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Sheikh SY, Hassan F, Shukla D, Bala S, Faruqui T, Akhter Y, Khan AR, Nasibullah M. A review on potential therapeutic targets for the treatment of leishmaniasis. Parasitol Int 2024; 100:102863. [PMID: 38272301 DOI: 10.1016/j.parint.2024.102863] [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: 05/30/2023] [Revised: 12/22/2023] [Accepted: 01/21/2024] [Indexed: 01/27/2024]
Abstract
Leishmania, a protozoan parasite, is responsible for the occurrence of leishmaniasis, a disease that is prevalent in tropical regions. Visceral Leishmaniasis (VL), also known as kala-azar in Asian countries, is one of the most significant forms of VL, along with Cutaneous Leishmaniasis (CL) and Mucocutaneous Leishmaniasis (ML). Management of this condition typically entails the use of chemotherapy as the sole therapeutic option. The current treatments for leishmaniasis present several drawbacks, including a multitude of side effects, prolonged treatment duration, disparate efficacy across different regions, and the emergence of resistance. To address this urgent need, it is imperative to identify alternative treatments that are both safer and more effective. The identification of appropriate pharmacological targets in conjunction with biological pathways constitutes the initial stage of drug discovery. In this review, we have addressed the key metabolic pathways that represent potential pharmacological targets as well as prominent treatment options for leishmaniasis.
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Affiliation(s)
- Sabahat Yasmeen Sheikh
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Firoj Hassan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Deepanjali Shukla
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Shashi Bala
- Department of Chemistry, Lucknow University, Lucknow 226026, India
| | - Tabrez Faruqui
- Department of Biosciences, Integral University, Lucknow 226026, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India
| | - Malik Nasibullah
- Department of Chemistry, Integral University, Dasauli, Kursi road, Lucknow 226026, India.
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Pal R, Teli G, Akhtar MJ, Matada GSP. Synthetic product-based approach toward potential antileishmanial drug development. Eur J Med Chem 2024; 263:115927. [PMID: 37976706 DOI: 10.1016/j.ejmech.2023.115927] [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: 08/19/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Leishmaniasis is a parasitic disease and is categorized as a tropically neglected disease (NTD) with no effective vaccines available. The available chemotherapeutics against leishmaniasis are associated with an increase in the incidence of toxicity and drug resistance. Consequently, targeting metabolic pathways and enzymes of parasites which differs from the mammalian host can be exploited to treat and overcome the resistance. The classical methods of identifying the structural fragments and the moieties responsible for the biological activities from the standard compounds and their modification are options for developing more effective novel compounds. Significant progress has been made in refining the development of potent non-toxic molecules and addressing the limitations of the current treatment available. Several examples of synthetic product-based approach utilizing their core heterocyclic rings including furan, pyrrole, thiazole, imidazole, pyrazole, triazole, quinazoline, quinoline, pyrimidine, coumarin, indole, acridine, oxadiazole, purine, chalcone, carboline, phenanthrene and metal containing derivatives and their structure-activity relationships are discussed in this review. It also analyses the groups/fragments interacting with the host cell receptors and will support the medicinal chemists with novel antileishmanial agents.
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Affiliation(s)
- Rohit Pal
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Ghanshyam Teli
- School of Pharmacy, Sangam University, Atoon, Bhilwara, 311001, Rajasthan, India
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, National University of Science and Technology, PO 620, PC 130, Azaiba Bousher, Muscat, Sultanate of Oman
| | - Gurubasavaraja Swamy Purawarga Matada
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India.
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Zhang Y, Zhao G, Yu L, Wang X, Meng Y, Mao J, Fu Z, Yin Y, Li J, Wang X, Guo C. Heat-shock protein 90α protects NME1 against degradation and suppresses metastasis of breast cancer. Br J Cancer 2023; 129:1679-1691. [PMID: 37731021 PMCID: PMC10645775 DOI: 10.1038/s41416-023-02435-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/28/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND NME1 has been exploited as a potential translational target for decades. Substantial efforts have been made to upregulate the expression of NME1 and restore its anti-metastasis function in metastatic cancer. METHODS Cycloheximide (CHX) chase assay was used to measure the steady-state protein stability of NME1 and HSP90α. The NME1-associating proteins were identified by immunoprecipitation combined with mass spectrometric analysis. Gene knockdown and overexpression were employed to examine the impact of HSP90AA1 on intracellular NME1 degradation. The motility and invasiveness of breast cancer cells were examined in vitro using wound healing and transwell invasion assays. The orthotopic spontaneous metastasis and intra-venous experimental metastasis assays were used to test the formation of metastasis in vivo, respectively. RESULTS HSP90α interacts with NME1 and increases NME1 lifetime by impeding its ubiquitin-proteasome-mediated degradation. HSP90α overexpression significantly inhibits the metastatic potential of breast cancer cells in vitro and in vivo. A novel cell-permeable peptide, OPT22 successfully mimics the HSP90α function and prolongs the life span of endogenous NME1, resulting in reduced metastasis of breast cancer. CONCLUSION These results not only reveal a new mechanism of NME1 degradation but also pave the way for the development of new and effective approaches to metastatic cancer therapy.
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Affiliation(s)
- Yanchao Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, People's Republic of China
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, People's Republic of China
| | - Guomeng Zhao
- Institute of Modern Biology, Nanjing University, Nanjing, People's Republic of China
| | - Liting Yu
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, People's Republic of China
| | - Xindong Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yao Meng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jinlei Mao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing People's Hospital, Nanjing, People's Republic of China
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing People's Hospital, Nanjing, People's Republic of China.
| | - Jinyao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, People's Republic of China.
| | - Xun Wang
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
| | - Changying Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, People's Republic of China.
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Galceran F, Digirolamo FA, Rengifo M, Reigada C, Saye M, Maciel BJ, Estecho IG, Errasti AE, Pereira CA, Miranda MR. Identifying inhibitors of Trypanosoma cruzi nucleoside diphosphate kinase 1 as potential repurposed drugs for Chagas' disease. Biochem Pharmacol 2023; 216:115766. [PMID: 37634596 DOI: 10.1016/j.bcp.2023.115766] [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: 05/30/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Trypanosoma cruzi is the causative agent of Chagas' disease, an endemic and neglected disease. The treatment is limited to only two drugs, benznidazole (BZL) and nifurtimox (NFX), introduced more than fifty years ago and no new advances have been made since then. Nucleoside diphosphate kinases (NDPK) are key metabolic enzymes which have gained interest as drug targets of pathogen organisms. Taking advantage of the computer-assisted drug repurposing approaches, in the present work we initiate a search of potential T. cruzi nucleoside diphosphate kinase 1 (TcNDPK1) inhibitors over an ∼ 12,000 compound structures database to find drugs targeted to this enzyme with trypanocidal activity. Four medicines were selected and evaluated in vitro, ketorolac (KET, an anti-inflamatory), dutasteride (DUT, used to treat benign prostatic hyperplasia), nebivolol and telmisartan (NEB and TEL, used to treat high blood pressure). The four compounds were weak inhibitors and presented different trypanocidal effect on epimastigotes, trypomastigotes and intracellular stages. NEB and TEL were the most active drugs with increased effect on intracellular stages, (IC50 = 2.25 µM and 13.21 µM respectively), and selectivity indexes of 13.01 and 8.59 respectively, showing comparable effect to BZL, the first line drug for Chagas' disease treatment. In addition, both presented positive interactions when combined with BZL. Finally, transgenic epimastigotes with increased expression of TcNDPK1 were more resistant to TEL and NEB, suggesting that TcNDPK1 is at least one of the molecular targets. In view of the results, NEB and TEL could be repurposed medicines for Chagas' disease therapy.
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Affiliation(s)
- Facundo Galceran
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Fabio A Digirolamo
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Marcos Rengifo
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Chantal Reigada
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Melisa Saye
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Belen J Maciel
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Ivana G Estecho
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andrea E Errasti
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Claudio A Pereira
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Mariana R Miranda
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina.
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Dhingra N, Kapoor K, Sharma S, Saxena A. Towards further understanding the structural insights of isoxazoles analogues against leishmaniasis using QSAR, molecular docking and molecular dynamics model. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Miranda MR, Sayé M, Reigada C, Galceran F, Rengifo M, Maciel BJ, Digirolamo FA, Pereira CA. Revisiting trypanosomatid nucleoside diphosphate kinases. Mem Inst Oswaldo Cruz 2022; 116:e210339. [PMID: 35170678 PMCID: PMC8833001 DOI: 10.1590/0074-02760210339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND An increasing amount of research has led to the positioning of nucleoside diphosphate kinases (NDPK/NDK) as key metabolic enzymes among all organisms. They contribute to the maintenance the intracellular di- and tri- phosphate nucleoside homeostasis, but they also are involved in widely diverse processes such as gene regulation, apoptosis, signal transduction and many other regulatory roles. OBJETIVE Examine in depth the NDPKs of trypanosomatid parasites responsible for devastating human diseases (e.g., Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp.) which deserve special attention. METHODS The earliest and latest advances in the topic were explored, focusing on trypanosomatid NDPK features, multifunctionality and suitability as molecular drug targets. FINDINGS Trypanosomatid NDPKs appear to play functions different from their host counterparts. Evidences indicate that they would perform key roles in the parasite metabolism such as nucleotide homeostasis, drug resistance, DNA damage responses and gene regulation, as well as host-parasite interactions, infection, virulence and immune evasion, placing them as attractive pharmacological targets. MAIN CONCLUSIONS NDPKs are very interesting multifunctional enzymes. In the present review, the potential of trypanosomatid NDPKs was highlighted, raising awareness of their value not only with respect to parasite biology but also as molecular targets.
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Affiliation(s)
- Mariana R Miranda
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina,+ Corresponding author: /
| | - Melisa Sayé
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Chantal Reigada
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Facundo Galceran
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Marcos Rengifo
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Belen J Maciel
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Fabio A Digirolamo
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Claudio A Pereira
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A Lanari, Buenos Aires, Argentina,Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas, Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
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7
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Gomez Barroso JA, Miranda MR, Pereira CA, Garratt RC, Aguilar CF. X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure. Acta Crystallogr D Struct Biol 2022; 78:30-42. [PMID: 34981759 DOI: 10.1107/s2059798321011219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
Trypanosoma cruzi is a flagellated protozoan parasite that causes Chagas disease, which represents a serious health problem in the Americas. Nucleoside diphosphate kinases (NDPKs) are key enzymes that are implicated in cellular energy management. TcNDPK1 is the canonical isoform in the T. cruzi parasite. TcNDPK1 has a cytosolic, perinuclear and nuclear distribution. It is also found in non-membrane-bound filaments adjacent to the nucleus. In the present work, X-ray diffraction and in vivo studies of TcNDPK1 are described. The structure reveals a novel, multi-hexameric, left-handed helical oligomer structure. The results of directed mutagenesis studies led to the conclusion that the microscopic TcNDPK1 granules observed in vivo in T. cruzi parasites are made up by the association of TcNDPK1 oligomers. In the absence of experimental data, analysis of the interactions in the X-ray structure of the TcNDPK1 oligomer suggests the probable assembly and disassembly steps: dimerization, assembly of the hexamer as a trimer of dimers, hexamer association to generate the left-handed helical oligomer structure and finally oligomer association in a parallel manner to form the microscopic TcNDPK1 filaments that are observed in vivo in T. cruzi parasites. Oligomer disassembly takes place on the binding of substrate in the active site of TcNDPK1, leading to dissociation of the hexamers. This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1.
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Affiliation(s)
- Juan Arturo Gomez Barroso
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Mariana Reneé Miranda
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Claudio Alejandro Pereira
- Laboratorio de Parasitología Molecular, Instituto de Investigaciones Médicas (IDIM), Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Richard Charles Garratt
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense No. 400, São Carlos, São Paulo 13566-590, Brazil
| | - Carlos Fernando Aguilar
- Laboratorio de Biología Molecular Estructural, Universidad Nacional de San Luis, Ejército de los Andes 950, 5700 San Luis, Argentina
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Gupta A, Sinha KM, Abdin MZ, Puri N, Selvapandiyan A. NDK/NME proteins: a host-pathogen interface perspective towards therapeutics. Curr Genet 2021; 68:15-25. [PMID: 34480234 DOI: 10.1007/s00294-021-01198-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022]
Abstract
No effective vaccine is available for any parasitic disease. The treatment to those is solely dependent on chemotherapy, which is always threatened due to development of drug resistance in bugs. This warrants identification of new drug targets. Here, we discuss Nucleoside diphosphate kinases (NDKs) of pathogens that alter host's intra and extracellular environment, as novel drug targets to simultaneously tackle multiple pathogens. NDKs having diverse functions, are highly conserved among prokaryotes and eukaryotes (the mammal NDKs are called NMEs [non-metastatic enzymes]). However, NDKs and NMEs have been separately analysed in the past for their structure and functions. The role of NDKs of pathogen in modulation of inflammation, phagocytosis, apoptosis, and ROS generation in host is known. Conversely, its combined contribution in host-pathogen interaction has not been studied yet. Through the sequence and domain analysis, we found that NDKs can be classified in two groups. One group comprised NMEs 1-4 and few NDKs of select essential protozoan parasites and the bacterium Mycobacterium tuberculosis. The other group included NME7 and the other NDKs of those parasites, posing challenges in the development of drugs specifically targeting pathogen NDKs, without affecting NME7. However, common drugs targeting group 2 NDKs of pathogens can be designed, as NME7 of group 2 is expressed only in ciliated host cells. This review thus analyses comparatively for the first time the structures and functions of human NMEs and pathogen NDKs and predicts the possibilities of NDKs as drug targets. In addition, pathogen NDKs have been now provided a nomenclature in alignment with the NMEs of humans.
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Affiliation(s)
- Ankit Gupta
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi, 110062, India
| | - Krishna Murari Sinha
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, Haryana, 122413, India
| | - Malik Z Abdin
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Niti Puri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Angamuthu Selvapandiyan
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi, 110062, India.
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Herrera-Acevedo C, Perdomo-Madrigal C, Muratov EN, Scotti L, Scotti MT. Discovery of Alternative Chemotherapy Options for Leishmaniasis through Computational Studies of Asteraceae. ChemMedChem 2021; 16:1234-1245. [PMID: 33336460 DOI: 10.1002/cmdc.202000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a complex disease caused by over 20 Leishmania species that primarily affects populations with poor socioeconomic conditions. Currently available drugs for treating leishmaniasis include amphotericin B, paromomycin, and pentavalent antimonials, which have been associated with several limitations, such as low efficacy, the development of drug resistance, and high toxicity. Natural products are an interesting source of new drug candidates. The Asteraceae family includes more than 23 000 species worldwide. Secondary metabolites that can be found in species from this family have been widely explored as potential new treatments for leishmaniasis. Recently, computational tools have become more popular in medicinal chemistry to establish experimental designs, identify new drugs, and compare the molecular structures and activities of novel compounds. Herein, we review various studies that have used computational tools to examine various compounds identified in the Asteraceae family in the search for potential drug candidates against Leishmania.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Camilo Perdomo-Madrigal
- School of Science, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 n° 55-37, Bogotá D.C., Colombia
| | - Eugene N Muratov
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
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10
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Nguyen S, Jovcevski B, Pukala TL, Bruning JB. Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase. FEBS J 2020; 288:2398-2417. [PMID: 33089641 DOI: 10.1111/febs.15607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals have been hindered by the limited knowledge of fundamental biological and structural mechanisms of A. fumigatus propagation. Biosynthesis of NTPs, the building blocks of DNA and RNA, is catalysed by NDK. An essential enzyme in A. fumigatus, NDK poses as an attractive target for novel antifungals. NDK exhibits broad substrate specificity across species, using both purines and pyrimidines, but the selectivity of such nucleosides in A. fumigatus NDK is unknown, impeding structure-guided inhibitor design. Structures of NDK in unbound- and NDP-bound states were solved, and NDK activity was assessed in the presence of various NTP substrates. We present the first instance of a unique substrate binding mode adopted by CDP and TDP specific to A. fumigatus NDK that illuminates the structural determinants of selectivity. Analysis of the oligomeric state reveals that A. fumigatus NDK adopts a hexameric assembly in both unbound- and NDP-bound states, contrary to previous reports suggesting it is tetrameric. Kinetic analysis revealed that ATP exhibited the greatest turnover rate (321 ± 33.0 s-1 ), specificity constant (626 ± 110.0 mm-1 ·s-1 ) and binding free energy change (-37.0 ± 3.5 kcal·mol-1 ). Comparatively, cytidine nucleosides displayed the slowest turnover rate (53.1 ± 3.7 s-1 ) and lowest specificity constant (40.2 ± 4.4 mm-1 ·s-1 ). We conclude that NDK exhibits nucleoside selectivity whereby adenine nucleosides are used preferentially compared to cytidine nucleosides, and these insights can be exploited to guide drug design. ENZYMES: Nucleoside-diphosphate kinase (EC 2.7.4.6). DATABASE: Structural data are available in the PDB database under the accession numbers: Unbound-NDK (6XP4), ADP-NDK (6XP7), GDP-NDK (6XPS), IDP-NDK (6XPU), UDP-NDK (6XPT), CDP-NDK (6XPW), TDP-NDK (6XPV).
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Affiliation(s)
- Stephanie Nguyen
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Australia
| | - Blagojce Jovcevski
- Adelaide Proteomics Centre, School of Physical Sciences, The University of Adelaide, Australia.,School of Agriculture, Food and Wine, The University of Adelaide, Australia
| | - Tara L Pukala
- Adelaide Proteomics Centre, School of Physical Sciences, The University of Adelaide, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Australia
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11
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Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Int J Mol Sci 2020; 21:ijms21186779. [PMID: 32947863 PMCID: PMC7554756 DOI: 10.3390/ijms21186779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/29/2022] Open
Abstract
Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Monomers are functionally independent from each other inside NDPK complexes and the nucleoside kinase catalytic mechanism involves transient phosphorylation of the conserved catalytic histidine. To be active, monomers must assemble into conserved head to tail dimers, which further assemble into hexamers or tetramers. The interfaces between these oligomeric states are very different but, surprisingly, the assembly structure barely affects the catalytic efficiency of the enzyme. While it has been shown that assembly into hexamers induces full formation of the catalytic site and stabilizes the complex, it is unclear why assembly into tetramers is required for function. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. However, we still lack the high resolution structural data of NDPK in complex with different partners, which is necessary for deciphering the mechanism of these diverse functions. In this review we discuss advances in the structure, folding and stability of NDPKs.
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12
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Synthesis of new N,S-acetal analogs derived from juglone with cytotoxic activity against Trypanossoma cruzi. J Bioenerg Biomembr 2020; 52:199-213. [PMID: 32418003 DOI: 10.1007/s10863-020-09834-8] [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: 09/06/2019] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
A series of 11 new N,S-acetal juglone derivatives were synthesized and evaluated against T. cruzi epimastigote forms. These compounds were obtained in good to moderate yields using a microwave irradiation protocol. Among all compounds, two N,S-acetal analogs, showed significant trypanocidal activity. Notably, one compound 11g exhibited selectivity index 10-fold higher than the reference drug benznidazole for epimastigote. The compound 11h was more effective for amastigote forms. Both prototypes exhibited S.I. higher than the benznidazole description. Thus, both compounds proving to be useful candidate molecules to further studies in infected animals.
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13
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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14
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Wang Y, Wang S, Nie X, Yang K, Xu P, Wang X, Liu M, Yang Y, Chen Z, Wang S. Molecular and structural basis of nucleoside diphosphate kinase-mediated regulation of spore and sclerotia development in the fungus Aspergillus flavus. J Biol Chem 2019; 294:12415-12431. [PMID: 31243100 DOI: 10.1074/jbc.ra119.007505] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
The fundamental biological function of nucleoside diphosphate kinase (NDK) is to catalyze the reversible exchange of the γ-phosphate between nucleoside triphosphate (NTP) and nucleoside diphosphate (NDP). This kinase also has functions that extend beyond its canonically defined enzymatic role as a phosphotransferase. However, the role of NDK in filamentous fungi, especially in Aspergillus flavus (A. flavus), is not yet known. Here we report that A. flavus has two NDK-encoding gene copies as assessed by qPCR. Using gene-knockout and complementation experiments, we found that AfNDK regulates spore and sclerotia development and is involved in plant virulence as assessed in corn and peanut seed-based assays. An antifungal test with the inhibitor azidothymidine suppressed AfNDK activity in vitro and prevented spore production and sclerotia formation in A. flavus, confirming AfNDK's regulatory functions. Crystallographic analysis of AfNDK, coupled with site-directed mutagenesis experiments, revealed three residues (Arg-104, His-117, and Asp-120) as key sites that contribute to spore and sclerotia development. These results not only enrich our knowledge of the regulatory role of this important protein in A. flavus, but also provide insights into the prevention of A. flavus infection in plants and seeds, as well as into the structural features relevant for future antifungal drug development.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sen Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyi Nie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kunlong Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Xu
- State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Xiuna Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengxin Liu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongshuai Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zhuo Chen
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; State Key Laboratory of Structural Chemistry and CAS Key Laboratory, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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15
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Dautant A, Henri J, Wales TE, Meyer P, Engen JR, Georgescauld F. Remodeling of the Binding Site of Nucleoside Diphosphate Kinase Revealed by X-ray Structure and H/D Exchange. Biochemistry 2019; 58:1440-1449. [PMID: 30785730 DOI: 10.1021/acs.biochem.8b01308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To be fully active and participate in the metabolism of phosphorylated nucleotides, most nucleoside diphosphate kinases (NDPKs) have to assemble into stable hexamers. Here we studied the role played by six intersubunit salt bridges R80-D93 in the stability of NDPK from the pathogen Mycobacterium tuberculosis ( Mt). Mutating R80 into Ala or Asn abolished the salt bridges. Unexpectedly, compensatory stabilizing mechanisms appeared for R80A and R80N mutants and we studied them by biochemical and structural methods. The R80A mutant crystallized into space group I222 that is unusual for NDPK, and its hexameric structure revealed the occurrence at the trimer interface of a stabilizing hydrophobic patch around the mutation. Functionally relevant, a trimer of the R80A hexamer showed a remodeling of the binding site. In this conformation, the cleft of the active site is more open, and then active His117 is more accessible to substrates. H/D exchange mass spectrometry analysis of the wild type and the R80A and R80N mutants showed that the remodeled region of the protein is highly solvent accessible, indicating that equilibrium between open and closed conformations is possible. We propose that such equilibrium occurs in vivo and explains how bulky substrates access the catalytic His117.
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Affiliation(s)
- Alain Dautant
- Université de Bordeaux , CNRS, Institut de Biochimie et Génétique Cellulaires, UMR5095 , 146 rue Léo Saignat , 33077 Bordeaux , France
| | - Julien Henri
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Philippe Meyer
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - John R Engen
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Florian Georgescauld
- Sorbonne Universités , UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France
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16
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Dumais M, Davies DR, Lin T, Staker BL, Myler PJ, Van Voorhis WC. Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties. Acta Crystallogr F Struct Biol Commun 2018; 74:373-384. [PMID: 29870023 PMCID: PMC5987747 DOI: 10.1107/s2053230x18007392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/16/2018] [Indexed: 01/13/2023] Open
Abstract
Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.
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Affiliation(s)
- Mitchell Dumais
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | | | - Tao Lin
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Bart L. Staker
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
| | - Peter J. Myler
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
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17
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Vijayakumar S, Das P. Recent progress in drug targets and inhibitors towards combating leishmaniasis. Acta Trop 2018; 181:95-104. [PMID: 29452111 DOI: 10.1016/j.actatropica.2018.02.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/24/2018] [Accepted: 02/11/2018] [Indexed: 12/22/2022]
Abstract
Lesihmaniasis is one of the major neglected tropical disease caused by the parasite of the genus Leishmania. The disease has more than one clinical forms and the visceral form is considered fatal. With the lack of potential vaccine, chemotherapy is the major treatment source considered for the control of the disease in the infected people. Drugs including amphotericin B and miltefosine are widely used for the treatment, however, development of resistance by the parasite towards the administered drug and high-toxicity of the drug are of major concern. Hence, more attention has been shown on identifying new targets, effective inhibitors, and better drug delivery system against the disease. This review deals with recent studies on drug targets and exploring their essentiality for the survival of Leishmania. Further, new inhibitors for those targets, novel anti-leishmanial peptides and vaccines against leishmaniasis were discussed. We believe that this pool of information will ease the researchers to gain knowledge and help in choosing right targets and design of new inhibitors against Leishmaniasis.
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18
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Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization. J Comput Aided Mol Des 2017; 31:547-562. [DOI: 10.1007/s10822-017-0022-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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19
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Pyrrole-indolinone SU11652 targets the nucleoside diphosphate kinase from Leishmania parasites. Biochem Biophys Res Commun 2017; 488:461-465. [PMID: 28499874 DOI: 10.1016/j.bbrc.2017.05.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/18/2023]
Abstract
Nucleoside diphosphate kinases (NDKs) are key enzymes in the purine-salvage pathway of trypanosomatids and have been associated with the maintenance of host-cell integrity for the benefit of the parasite, being potential targets for rational drug discovery and design. The NDK from Leishmania major (LmNDK) and mutants were expressed and purified to homogeneity. Thermal shift assays were employed to identify potential inhibitors for LmNDK. Calorimetric experiments, site-directed mutagenesis and molecular docking analysis were performed to validate the interaction and to evaluate the structural basis of ligand recognition. Furthermore, the anti-leishmanial activity of the newly identified and validated compound was tested in vitro against different Leishmania species. The molecule SU11652, a Sunitinib analog, was identified as a potential inhibitor for LmNDK and structural studies indicated that this molecule binds to the active site of LmNDK in a similar conformation to nucleotides, mimicking natural substrates. Isothermal titration calorimetry experiments combined with site-directed mutagenesis revealed that the residues H50 and H117, considered essential for catalysis, play an important role in ligand binding. In vitro cell studies showed that SU11652 had similar efficacy to Amphotericin b against some Leishmania species. Together, our results indicate the pyrrole-indolinone SU11652 as a promising scaffold for the rational design of new drugs targeting the enzyme NDK from Leishmania parasites.
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20
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Santana AG, Gracher AHP, Rüdiger AL, Zanchin NIT, Carvalho PC, Cipriani TR, de Arruda Campos Brasil de Souza T. Identification of potential targets for an anticoagulant pectin. J Proteomics 2017; 151:243-250. [DOI: 10.1016/j.jprot.2016.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/25/2016] [Accepted: 06/09/2016] [Indexed: 01/03/2023]
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21
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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22
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Vieira PS, de Giuseppe PO, de Oliveira AHC, Murakami MT. The role of the C-terminus and Kpn loop in the quaternary structure stability of nucleoside diphosphate kinase from Leishmania parasites. J Struct Biol 2015; 192:336-341. [PMID: 26410384 DOI: 10.1016/j.jsb.2015.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 01/18/2023]
Abstract
Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. Moreover, it is secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. Here, we report the crystal structures of three mutants of the NDK from Leishmania major (LmNDK) that affects the stability of the hexameric biological assembly including P95S, Δ5Ct (lacking the last five residues) and the double mutant P100S/Δ5Ct. Although P95S and Δ5Ct variants conserve the hexameric structure of the wild-type protein, the double mutant becomes a dimer as shown by in solution studies. Free energy calculation of dimer-dimer interfaces and enzymatic assays indicate that P95S, Δ5Ct and P100S/Δ5Ct mutations progressively decrease the hexamer stability and enzyme activity. These results demonstrate that the mutated regions play a role in protein function through stabilizing the quaternary arrangement.
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Affiliation(s)
- Plínio Salmazo Vieira
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Priscila Oliveira de Giuseppe
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | | | - Mario Tyago Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.
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23
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Crystal structure and biophysical characterization of the nucleoside diphosphate kinase from Leishmania braziliensis. BMC STRUCTURAL BIOLOGY 2015; 15:2. [PMID: 25643978 PMCID: PMC4322457 DOI: 10.1186/s12900-015-0030-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/15/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite Leishmania to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions. RESULTS We report the crystal structure and biophysical characterization of the NDK from Leishmania braziliensis (LbNDK). The subunit consists of six α-helices along with a core of four β-strands arranged in a β2β3β1β4 antiparallel topology order. In contrast to the NDK from L. major, the LbNDK C-terminal extension is partially unfolded. SAXS data showed that LbNDK forms hexamers in solution in the pH range from 7.0 to 4.0, a hydrodynamic behavior conserved in most eukaryotic NDKs. However, DSF assays show that acidification and alkalization decrease the hexamer stability. CONCLUSIONS Our results support that LbNDK remains hexameric in pH conditions akin to that faced by this enzyme when secreted by Leishmania amastigotes in the parasitophorous vacuoles (pH 4.7 to 5.3). The unusual unfolded conformation of LbNDK C-terminus decreases the surface buried in the trimer interface exposing new regions that might be explored for the development of compounds designed to disturb enzyme oligomerization, which may impair the important nucleotide salvage pathway in these parasites.
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24
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Nagle A, Khare S, Kumar AB, Supek F, Buchynskyy A, Mathison CJN, Chennamaneni N, Pendem N, Buckner FS, Gelb M, Molteni V. Recent developments in drug discovery for leishmaniasis and human African trypanosomiasis. Chem Rev 2014; 114:11305-47. [PMID: 25365529 PMCID: PMC4633805 DOI: 10.1021/cr500365f] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 02/08/2023]
Affiliation(s)
- Advait
S. Nagle
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Shilpi Khare
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Arun Babu Kumar
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Frantisek Supek
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Andriy Buchynskyy
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Casey J. N. Mathison
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Naveen
Kumar Chennamaneni
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Nagendar Pendem
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Frederick S. Buckner
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Michael
H. Gelb
- Departments of Chemistry, Biochemistry, and Medicine, University
of Washington, Seattle, Washington 98195, United States
| | - Valentina Molteni
- Genomics
Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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25
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Paul MLS, Kaur A, Geete A, Sobhia ME. Essential gene identification and drug target prioritization in Leishmania species. MOLECULAR BIOSYSTEMS 2014; 10:1184-95. [PMID: 24643243 DOI: 10.1039/c3mb70440h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Leishmaniasis is one of the neglected tropical diseases (NTDs), mainly affecting impoverished communities and having varied ranges of pathogenicity according to the diverse spectrum of clinical manifestations. It is endemic in many countries and poses major challenges to healthcare systems in developing countries. Despite the fact that most of the current mono and combination therapies are found to be failures, clear perception of gene essentiality for parasite survival are now desideratum to identify potential biochemical targets through selection. Here we used the metabolic network of L. major, to perform a comprehensive set of in silico deletion mutants and have systematically recognized a clearly defined set of essential proteins by combining several essential criteria. In this paper we summarize the efforts to prioritize potential drug targets up to a five-fold enrichment compared with a random selection.
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Affiliation(s)
- M L Stanly Paul
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali, India-160062.
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López-Zavala AA, Quintero-Reyes IE, Carrasco-Miranda JS, Stojanoff V, Weichsel A, Rudiño-Piñera E, Sotelo-Mundo RR. Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates. Acta Crystallogr F Struct Biol Commun 2014; 70:1150-4. [PMID: 25195883 PMCID: PMC4157410 DOI: 10.1107/s2053230x1401557x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/03/2014] [Indexed: 12/21/2022] Open
Abstract
Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK from Litopenaeus vannamei (LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry, LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyes et al. (2012), J. Bioenerg. Biomembr. 44, 325-331]. In order to investigate the differences in selectivity, LvNDK was crystallized as binary complexes with both acceptor (dADP and dCDP) and donor (ADP) phosphate-group nucleoside diphosphate substrates and their structures were determined. The three structures with purine or pyrimidine nucleotide ligands are all hexameric. Also, the binding of deoxy or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 2'-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide. Because of this, shrimp NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism.
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Affiliation(s)
- Alonso A. López-Zavala
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, 83304 Sonora, Mexico
| | - Idania E. Quintero-Reyes
- Universidad de Sonora, Blvd Bordo Nuevo s/n, Ejido Providencia, 85039 Cd Obregón, Sonora, Mexico
| | - Jesús S. Carrasco-Miranda
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, 83304 Sonora, Mexico
| | - Vivian Stojanoff
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Andrzej Weichsel
- Macromolecular Crystallography Core, The University of Arizona, Biological Sciences West, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, 62210 Morelos, Mexico
| | - Rogerio R. Sotelo-Mundo
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, 83304 Sonora, Mexico
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Braga MS, Neves LX, Campos JM, Roatt BM, de Oliveira Aguiar Soares RD, Braga SL, de Melo Resende D, Reis AB, Castro-Borges W. Shotgun proteomics to unravel the complexity of the Leishmania infantum exoproteome and the relative abundance of its constituents. Mol Biochem Parasitol 2014; 195:43-53. [PMID: 25017697 DOI: 10.1016/j.molbiopara.2014.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 01/27/2023]
Abstract
The exoproteome of some Leishmania species has revealed important insights into host-parasite interaction, paving the way for the proposal of novel disease-oriented interventions. The focus of the present investigation constituted the molecular profile of the L. infantum exoproteome revealed by a shotgun proteomic approach. Promastigotes under logarithmic phase of growth were obtained and harvested by centrifugation at different time points. Cell integrity was evaluated through the counting of viable parasites using propidium iodide labeling, followed by flow cytometry analysis. The 6h culture supernatant, operationally defined here as exoproteome, was then conditioned to in solution digestion and the resulting peptides submitted to mass spectrometry. A total of 102 proteins were identified and categorized according to their cellular function. Their relative abundance index (emPAI) allowed inference that the L. infantum exoproteome is a complex mixture dominated by molecules particularly involved in nucleotide metabolism and antioxidant activity. Bioinformatic analyses support that approximately 60% of the identified proteins are secreted, of which, 85% possibly reach the extracellular milieu by means of non-classic pathways. At last, sera from naturally infected animals, carriers of differing clinical forms of Canine Visceral Leishmaniasis (CVL), were used to test the immunogenicity associated to the L. infantum exoproteome. Western blotting experiments revealed that this sub-proteome was useful at discriminating symptomatic animals from those exhibiting other clinical forms of the disease. Collectively, the molecular characterization of the L. infantum exoproteome and the preliminary immunoproteomic assays opened up new research avenues related to treatment, prognosis and diagnosis of CVL.
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Affiliation(s)
- Micheline Soares Braga
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Leandro Xavier Neves
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Jonatan Marques Campos
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Bruno Mendes Roatt
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | | | - Samuel Leôncio Braga
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Daniela de Melo Resende
- Laboratório de Pesquisas Clínicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Grupo Informática de Biossistemas, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, Minas Gerais, Brazil
| | - Alexandre Barbosa Reis
- Laboratório de Imunopatologia, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil; Laboratório de Pesquisas Clínicas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - William Castro-Borges
- Laboratório de Enzimologia e Proteômica, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.
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Ogungbe IV, Erwin WR, Setzer WN. Antileishmanial phytochemical phenolics: molecular docking to potential protein targets. J Mol Graph Model 2014; 48:105-17. [PMID: 24463105 DOI: 10.1016/j.jmgm.2013.12.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 12/21/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022]
Abstract
A molecular docking analysis has been carried out to examine potential Leishmania protein targets of antiprotozoal plant-derived polyphenolic compounds. A total of 352 phenolic phytochemicals, including 10 aurones, six cannabinoids, 34 chalcones, 20 chromenes, 52 coumarins, 92 flavonoids, 41 isoflavonoids, 52 lignans, 25 quinones, eight stilbenoids, nine xanthones, and three miscellaneous phenolic compounds, were used in the virtual screening study using 24 Leishmania enzymes (52 different protein structures from the Protein Data Bank). Noteworthy protein targets were Leishmania dihydroorotate dehydrogenase, N-myristoyl transferase, phosphodiesterase B1, pteridine reductase, methionyl-tRNA synthetase, tyrosyl-tRNA synthetase, uridine diphosphate-glucose pyrophosphorylase, nicotinamidase, and glycerol-3-phosphate dehydrogenase. Based on in-silico analysis of antiparasitic polyphenolics in this study, two aurones, one chalcone, five coumarins, six flavonoids, one isoflavonoid, three lignans, and one stilbenoid, can be considered to be promising drug leads worthy of further investigation.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William R Erwin
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Interactions of antiparasitic alkaloids with Leishmania protein targets: a molecular docking analysis. Future Med Chem 2013; 5:1777-99. [DOI: 10.4155/fmc.13.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background: Leishmaniasis is a collection of chronic diseases caused by protozoa of the genus Leishmania. Current antileishmanial chemotherapeutics have demonstrated adverse side effects and therefore R&D into new safer alternative treatments are needed. Methods: A molecular docking analysis has been carried out to assess possible Leishmania biochemical targets of antiparasitic alkaloids. A total of 209 antiparasitic alkaloids were docked with 24 Leishmania protein targets. Results: The strongest docking alkaloid ligands were flinderoles A and B and juliflorine with Leishmania major methionyl-tRNA synthetase; juliflorine, juliprosine, prosopilosidine and prosopilosine with Leishmania mexicana glycerol-3-phosphate dehydrogenase; and ancistrogriffithine A with L. major N-myristoyl transferase. Conclusion: This molecular docking study has provided evidence for what classes and structural types of alkaloids may be targeting specific Leishmania protein targets.
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In-silico Leishmania target selectivity of antiparasitic terpenoids. Molecules 2013; 18:7761-847. [PMID: 23823876 PMCID: PMC6270436 DOI: 10.3390/molecules18077761] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 01/21/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), like leishmaniasis, are major causes of mortality in resource-limited countries. The mortality associated with these diseases is largely due to fragile healthcare systems, lack of access to medicines, and resistance by the parasites to the few available drugs. Many antiparasitic plant-derived isoprenoids have been reported, and many of them have good in vitro activity against various forms of Leishmania spp. In this work, potential Leishmania biochemical targets of antiparasitic isoprenoids were studied in silico. Antiparasitic monoterpenoids selectively docked to L. infantum nicotinamidase, L. major uridine diphosphate-glucose pyrophosphorylase and methionyl t-RNA synthetase. The two protein targets selectively targeted by germacranolide sesquiterpenoids were L. major methionyl t-RNA synthetase and dihydroorotate dehydrogenase. Diterpenoids generally favored docking to L. mexicana glycerol-3-phosphate dehydrogenase. Limonoids also showed some selectivity for L. mexicana glycerol-3-phosphate dehydrogenase and L. major dihydroorotate dehydrogenase while withanolides docked more selectively with L. major uridine diphosphate-glucose pyrophosphorylase. The selectivity of the different classes of antiparasitic compounds for the protein targets considered in this work can be explored in fragment- and/or structure-based drug design towards the development of leads for new antileishmanial drugs.
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31
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Sinha DK, Atray I, Bentur JS, Nair S. Expression of Orseolia oryzae nucleoside diphosphate kinase (OoNDPK) is enhanced in rice gall midge feeding on susceptible rice hosts and its over-expression leads to salt tolerance in Escherichia coli. INSECT MOLECULAR BIOLOGY 2012; 21:593-603. [PMID: 23126268 DOI: 10.1111/j.1365-2583.2012.01163.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The Asian rice gall midge, Orseolia oryzae, is a major dipteran pest of rice, with many known biotypes. The present investigation was initiated to understand the molecular mechanisms of infestation for developing novel integrated pest management strategies. We isolated and characterized a gene, nucleoside diphosphate kinase (OoNDPK), from the rice gall midge, encoding a protein with 169 amino acid residues and with a secretory signal sequence - an observation that assumes significance as salivary gland secretions have been implicated to play a major role in insect-plant interactions. Furthermore, up-regulation (> 18 folds) of OoNDPK was observed in the salivary glands of maggots feeding on susceptible host in contrast to those feeding on resistant host. Phylogenetic analysis revealed similarity of OoNDPK with its dipteran orthologues. 3DLigandSite analysis, of the predicted OoNDPK and its orthologues, revealed phenylalanine and tyrosine residues to be specifically present in NDPK proteins from the plant feeders. Results suggest secretion of OoNDPK into the host plant and its probable involvement in gall midge-rice interaction. Using the coleoptile cell elongation assay, we demonstrated that the recombinant OoNDPK is capable of causing elongation of rice coleoptile cells. Additionally, heterologous expression of OoNDPK in Escherichia coli increased the tolerance of these cells to salt (NaCl; up to 1 mM), hinting at the involvement of this gene in abiotic stress response as well.
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Affiliation(s)
- D K Sinha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Silva TS, Cordeiro OD, Matos ED, Wulff T, Dias JP, Jessen F, Rodrigues PM. Effects of preslaughter stress levels on the post-mortem sarcoplasmic proteomic profile of gilthead seabream muscle. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:9443-53. [PMID: 22906076 DOI: 10.1021/jf301766e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fish welfare is an important concern in aquaculture, not only due to the ethical implications but also for productivity and quality-related reasons. The purpose of this study was to track soluble proteome expression in post-mortem gilthead seabream muscle and to observe how preslaughter stress affects these post-mortem processes. For the experiment, two groups of gilthead seabream (n = 5) were subjected to distinct levels of preslaughter stress, with three muscle samples being taken from each fish. Proteins were extracted from the muscle samples, fractionated, and separated by 2DE. Protein identification was performed by MALDI-TOF-TOF MS. Analysis of the results indicates changes on several cellular pathways, with some of these changes being attributable to oxidative and proteolytic activity on sarcoplasmic proteins, together with leaking of myofibrillar proteins. These processes appear to have been hastened by preslaughter stress, confirming that it induces clear post-mortem changes in the muscle proteome of gilthead seabream.
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Affiliation(s)
- Tomé S Silva
- CIMAR/CCMAR, Centre of Marine Sciences of Algarve, University of Algarve, Faro, Portugal.
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Addis MF, Pisanu S, Preziosa E, Bernardini G, Pagnozzi D, Roggio T, Uzzau S, Saroglia M, Terova G. 2D DIGE/MS to investigate the impact of slaughtering techniques on postmortem integrity of fish filet proteins. J Proteomics 2012; 75:3654-64. [DOI: 10.1016/j.jprot.2012.04.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/27/2012] [Accepted: 04/17/2012] [Indexed: 02/05/2023]
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34
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Spooner R, Yilmaz Ö. Nucleoside-diphosphate-kinase: a pleiotropic effector in microbial colonization under interdisciplinary characterization. Microbes Infect 2012; 14:228-37. [PMID: 22079150 PMCID: PMC3277739 DOI: 10.1016/j.micinf.2011.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 10/07/2011] [Accepted: 10/07/2011] [Indexed: 12/20/2022]
Abstract
Emerging evidence identifies multiple roles for nucleoside-diphosphate-kinase in host-microbe interaction. We provide the first synopsis of utilization of this molecule by various microorganisms during colonization of host tissues. Additionally, we propose novel mechanisms this effector may participate in, which could be crucial for microbial adaptation in chronic host infection.
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Affiliation(s)
- Ralee Spooner
- Department of Periodontology, University of Florida, Gainesville, FL 32610, USA
| | - Özlem Yilmaz
- Department of Periodontology, University of Florida, Gainesville, FL 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
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