via transcriptional and translational regulations and long-time cultivation makes them struggle to convert to virulent metacyclics. At the genomic level very subtle plasticity was observed between the early and the late passages mostly in defense-related, nutrient acquisition and signal transduction genes. Chromosome Copy number variation is seen in the early and late passages involving several genes that may be playing a role in pathogenicity. Our study highlights the importance of ABC transporters and calpain like cysteine proteases in parasite virulence in cultured promastigotes. Interestingly, these proteins are emerging as important patho-adaptive factors in clinical isolates of Leishmania. We found that the currently available genome of Leishmania in the NCBI database are from late passages. Our early passage genome can act as a reference for future studies on virulent isolates of Leishmania. The annotated leads from this study can be used for virulence surveillance and therapeutic studies in the Indian subcontinent.
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Affiliation(s)
- Roma Sinha
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mathu Malar C
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Raghwan
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhadeep Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Sonali Das
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mohammad Shadab
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rukhsana Chowdhury
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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17
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Nayak A, Akpunarlieva S, Barrett M, Burchmore R. A defined medium for Leishmania culture allows definition of essential amino acids. Exp Parasitol 2018; 185:39-52. [PMID: 29326050 DOI: 10.1016/j.exppara.2018.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 10/18/2022]
Abstract
Axenic culture of Leishmania is generally performed in rich, serum-supplemented media which sustain robust growth over multiple passages. The use of such undefined media, however, obscures proteomic analyses and confounds the study of metabolism. We have established a simple, defined culture medium that supports the sustained growth of promastigotes over multiple passages and which yields parasites that have similar infectivity to macrophages to parasites grown in a conventional semi-defined medium. We have exploited this medium to investigate the amino acid requirements of promastigotes in culture and have found that phenylalanine, tryptophan, arginine, leucine, lysine and valine are essential for viability in culture. Most of the 20 proteogenic amino acids promote growth of Leishmania promastigotes, with the exception of alanine, asparagine, and glycine. This defined medium will be useful for further studies of promastigote substrate requirements, and will facilitate future proteomic and metabolomic analyses.
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Affiliation(s)
- Archana Nayak
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Snezhana Akpunarlieva
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michael Barrett
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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18
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Gomes MN, Alcântara LM, Neves BJ, Melo-Filho CC, Freitas-Junior LH, Moraes CB, Ma R, Franzblau SG, Muratov E, Andrade CH. Computer-aided discovery of two novel chalcone-like compounds active and selective against Leishmania infantum. Bioorg Med Chem Lett 2017; 27:2459-2464. [PMID: 28434763 PMCID: PMC6020026 DOI: 10.1016/j.bmcl.2017.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 01/09/2023]
Abstract
Leishmaniasis are infectious diseases caused by parasites of genus Leishmania that affect affects 12 million people in 98 countries mainly in Africa, Asia, and Latin America. Effective treatments for this disease are urgently needed. In this study, we present a computer-aided approach to investigate a set of 32 recently synthesized chalcone and chalcone-like compounds to act as antileishmanial agents. As a result, nine most promising compounds and three potentially inactive compounds were experimentally evaluated against Leishmania infantum amastigotes and mammalian cells. Four compounds exhibited EC50 in the range of 6.2-10.98μM. In addition, two compounds, LabMol-65 and LabMol-73, exhibited cytotoxicity in macrophages >50μM that resulted in better selectivity compared to standard drug amphotericin B. These two compounds also demonstrated low cytotoxicity and high selectivity towards Vero cells. The results of target fishing followed by homology modeling and docking studies suggest that these chalcone compounds could act in Leishmania because of their interaction with cysteine proteases, such as procathepsin L. Finally, we have provided structural recommendations for designing new antileishmanial chalcones.
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Affiliation(s)
- Marcelo N Gomes
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil
| | - Laura M Alcântara
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil. d Instituto Butantan - Sao Paulo, Sao Paulo 05503-900, Brazil
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil; Postgraduate Program on Society, Technology and Enviroment, University Center of Anápolis/UniEVANGELICA, Anápolis, Goiás 75083-515, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil
| | | | - Carolina B Moraes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil. d Instituto Butantan - Sao Paulo, Sao Paulo 05503-900, Brazil
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States; Department of Chemical Technology, Odessa National Polytechnic University, Odessa 65000, Ukraine; Currently Visiting Professor at Universidade Federal de Goias, Goiania, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goias, Rua 240, Qd.87, Setor Leste Universitário, Goiania, Goias 74605-510, Brazil.
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Rationale for selection of developmentally regulated genes as vaccine candidates against Leishmania infantum infection. Vaccine 2016; 34:5474-5478. [DOI: 10.1016/j.vaccine.2016.08.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 01/20/2023]
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20
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Proteome profiling of the growth phases of Leishmania pifanoi promastigotes in axenic culture reveals differential abundance of immunostimulatory proteins. Acta Trop 2016; 158:240-247. [PMID: 26992294 DOI: 10.1016/j.actatropica.2016.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/28/2016] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
Abstract
Leishmaniasis is a term that encompasses a compendium of neglected tropical diseases caused by dimorphic and digenetic protozoan parasites from the genus Leishmania (Kinetoplastida: Trypanosomatidae). The clinical manifestations of neotropical cutaneous leishmaniasis (NCL) caused by Leishmania pifanoi and other species of the "Leishmania mexicana complex" mainly correspond to anergic diffuse cutaneous leishmaniasis (ADCL), which is the origin of considerable morbidity. Despite the outstanding advances in the characterization of the trypanosomatid genomes and proteomes, the biology of this species has been scarcely explored. However, the close relation of L. pifanoi to the sequenced species L. mexicana and others included in the "L. mexicana complex" allowed us to perform a two-dimension electrophoresis (2DE) approach to the promastigote proteome at the differential expression level. Protein identifications were performed by matrix-assisted laser desorption-ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). This insight has revealed similarities and differences between L. pifanoi and other species responsible for cutaneous and visceral leishmaniasis. Interestingly, certain proteins that were previously described as immunostimulatory (elongation factor 1β, trypanothione peroxidase, heat shock protein 70, enolase, GDP-forming succinyl-CoA and aldehyde dehydrogenase) are more abundant in the final growth stages of promastigotes (late-logarithmic and/or stationary phase) in the case of L. pifanoi.
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Alcolea PJ, Alonso A, Domínguez M, Parro V, Jiménez M, Molina R, Larraga V. Influence of the Microenvironment in the Transcriptome of Leishmania infantum Promastigotes: Sand Fly versus Culture. PLoS Negl Trop Dis 2016; 10:e0004693. [PMID: 27163123 PMCID: PMC4862625 DOI: 10.1371/journal.pntd.0004693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 04/14/2016] [Indexed: 01/04/2023] Open
Abstract
Zoonotic visceral leishmaniasis is a vector-borne disease caused by Leishmania infantum in the Mediterranean Basin, where domestic dogs and wild canids are the main reservoirs. The promastigote stage replicates and develops within the gut of blood-sucking phlebotomine sand flies. Mature promastigotes are injected in the dermis of the mammalian host and differentiate into the amastigote stage within parasitophorous vacuoles of phagocytic cells. The major vector of L. infantum in Spain is Phlebotomus perniciosus. Promastigotes are routinely axenized and cultured to mimic in vitro the conditions inside the insect gut, which allows for most molecular, cellular, immunological and therapeutical studies otherwise inviable. Culture passages are known to decrease infectivity, which is restored by passage through laboratory animals. The most appropriate source of promastigotes is the gut of the vector host but isolation of the parasite is technically challenging. In fact, this option is not viable unless small samples are sufficient for downstream applications like promastigote cultures and nucleic acid amplification. In this study, in vitro infectivity and differential gene expression have been studied in cultured promastigotes at the stationary phase and in promastigotes isolated from the stomodeal valve of the sand fly P. perniciosus. About 20 ng RNA per sample could be isolated. Each sample contained L. infantum promastigotes from 20 sand flies. RNA was successfully amplified and processed for shotgun genome microarray hybridization analysis. Most differentially regulated genes are involved in regulation of gene expression, intracellular signaling, amino acid metabolism and biosynthesis of surface molecules. Interestingly, meta-analysis by hierarchical clustering supports that up-regulation of 22.4% of the differentially regulated genes is specifically enhanced by the microenvironment (i.e. sand fly gut or culture). The correlation between cultured and naturally developed promastigotes is strong but not very high (Pearson coefficient R2 = 0.727). Therefore, the influence of promastigote culturing should be evaluated case-by-case in experimentation. The protozoan parasite Leishmania infantum causes visceral leishmaniasis in humans and is responsible for a recent outbreak reported in central Spain. Domestic dogs and wild canids are the main reservoirs. The life cycle of the parasite involves two stages and two hosts. The motile promastigote stage differentiates within the gut of the sand fly vector host and develops into non-motile amastigotes within phagocytes of the mammalian host. Promastigotes are routinely cultured in liquid media because it is assumed that they mimic the conditions within the gut of the insect. Therefore, the culture model is used in most studies about the biology of the parasite, pathogenesis and development of vaccines and new compounds for treatment. Isolating promastigotes from the natural microenvironment (i.e. the vector host) is desirable but technically challenging. We were able to perform a high-throughput analysis of gene expression thanks to mRNA amplification. The over-expressed genes detected may influence life cycle progression depending on the promastigote microenvironment (i.e. culture or vector host). Upcoming studies based on these results may reveal new therapeutic targets or vaccine candidates. Our results suggest that evaluating the influence of cultures in experimentation is convenient.
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Affiliation(s)
- Pedro J. Alcolea
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
| | - Ana Alonso
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mercedes Domínguez
- Unidad de Inmunología Microbiana, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Víctor Parro
- Laboratorio de Ecología Molecular, Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial “Esteban Terradas”—Consejo Superior de Investigaciones Científicas, Torrejón de Ardoz, Madrid, Spain
| | - Maribel Jiménez
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ricardo Molina
- Unidad de Entomología Médica, Servicio de Parasitología, Centro Nacional de Microbiología, Virología e Inmunología Sanitarias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Vicente Larraga
- Laboratorio de Parasitología Molecular, Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Nasir N, Anant A, Vyas R, Biswal BK. Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities. Sci Rep 2016; 6:18880. [PMID: 26738801 PMCID: PMC4703992 DOI: 10.1038/srep18880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/30/2015] [Indexed: 01/07/2023] Open
Abstract
Aminotransferases of subfamily Iβ, which include histidinol phosphate aminotransferases (HspATs) and aromatic amino acid aminotransferases (ArATs), are structurally similar but possess distinct substrate specificities. This study, encompassing structural and biochemical characterisation of HspAT and ArAT from Mycobacterium tuberculosis demonstrates that the residues lining the substrate binding pocket and N-terminal lid are the primary determinants of their substrate specificities. In mHspAT, hydrophilic residues in the substrate binding pocket and N-terminal lid allow the entry and binding of its preferential substrate, Hsp. On the other hand, the hydrophobic nature of both the substrate binding pocket and the N-terminal lid of mArAT is responsible for the discrimination of a polar substrate such as Hsp, while facilitating the binding of Phe and other aromatic residues such as Tyr and Trp. In addition, the present study delineates the ligand induced conformational rearrangements, providing insights into the plasticity of aminotransferases. Furthermore, the study also demonstrates that the adventitiously bound ligand 2-(N-morpholino)ethanesulfonic acid (MES) is indeed a specific inhibitor of HspAT. These results suggest that previously untapped morpholine-ring scaffold compounds could be explored for the design of new anti-TB agents.
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Affiliation(s)
- Nazia Nasir
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Avishek Anant
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Rajan Vyas
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Bichitra Kumar Biswal
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India,
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Westrop GD, Williams RAM, Wang L, Zhang T, Watson DG, Silva AM, Coombs GH. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism. PLoS One 2015; 10:e0136891. [PMID: 26368322 PMCID: PMC4569581 DOI: 10.1371/journal.pone.0136891] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/09/2015] [Indexed: 01/09/2023] Open
Abstract
Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.
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Affiliation(s)
- Gareth D. Westrop
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Roderick A. M. Williams
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, United Kingdom
| | - Lijie Wang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Tong Zhang
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Ana Marta Silva
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Graham H. Coombs
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail:
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