1
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Dick CF, Alcantara CL, Carvalho-Kelly LF, Lacerda-Abreu MA, Cunha-E-Silva NL, Meyer-Fernandes JR, Vieyra A. Iron Uptake Controls Trypanosoma cruzi Metabolic Shift and Cell Proliferation. Antioxidants (Basel) 2023; 12:antiox12050984. [PMID: 37237850 DOI: 10.3390/antiox12050984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: Ionic transport in Trypanosoma cruzi is the object of intense studies. T. cruzi expresses a Fe-reductase (TcFR) and a Fe transporter (TcIT). We investigated the effect of Fe depletion and Fe supplementation on different structures and functions of T. cruzi epimastigotes in culture. (2) Methods: We investigated growth and metacyclogenesis, variations of intracellular Fe, endocytosis of transferrin, hemoglobin, and albumin by cell cytometry, structural changes of organelles by transmission electron microscopy, O2 consumption by oximetry, mitochondrial membrane potential measuring JC-1 fluorescence at different wavelengths, intracellular ATP by bioluminescence, succinate-cytochrome c oxidoreductase following reduction of ferricytochrome c, production of H2O2 following oxidation of the Amplex® red probe, superoxide dismutase (SOD) activity following the reduction of nitroblue tetrazolium, expression of SOD, elements of the protein kinase A (PKA) signaling, TcFR and TcIT by quantitative PCR, PKA activity by luminescence, glyceraldehyde-3-phosphate dehydrogenase abundance and activity by Western blotting and NAD+ reduction, and glucokinase activity recording NADP+ reduction. (3) Results: Fe depletion increased oxidative stress, inhibited mitochondrial function and ATP formation, increased lipid accumulation in the reservosomes, and inhibited differentiation toward trypomastigotes, with the simultaneous metabolic shift from respiration to glycolysis. (4) Conclusion: The processes modulated for ionic Fe provide energy for the T. cruzi life cycle and the propagation of Chagas disease.
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Affiliation(s)
- Claudia F Dick
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - Carolina L Alcantara
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - Luiz F Carvalho-Kelly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Marco Antonio Lacerda-Abreu
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Narcisa L Cunha-E-Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
| | - José R Meyer-Fernandes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Adalberto Vieyra
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro/CENABIO, Rio de Janeiro 21941-902, RJ, Brazil
- Programa de Pós-Graduação em Biomedicina Translacional /BIOTRANS, Universidade do Grande Rio, Duque de Caxias 25071-202, RJ, Brazil
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2
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Santiago C, Ortega-Tenezaca B, Barbolla I, Fundora-Ortiz B, Arrasate S, Dea-Ayuela MA, González-Díaz H, Sotomayor N, Lete E. Prediction of Antileishmanial Compounds: General Model, Preparation, and Evaluation of 2-Acylpyrrole Derivatives. J Chem Inf Model 2022; 62:3928-3940. [PMID: 35946598 PMCID: PMC9986876 DOI: 10.1021/acs.jcim.2c00731] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, the SOFT.PTML tool has been used to pre-process a ChEMBL dataset of pre-clinical assays of antileishmanial compound candidates. A comparative study of different ML algorithms, such as logistic regression (LOGR), support vector machine (SVM), and random forests (RF), has shown that the IFPTML-LOGR model presents excellent values of specificity and sensitivity (81-98%) in training and validation series. The use of this software has been illustrated with a practical case study focused on a series of 28 derivatives of 2-acylpyrroles 5a,b, obtained through a Pd(II)-catalyzed C-H radical acylation of pyrroles. Their in vitro leishmanicidal activity against visceral (L. donovani) and cutaneous (L. amazonensis) leishmaniasis was evaluated finding that compounds 5bc (IC50 = 30.87 μM, SI > 10.17) and 5bd (IC50 = 16.87 μM, SI > 10.67) were approximately 6-fold more selective than the drug of reference (miltefosine) in in vitro assays against L. amazonensis promastigotes. In addition, most of the compounds showed low cytotoxicity, CC50 > 100 μg/mL in J774 cells. Interestingly, the IFPMTL-LOGR model predicts correctly the relative biological activity of these series of acylpyrroles. A computational high-throughput screening (cHTS) study of 2-acylpyrroles 5a,b has been performed calculating >20,700 activity scores vs a large space of 647 assays involving multiple Leishmania species, cell lines, and potential target proteins. Overall, the study demonstrates that the SOFT.PTML all-in-one strategy is useful to obtain IFPTML models in a friendly interface making the work easier and faster than before. The present work also points to 2-acylpyrroles as new lead compounds worthy of further optimization as antileishmanial hits.
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Affiliation(s)
- Carlos Santiago
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
| | - Bernabé Ortega-Tenezaca
- Department of Computer Science and Information Technologies, University of A Coruña (UDC), 15071, A Coruña, Spain
| | - Iratxe Barbolla
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.,BIOFISIKA. Basque Center for Biophysics CSIC-UPV/EHU, 48940, Bilbao, Spain
| | - Brenda Fundora-Ortiz
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
| | - Sonia Arrasate
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
| | - María Auxiliadora Dea-Ayuela
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, 46115 Alfara del Patriarca, Valencia, Spain
| | - Humberto González-Díaz
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain.,BIOFISIKA. Basque Center for Biophysics CSIC-UPV/EHU, 48940, Bilbao, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Nuria Sotomayor
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
| | - Esther Lete
- Departamento de Química Orgánica e Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco / Euskal Herriko Unibertsitatea UPV/EHU, Apdo. 644, 48080 Bilbao, Spain
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3
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Lin C, Jaén Batista DDG, Mazzeti AL, Donola Girão R, de Oliveira GM, Karalic I, Hulpia F, Soeiro MDNC, Maes L, Caljon G, Van Calenbergh S. N 6-modification of 7-Deazapurine nucleoside analogues as Anti-Trypanosoma cruzi and anti-Leishmania agents: Structure-activity relationship exploration and In vivo evaluation. Eur J Med Chem 2022; 231:114165. [PMID: 35144125 DOI: 10.1016/j.ejmech.2022.114165] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022]
Abstract
Chagas disease and leishmaniasis are two poverty-related neglected tropical diseases that cause high mortality and morbidity. Current treatments suffer from severe limitations and novel, safer and more effective drugs are urgently needed. Both Trypanosoma cruzi and Leishmania are auxotrophic for purines and absolutely depend on uptake and assimilation of host purines. This led us to successfully explore purine nucleoside analogues as chemotherapeutic agents against these and other kinetoplastid infections. This study extensively explored the modification of the 6-amino group of tubercidin, a natural product with trypanocidal activity but unacceptable toxicity for clinical use. We found that mono-substitution of the amine with short alkyls elicits potent and selective antitrypanosomal and antileishmanial activity. The methyl analogue 15 displayed the best in vitro activity against both T. cruzi and L. infantum and high selectivity versus host cells. Oral administration for five consecutive days in an acute Chagas disease mouse model resulted in significantly reduced peak parasitemia levels (75, 89 and 96% with 12.5, 25 and 50 mg/kg/day, respectively). as well as increased animal survival rates with the lower doses (83 and 67% for 12.5 and 25 mg/kg/day, respectively).
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Affiliation(s)
- Cai Lin
- Laboratory for Medicinal Chemistry (Campus Heymans), Ghent University, Ottergemsesteenweg 460, B-9000, Gent, Belgium
| | - Denise da Gama Jaén Batista
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz (FIOCRUZ), Fundação Oswaldo Cruz, Rio de Janeiro, Avenida Brasil 4365, Manguinhos, 21040-360, Rio de Janeiro, Brazil
| | - Ana Lia Mazzeti
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz (FIOCRUZ), Fundação Oswaldo Cruz, Rio de Janeiro, Avenida Brasil 4365, Manguinhos, 21040-360, Rio de Janeiro, Brazil
| | - Roberson Donola Girão
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz (FIOCRUZ), Fundação Oswaldo Cruz, Rio de Janeiro, Avenida Brasil 4365, Manguinhos, 21040-360, Rio de Janeiro, Brazil
| | - Gabriel Melo de Oliveira
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz (FIOCRUZ), Fundação Oswaldo Cruz, Rio de Janeiro, Avenida Brasil 4365, Manguinhos, 21040-360, Rio de Janeiro, Brazil
| | - Izet Karalic
- Laboratory for Medicinal Chemistry (Campus Heymans), Ghent University, Ottergemsesteenweg 460, B-9000, Gent, Belgium
| | - Fabian Hulpia
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Maria de Nazaré C Soeiro
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz (FIOCRUZ), Fundação Oswaldo Cruz, Rio de Janeiro, Avenida Brasil 4365, Manguinhos, 21040-360, Rio de Janeiro, Brazil
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Infla-Med Centre of Excellence, University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (Campus Heymans), Ghent University, Ottergemsesteenweg 460, B-9000, Gent, Belgium.
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4
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Li NS, Koo SC, Piccirilli JA. Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'- S-phosphorothiolate Linkage. J Org Chem 2021; 86:13231-13244. [PMID: 34533968 PMCID: PMC8491167 DOI: 10.1021/acs.joc.1c01059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Oligoribonucleotides
containing a photocaged 2′-amino-5′-S-phophorothiolate linkage have potential applications as
therapeutic agents and biological probes to investigate the RNA structure
and function. We envisioned that oligoribonucleotides containing a
2′-amino-5′-S-phosphorothiolate linkage
could provide an approach to identify the general base within catalytic
RNAs by chemogenetic suppression. To enable preliminary tests of this
idea, we developed synthetic approaches to a dinucleotide, trinucleotide,
and oligoribonucleotide containing a photocaged 2′-amino-5′-S-phosphorothiolate linkage. We incorporated the photocaged
2′-amino-5′-S-phosphorothiolate linkage
into an oligoribonucleotide substrate for the hepatitis delta virus
(HDV) ribozyme and investigated the pH dependence of its cleavage
following UV irradiation both in the presence and absence of the ribozyme.
The substrate exhibited a pH-rate profile characteristic of the modified
linkage but reacted slower when bound to the ribozyme. Cleavage inhibition
by the HDV ribozyme could reflect a non-productive ground-state interaction
with the modified substrate’s nucleophilic 2′-NH2 or a poor fit of the modified transition state at the ribozyme’s
active site.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
| | - Selene C Koo
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
| | - Joseph A Piccirilli
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States.,Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
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5
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Chopra B, Dhingra AK. Natural products: A lead for drug discovery and development. Phytother Res 2021; 35:4660-4702. [PMID: 33847440 DOI: 10.1002/ptr.7099] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/29/2022]
Abstract
Natural products are used since ancient times in folklore for the treatment of various ailments. Plant-derived products have been recognized for many years as a source of therapeutic agents and structural diversity. A literature survey has been carried out to determine the utility of natural molecules and their modified analogs or derivatives as pharmacological active entities. This review presents a study on the importance of natural products in terms of drug discovery and development. It describes how the natural components can be utilized after small modifications in new perspectives. Various new modifications in structure offer a unique opportunity to establish a new molecular entity with better pharmacological potential. It was concluded that in this current era, new attempts are taken to utilize the compounds derived from natural sources as novel drug candidates, with a focus to find and discover new effective molecules that were referred to as "new entities of natural product drug discovery."
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Affiliation(s)
- Bhawna Chopra
- Department of Pharmaceutical Chemistry, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, India
| | - Ashwani Kumar Dhingra
- Department of Pharmaceutical Chemistry, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, India
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6
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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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7
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Eyssen LEA, Coetzer TH. Validation of ligands targeting metacaspase-2 (MCA2) from Trypanosoma brucei brucei and their application to MCA5 from T. congolense as possible trypanocides. J Mol Graph Model 2020; 97:107579. [PMID: 32197135 DOI: 10.1016/j.jmgm.2020.107579] [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: 11/19/2019] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 11/29/2022]
Abstract
Metacaspases (MCAs) are ideal drug and diagnostic targets for animal and human African trypanosomiasis, as these cysteine peptidases are absent from the metazoan kingdom and have been implicated in the parasite cell cycle and cell death. Tsetse fly-transmitted trypanosomes that live free in the bloodstream and/or cerebrospinal fluid of the mammalian host cause animal and human African trypanosomiasis (nagana or sleeping sickness respectively). Chemotherapy and chemoprophylaxis are the main forms of control, but in contrast to human trypanocides, the veterinary drugs are old and drug resistance is on the increase. A peptidomimetic library targeting the MCA2 from Trypanosoma brucei brucei has ligands with low IC50 values, some of which were antiparasitic. This study validates the inhibitory activity of these ligands using the protein structure solved by X-ray diffraction after the ligand library was published. Water molecules were shown to be important in substrate binding and strategies to improve the efficacy of these ligands are highlighted. These ligands appear to be pan-specific as they were docked into the active site of the homology modelled MCA5 of animal infective Trypanosoma congolense with similar binding energies and conformations.
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Affiliation(s)
- L E-A Eyssen
- Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa
| | - Theresa Ht Coetzer
- Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa.
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8
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Discovery of Novel TASK-3 Channel Blockers Using a Pharmacophore-Based Virtual Screening. Int J Mol Sci 2019; 20:ijms20164014. [PMID: 31426491 PMCID: PMC6720600 DOI: 10.3390/ijms20164014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
TASK-3 is a two-pore domain potassium (K2P) channel highly expressed in the hippocampus, cerebellum, and cortex. TASK-3 has been identified as an oncogenic potassium channel and it is overexpressed in different cancer types. For this reason, the development of new TASK-3 blockers could influence the pharmacological treatment of cancer and several neurological conditions. In the present work, we searched for novel TASK-3 blockers by using a virtual screening protocol that includes pharmacophore modeling, molecular docking, and free energy calculations. With this protocol, 19 potential TASK-3 blockers were identified. These molecules were tested in TASK-3 using patch clamp, and one blocker (DR16) was identified with an IC50 = 56.8 ± 3.9 μM. Using DR16 as a scaffold, we designed DR16.1, a novel TASK-3 inhibitor, with an IC50 = 14.2 ± 3.4 μM. Our finding takes on greater relevance considering that not many inhibitory TASK-3 modulators have been reported in the scientific literature until today. These two novel TASK-3 channel inhibitors (DR16 and DR16.1) are the first compounds found using a pharmacophore-based virtual screening and rational drug design protocol.
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9
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Duschak VG. Major Kinds of Drug Targets in Chagas Disease or American Trypanosomiasis. Curr Drug Targets 2019; 20:1203-1216. [PMID: 31020939 DOI: 10.2174/1389450120666190423160804] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/22/2022]
Abstract
American Trypanosomiasis, a parasitic infection commonly named Chagas disease, affects millions of people all over Latin American countries. Presently, the World Health Organization (WHO) predicts that the number of international infected individuals extends to 7 to 8 million, assuming that more than 10,000 deaths occur annually. The transmission of the etiologic agent, Trypanosoma cruzi, through people migrating to non-endemic world nations makes it an emergent disease. The best promising targets for trypanocidal drugs may be classified into three main groups: Group I includes the main molecular targets that are considered among specific enzymes involved in the essential processes for parasite survival, principally Cruzipain, the major antigenic parasite cysteine proteinase. Group II involves biological pathways and their key specific enzymes, such as Sterol biosynthesis pathway, among others, specific antioxidant defense mechanisms, and bioenergetics ones. Group III includes the atypical organelles /structures present in the parasite relevant clinical forms, which are absent or considerably different from those present in mammals and biological processes related to them. These can be considered potential targets to develop drugs with extra effectiveness and fewer secondary effects than the currently used therapeutics. An improved distinction between the host and the parasite targets will help fight against this neglected disease.
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Affiliation(s)
- Vilma G Duschak
- National Council of Scientific and Technical Reasearch (CONICET) Researcher, Area of Protein Biochemistry and Parasite Glycobiology, Research Department, National Institute of Parasitology (INP), "Dr. Mario Fatala Chaben", ANLIS-Malbran, National Health Secretary, Av. Paseo Colon 568, Lab 506, Ciudad Autonoma de Buenos Aires (1063), Buenos Aires, Argentina
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10
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Gómez S, Querol-García J, Sánchez-Barrón G, Subias M, González-Alsina À, Franco-Hidalgo V, Albertí S, Rodríguez de Córdoba S, Fernández FJ, Vega MC. The Antimicrobials Anacardic Acid and Curcumin Are Not-Competitive Inhibitors of Gram-Positive Bacterial Pathogenic Glyceraldehyde-3-Phosphate Dehydrogenase by a Mechanism Unrelated to Human C5a Anaphylatoxin Binding. Front Microbiol 2019; 10:326. [PMID: 30863383 PMCID: PMC6400076 DOI: 10.3389/fmicb.2019.00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
The ubiquitous and highly abundant glycolytic enzyme D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is pivotal for the energy and carbon metabolism of most organisms, including human pathogenic bacteria. For bacteria that depend mostly on glycolysis for survival, GAPDH is an attractive target for inhibitor discovery. The availability of high-resolution structures of GAPDH from various pathogenic bacteria is central to the discovery of new antibacterial compounds. We have determined the X-ray crystal structures of two new GAPDH enzymes from Gram-positive bacterial pathogens, Streptococcus pyogenes and Clostridium perfringens. These two structures, and the recent structure of Atopobium vaginae GAPDH, reveal details in the active site that can be exploited for the design of novel inhibitors based on naturally occurring molecules. Two such molecules, anacardic acid and curcumin, have been found to counter bacterial infection in clinical settings, although the cellular targets responsible for their antimicrobial properties remain unknown. We show that both anacardic acid and curcumin inhibit GAPDH from two bacterial pathogens through uncompetitive and non-competitive mechanisms, suggesting GAPDH as a relevant pharmaceutical target for antibacterial development. Inhibition of GAPDH by anacardic acid and curcumin seems to be unrelated to the immune evasion function of pathogenic bacterial GAPDH, since neither natural compound interfere with binding to the human C5a anaphylatoxin.
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Affiliation(s)
- Sara Gómez
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Javier Querol-García
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Gara Sánchez-Barrón
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
| | - Marta Subias
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | - Àlex González-Alsina
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | | | - Sebastián Albertí
- Institut Universitari d'Investigació en Ciències de la Salut, University of the Balearic Islands, Mallorca, Spain
| | - Santiago Rodríguez de Córdoba
- Center for Biological Research, Spanish National Research Council, Madrid, Spain.,CIBER de Enfermedades Raras, Madrid, Spain
| | | | - M Cristina Vega
- Center for Biological Research, Spanish National Research Council, Madrid, Spain
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11
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Dhal AK, Pani A, Mahapatra RK, Yun SI. In-silico screening of small molecule inhibitors against Lactate Dehydrogenase (LDH) of Cryptosporidium parvum. Comput Biol Chem 2018; 77:44-51. [PMID: 30240985 DOI: 10.1016/j.compbiolchem.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/30/2018] [Accepted: 09/02/2018] [Indexed: 10/28/2022]
Abstract
Cryptosporidium parvum is a protozoan parasite which causes waterborne diseases known as Cryptosporidiosis. It is an acute enteric diarrheal disease being severe in the case of immunocompromised individuals and children. C. parvum mainly depends on the glycolysis process for energy production and LDH (Lactate Dehydrogenase) is a key controller of this process. In this study from different in-silico approaches such as structure-based, ligand-based and de novo drug design; a total of 40 compounds were selected for docking studies against LDH. The study reported a compound CHEMBL1784973 from Pathogen Box as the best inhibitor in terms of docking score and pharmacophoric features. Furthermore, the binding mode of the best-reported inhibitor was validated through molecular dynamics simulation for a time interval of 70 ns in water environment. The findings resulted in the stable conformation of the inhibitor in the active site of the protein. This study will be helpful for experimental validation.
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Affiliation(s)
- Ajit Kumar Dhal
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Alok Pani
- Department of Food Science and Technology, Chonbuk National University, Jeonju 561756, South Korea
| | | | - Soon-Il Yun
- Department of Food Science and Technology, Chonbuk National University, Jeonju 561756, South Korea.
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12
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Querol-García J, Fernández FJ, Marin AV, Gómez S, Fullà D, Melchor-Tafur C, Franco-Hidalgo V, Albertí S, Juanhuix J, Rodríguez de Córdoba S, Regueiro JR, Vega MC. Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from the Gram-Positive Bacterial Pathogen A. vaginae, an Immunoevasive Factor that Interacts with the Human C5a Anaphylatoxin. Front Microbiol 2017; 8:541. [PMID: 28443070 PMCID: PMC5385343 DOI: 10.3389/fmicb.2017.00541] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive anaerobic human pathogenic bacterium Atopobium vaginae causes most diagnosed cases of bacterial vaginosis as well as opportunistic infections in immunocompromised patients. In addition to its well-established role in carbohydrate metabolism, D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Streptococcus pyogenes and S. pneumoniae have been reported to act as extracellular virulence factors during streptococcal infections. Here, we report the crystal structure of GAPDH from A. vaginae (AvGAPDH) at 2.19 Å resolution. The refined model has a crystallographic Rfree of 22.6%. AvGAPDH is a homotetramer wherein each subunit is bound to a nicotinamide adenine dinucleotide (NAD+) molecule. The AvGAPDH enzyme fulfills essential glycolytic as well as moonlight (non-glycolytic) functions, both of which might be targets of chemotherapeutic intervention. We report that AvGAPDH interacts in vitro with the human C5a anaphylatoxin and inhibits C5a-specific granulocyte chemotaxis, thereby suggesting the participation of AvGAPDH in complement-targeted immunoevasion in a context of infection. The availability of high-quality structures of AvGAPDH and other homologous virulence factors from Gram-positive pathogens is critical for drug discovery programs. In this study, sequence and structural differences between AvGAPDH and related bacterial and eukaryotic GAPDH enzymes are reported in an effort to understand how to subvert the immunoevasive properties of GAPDH and evaluate the potential of AvGAPDH as a druggable target.
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Affiliation(s)
- Javier Querol-García
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Francisco J Fernández
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain.,Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain.,Abvance Biotech srlMadrid, Spain
| | - Ana V Marin
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - Sara Gómez
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Daniel Fullà
- ALBA Synchrotron, Cerdanyola del VallèsCatalonia, Spain
| | - Cecilia Melchor-Tafur
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - Virginia Franco-Hidalgo
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | | | | | - Santiago Rodríguez de Córdoba
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
| | - José R Regueiro
- Department of Immunology, Complutense University School of MedicineMadrid, Spain.,Hospital 12 de Octubre Health Research InstituteMadrid, Spain
| | - M Cristina Vega
- Integrated Protein Science for Biomedicine & Biotechnology and Ciber de Enfermedades Raras, Center for Biological Research (CIB-CSIC)Madrid, Spain
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13
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Abstract
Aside from its well-established role in glycolysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been shown to possess many key functions in cells. These functions are regulated by protein oligomerization , biomolecular interactions, post-translational modifications , and variations in subcellular localization . Several GAPDH functions and regulatory mechanisms overlap with one another and converge around its role in intermediary metabolism. Several structural determinants of the protein dictate its function and regulation. GAPDH is ubiquitously expressed and is found in all domains of life. GAPDH has been implicated in many diseases, including those of pathogenic, cardiovascular, degenerative, diabetic, and tumorigenic origins. Understanding the mechanisms by which GAPDH can switch between its functions and how these functions are regulated can provide insights into ways the protein can be modulated for therapeutic outcomes.
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14
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Oslovsky VE, Drenichev MS, Mikhailov SN. Regioselective 1-N-Alkylation and Rearrangement of Adenosine Derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:475-99. [PMID: 26158567 DOI: 10.1080/15257770.2015.1016169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Several methods for the preparation of some N(6)-substituted adenosines based on selective 1-N-alkylation with subsequent Dimroth rearrangement were developed. The proposed methods seem to be effective for the preparation of natural N(6)-isopentenyl- and N(6)-benzyladenosines, which are known to possess pronounced biological activities. Direct 1-N-alkylation of 2',3',5'-tri-O-acetyladenosine and 3',5'-di-O-acetyl-2'-deoxyadenosine with alkyl halides in N,N-dimethylformamide (DMF) in the presence of BaCO3 and KI gave 1-N-substituted derivatives with quantitative yields, whereas 1-N-alkylation of adenosine was accompanied by significant O-alkylation. Moreover, the reaction of trimethylsilyl derivatives of N(6)-acetyl-2',3',5'-tri-O-acetyladenosine and N(6)-acetyl-3',5'-di-O-acetyl-2'-deoxyadenosine with alkyl halides leads to the formation of the stable 1-N-substituted adenosines. Dimroth rearrangement of 1-N-substituted adenosines in aqueous ammonia yields pure N(6)-substituted adenosines.
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Affiliation(s)
- Vladimir E Oslovsky
- a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow , Russian Federation
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15
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Bruno S, Margiotta M, Pinto A, Cullia G, Conti P, De Micheli C, Mozzarelli A. Selectivity of 3-bromo-isoxazoline inhibitors between human and Plasmodium falciparum glyceraldehyde-3-phosphate dehydrogenases. Bioorg Med Chem 2016; 24:2654-9. [DOI: 10.1016/j.bmc.2016.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 01/09/2023]
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16
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Ramírez D. Computational Methods Applied to Rational Drug Design. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2016; 10:7-20. [PMID: 27708723 PMCID: PMC5039900 DOI: 10.2174/1874104501610010007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/22/2022]
Abstract
Due
to the synergic relationship between medical chemistry, bioinformatics and
molecular simulation, the development of new accurate computational tools for
small molecules drug design has been rising over the last years. The main result
is the increased number of publications where computational techniques such as
molecular docking, de novo design as well as virtual screening have been
used to estimate the binding mode, site and energy of novel small molecules. In
this work I review some tools, which enable the study of biological systems at
the atomistic level, providing relevant information and thereby, enhancing the
process of rational drug design.
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Affiliation(s)
- David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla, Talca, Chile
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17
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Njogu PM, Guantai EM, Pavadai E, Chibale K. Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis. ACS Infect Dis 2016; 2:8-31. [PMID: 27622945 DOI: 10.1021/acsinfecdis.5b00093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).
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Affiliation(s)
- Peter M. Njogu
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Eric M. Guantai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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18
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Cook WJ, Senkovich O, Hernandez A, Speed H, Chattopadhyay D. Biochemical and structural characterization of Cryptosporidium parvum Lactate dehydrogenase. Int J Biol Macromol 2014; 74:608-19. [PMID: 25542170 DOI: 10.1016/j.ijbiomac.2014.12.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
The protozoan parasite Cryptosporidium parvum causes waterborne diseases worldwide. There is no effective therapy for C. parvum infection. The parasite depends mainly on glycolysis for energy production. Lactate dehydrogenase is a major regulator of glycolysis. This paper describes the biochemical characterization of C. parvum lactate dehydrogenase and high resolution crystal structures of the apo-enzyme and four ternary complexes. The ternary complexes capture the enzyme bound to NAD/NADH or its 3-acetylpyridine analog in the cofactor binding pocket, while the substrate binding site is occupied by one of the following ligands: lactate, pyruvate or oxamate. The results reveal distinctive features of the parasitic enzyme. For example, C. parvum lactate dehydrogenase prefers the acetylpyridine analog of NADH as a cofactor. Moreover, it is slightly less sensitive to gossypol inhibition compared with mammalian lactate dehydrogenases and not inhibited by excess pyruvate. The active site loop and the antigenic loop in C. parvum lactate dehydrogenase are considerably different from those in the human counterpart. Structural features and enzymatic properties of C. parvum lactate dehydrogenase are similar to enzymes from related parasites. Structural comparison with malate dehydrogenase supports a common ancestry for the two genes.
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Affiliation(s)
- William J Cook
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Olga Senkovich
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Agustin Hernandez
- Instituto de Bioquímica Vegetal y Fotosintesis (CSIC/U. Sevilla), Avda. Americo Vespucio 49, Seville 41092, Spain
| | - Haley Speed
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Debasish Chattopadhyay
- Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, United States; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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19
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Tararov VI, Tijsma A, Kolyachkina SV, Oslovsky VE, Neyts J, Drenichev MS, Leyssen P, Mikhailov SN. Chemical modification of the plant isoprenoid cytokinin N(6)-isopentenyladenosine yields a selective inhibitor of human enterovirus 71 replication. Eur J Med Chem 2014; 90:406-13. [PMID: 25461889 DOI: 10.1016/j.ejmech.2014.11.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 01/30/2023]
Abstract
In this study, we demonstrate that N(6)-isopentenyladenosine, which essentially is a plant cytokinin-like compound, exerts a potent and selective antiviral effect on the replication of human enterovirus 71 with an EC50 of 1.0 ± 0.2 μM and a selectivity index (SI) of 5.7. The synthesis of analogs with modification of the N(6)-position did not result in a lower EC50 value. However, in particular with the synthesis of N(6)-(5-hexene-2-yne-1-yl)adenosine (EC50 = 4.3 ± 1.5 μM), the selectivity index was significantly increased: because of a reduction in the adverse effect of this compound on the host cells, an SI > 101 could be calculated. With this study, we for the first time provide proof that a compound class that is based on the plant cytokinin skeleton offers an interesting starting point for the development of novel antivirals against mammalian viruses, in the present context in particular against enterovirus 71.
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Affiliation(s)
- Vitali I Tararov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Aloys Tijsma
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Svetlana V Kolyachkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Vladimir E Oslovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Johan Neyts
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Mikhail S Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation
| | - Pieter Leyssen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Virology and Chemotherapy, Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Sergey N Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow 119991, Russian Federation.
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20
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Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, de Castro Soares S, Almeida S, Ali A, Islam A, Póvoa FD, de Abreu VAC, Jain N, Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira RS. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15 Suppl 7:S3. [PMID: 25573232 PMCID: PMC4243142 DOI: 10.1186/1471-2164-15-s7-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
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21
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Bruno S, Pinto A, Paredi G, Tamborini L, De Micheli C, La Pietra V, Marinelli L, Novellino E, Conti P, Mozzarelli A. Discovery of Covalent Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase, A Target for the Treatment of Malaria. J Med Chem 2014; 57:7465-71. [DOI: 10.1021/jm500747h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Stefano Bruno
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
- Istituto di Bioscienze e Biorisorse, CNR, 80131 Napoli, Italy
| | - Andrea Pinto
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Gianluca Paredi
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
| | - Lucia Tamborini
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Carlo De Micheli
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Valeria La Pietra
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Luciana Marinelli
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli Federico II, Via Montesano,
49, 80138 Napoli, Italy
| | - Paola Conti
- Dipartimento
di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Mozzarelli
- Dipartimento
di Farmacia and Centro Siteia.Parma, Università di Parma, Parco Area
delle Scienze 23/A, 43124 Parma, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, 00136 Roma, Italy
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22
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A pharmacophore-based virtual screening approach for the discovery of Trypanosoma cruzi GAPDH inhibitors. Future Med Chem 2014; 5:2019-35. [PMID: 24215344 DOI: 10.4155/fmc.13.166] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chagas disease is a major cause of morbidity and death for millions of people in Latin America. The drugs currently available exhibit poor efficacy and severe side effects. Therefore, there is an urgent need for new, safe and effective drugs against Chagas disease. The vital dependence on glycolysis as energy source makes the glycolytic enzymes of Trypanosoma cruzi, the causative agent of Chagas disease, attractive targets for drug design. In this work, glyceraldehyde-3-phosphate dehydrogenase from T. cruzi (TcGAPDH) was employed as molecular target for the discovery of new inhibitors as hits. RESULTS Integrated protein-based pharmacophore and structure-based virtual screening approaches resulted in the identification of three hits from three chemical classes with moderate inhibitory activity against TcGAPDH. The inhibitors showed IC50 values in the high micromolar range. CONCLUSION The new chemotypes are attractive molecules for future medicinal chemistry efforts aimed at developing new lead compounds for Chagas disease.
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23
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RVC, Andricopulo AD, de Sousa AG, da Silva ABF. Pattern recognition techniques applied to the study of leishmanial glyceraldehyde-3-phosphate dehydrogenase inhibition. Int J Mol Sci 2014; 15:3186-203. [PMID: 24566143 PMCID: PMC3958905 DOI: 10.3390/ijms15023186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 11/16/2022] Open
Abstract
Chemometric pattern recognition techniques were employed in order to obtain Structure-Activity Relationship (SAR) models relating the structures of a series of adenosine compounds to the affinity for glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). A training set of 49 compounds was used to build the models and the best ones were obtained with one geometrical and four electronic descriptors. Classification models were externally validated by predictions for a test set of 14 compounds not used in the model building process. Results of good quality were obtained, as verified by the correct classifications achieved. Moreover, the results are in good agreement with previous SAR studies on these molecules, to such an extent that we can suggest that these findings may help in further investigations on ligands of LmGAPDH capable of improving treatment of leishmaniasis.
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Affiliation(s)
- Norka B H Lozano
- Instituto de Química de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
| | - Rafael F Oliveira
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Karen C Weber
- Universidade Federal da Paraíba, João Pessoa (PB), 58051-900, Brazil.
| | - Kathia M Honorio
- Escola de Artes Ciências e Humanidades, USP, São Paulo (SP), 03828-000, Brazil.
| | - Rafael V C Guido
- Instituto de Física de São Carlos, USP, São Carlos (SP), 13566-590, Brazil.
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24
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Integration of methods in cheminformatics and biocalorimetry for the design of trypanosomatid enzyme inhibitors. Future Med Chem 2014; 6:17-33. [DOI: 10.4155/fmc.13.185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The enzyme GAPDH, which acts in the glycolytic pathway, is seen as a potential target for pharmaceutical intervention of Chagas disease. Results: Herein, we report the discovery of new Trypanosoma cruzi GAPDH (TcGAPDH) inhibitors from target- and ligand-based virtual screening protocols using isothermal titration calorimetry (ITC) and molecular dynamics. Molecular dynamics simulations were used to gain insight on the binding poses of newly identified inhibitors acting at the TcGAPDH substrate (G3P) site. Conclusion: Nequimed125, the most potent inhibitor to act upon TcGAPDH so far, which sits on the G3P site without any contact with the co-factor (NAD+) site, underpins the result obtained by ITC that it is a G3P-competitive inhibitor. Molecular dynamics simulation provides biding poses of TcGAPDH inhibitors that correlate with mechanisms of inhibition observed by ITC. Overall, a new class of dihydroindole compounds that act upon TcGAPDH through a competitive mechanism of inhibition as proven by ITC measurements also kills T. cruzi.
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25
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Lüscher A, Lamprea-Burgunder E, Graf FE, de Koning HP, Mäser P. Trypanosoma brucei adenine-phosphoribosyltransferases mediate adenine salvage and aminopurinol susceptibility but not adenine toxicity. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2013; 4:55-63. [PMID: 24596669 PMCID: PMC3940079 DOI: 10.1016/j.ijpddr.2013.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 11/30/2022]
Abstract
African trypanosomes possess two distinct adenine phosphoribosyltransferases. Trypanosoma brucei TbAPRT1 is cytosolic, TbAPRT2 localizes to the glycosome. Aprt1,2 null mutants are viable but do not incorporate adenine into nucleotides. Aprt1,2 null mutants are resistant to aminopurinol but still sensitive to adenine. Aminopurinol is a trypanocide with submicromolar activity against T. brucei.
African trypanosomes, like all obligate parasitic protozoa, cannot synthesize purines de novo and import purines from their hosts to build nucleic acids. The purine salvage pathways of Trypanosoma brucei being redundant, none of the involved enzymes is likely to be essential. Nevertheless they can be of pharmacological interest due to their role in activation of purine nucleobase or nucleoside analogues, which only become toxic when converted to nucleotides. Aminopurine antimetabolites, in particular, are potent trypanocides and even adenine itself is toxic to trypanosomes at elevated concentrations. Here we report on the T. brucei adenine phosphoribosyltransferases TbAPRT1 and TbAPRT2, encoded by the two genes Tb927.7.1780 and Tb927.7.1790, located in tandem on chromosome seven. The duplication is syntenic in all available Trypanosoma genomes but not in Leishmania. While TbAPRT1 is cytosolic, TbAPRT2 possesses a glycosomal targeting signal and co-localizes with the glycosomal marker aldolase. Interestingly, the distribution of glycosomal targeting signals among trypanosomatid adenine phosphoribosyltransferases is not consistent with their phylogeny, indicating that the acquisition of adenine salvage to the glycosome happened after the radiation of Trypanosoma. Double null mutant T. brucei Δtbaprt1,2 exhibited no growth phenotype but no longer incorporated exogenous adenine into the nucleotide pool. This, however, did not reduce their sensitivity to adenine. The Δtbaprt1,2 trypanosomes were resistant to the adenine isomer aminopurinol, indicating that it is activated by phosphoribosyl transfer. Aminopurinol was about 1000-fold more toxic to bloodstream-form T. brucei than the corresponding hypoxanthine isomer allopurinol. Aminopurinol uptake was not dependent on the aminopurine permease P2 that has been implicated in drug resistance.
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Affiliation(s)
- Alexandra Lüscher
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | | | - Fabrice E Graf
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ; University of Basel, 4000 Basel, Switzerland
| | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8RA, UK
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ; University of Basel, 4000 Basel, Switzerland
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Frączek T, Siwek A, Paneth P. Assessing Molecular Docking Tools for Relative Biological Activity Prediction: A Case Study of Triazole HIV-1 NNRTIs. J Chem Inf Model 2013; 53:3326-42. [DOI: 10.1021/ci400427a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tomasz Frączek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
| | - Agata Siwek
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
- Department
of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodzki 4a, 20-093 Lublin, Poland
| | - Piotr Paneth
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, Zeromskiego
116, 90-924 Lodz, Poland
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Lozano NBH, Oliveira RF, Weber KC, Honorio KM, Guido RV, Andricopulo AD, Da Silva ABF. Identification of electronic and structural descriptors of adenosine analogues related to inhibition of leishmanial glyceraldehyde-3-phosphate dehydrogenase. Molecules 2013; 18:5032-50. [PMID: 23629757 PMCID: PMC6269754 DOI: 10.3390/molecules18055032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/27/2013] [Accepted: 04/28/2013] [Indexed: 11/24/2022] Open
Abstract
Quantitative structure-activity relationship (QSAR) studies were performed in order to identify molecular features responsible for the antileishmanial activity of 61 adenosine analogues acting as inhibitors of the enzyme glyceraldehyde 3-phosphate dehydrogenase of Leishmania mexicana (LmGAPDH). Density functional theory (DFT) was employed to calculate quantum-chemical descriptors, while several structural descriptors were generated with Dragon 5.4. Variable selection was undertaken with the ordered predictor selection (OPS) algorithm, which provided a set with the most relevant descriptors to perform PLS, PCR and MLR regressions. Reliable and predictive models were obtained, as attested by their high correlation coefficients, as well as the agreement between predicted and experimental values for an external test set. Additional validation procedures were carried out, demonstrating that robust models were developed, providing helpful tools for the optimization of the antileishmanial activity of adenosine compounds.
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Affiliation(s)
- Norka B. H. Lozano
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
| | - Rafael F. Oliveira
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Karen C. Weber
- Departamento de Química, Universidade Federal da Paraiba, João Pessoa, PB 13083-970, Brazil; E-Mails: (R.F.O.); (K.W.C.)
| | - Kathia M. Honorio
- Centro de Ciência Naturais e Humanas, Universidade Federal do ABC, Santo Andre, SP 09210-170, Brazil; E-Mail:
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP 03828-000, Brazil; E-Mail:
| | - Rafael V. Guido
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Adriano D. Andricopulo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP 13560-590, Brazil; E-Mails: (R.V.G.); (A.D.A.)
| | - Albérico B. F. Da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP 13566-590, Brazil; E-Mail:
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de Oliveira OV, dos Santos JD, Freitas LC. Molecular dynamics simulation of the gGAPDH–NAD+complex fromTrypanosoma cruzi. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.696112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Translocation of solutes and proteins across the glycosomal membrane of trypanosomes; possibilities and limitations for targeting with trypanocidal drugs. Parasitology 2012; 140:1-20. [PMID: 22914253 DOI: 10.1017/s0031182012001278] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Glycosomes are specialized peroxisomes found in all kinetoplastid organisms. The organelles are unique in harbouring most enzymes of the glycolytic pathway. Matrix proteins, synthesized in the cytosol, cofactors and metabolites have to be transported across the membrane. Recent research on Trypanosoma brucei has provided insight into how these translocations across the membrane occur, although many details remain to be elucidated. Proteins are imported by a cascade of reactions performed by specialized proteins, called peroxins, in which a cytosolic receptor with bound matrix protein inserts itself in the membrane to deliver its cargo into the organelle and is subsequently retrieved from the glycosome to perform further rounds of import. Bulky solutes, such as cofactors and acyl-CoAs, seem to be translocated by specific transporter molecules, whereas smaller solutes such as glycolytic intermediates probably cross the membrane through pore-forming channels. The presence of such channels is in apparent contradiction with previous results that suggested a low permeability of the glycosomal membrane. We propose 3 possible, not mutually exclusive, solutions for this paradox. Glycosomal glycolytic enzymes have been validated as drug targets against trypanosomatid-borne diseases. We discuss the possible implications of the new data for the design of drugs to be delivered into glycosomes.
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Granchi C, Minutolo F. Anticancer agents that counteract tumor glycolysis. ChemMedChem 2012; 7:1318-50. [PMID: 22684868 PMCID: PMC3516916 DOI: 10.1002/cmdc.201200176] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/04/2012] [Indexed: 12/12/2022]
Abstract
Can we consider cancer to be a "metabolic disease"? Tumors are the result of a metabolic selection, forming tissues composed of heterogeneous cells that generally express an overactive metabolism as a common feature. In fact, cancer cells have increased needs for both energy and biosynthetic intermediates to support their growth and invasiveness. However, their high proliferation rate often generates regions that are insufficiently oxygenated. Therefore, their carbohydrate metabolism must rely mostly on a glycolytic process that is uncoupled from oxidative phosphorylation. This metabolic switch, also known as the Warburg effect, constitutes a fundamental adaptation of tumor cells to a relatively hostile environment, and supports the evolution of aggressive and metastatic phenotypes. As a result, tumor glycolysis may constitute an attractive target for cancer therapy. This approach has often raised concerns that antiglycolytic agents may cause serious side effects toward normal cells. The key to selective action against cancer cells can be found in their hyperbolic addiction to glycolysis, which may be exploited to generate new anticancer drugs with minimal toxicity. There is growing evidence to support many glycolytic enzymes and transporters as suitable candidate targets for cancer therapy. Herein we review some of the most relevant antiglycolytic agents that have been investigated thus far for the treatment of cancer.
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Affiliation(s)
- Carlotta Granchi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa (Italy)
| | - Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa (Italy)
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Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Bochkov DV, Sysolyatin SV, Kalashnikov AI, Surmacheva IA. Shikimic acid: review of its analytical, isolation, and purification techniques from plant and microbial sources. J Chem Biol 2012; 5:5-17. [PMID: 22826715 PMCID: PMC3251648 DOI: 10.1007/s12154-011-0064-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/14/2011] [Indexed: 11/26/2022] Open
Abstract
Shikimic acid properties and its available analytical techniques are discussed. Plants having the highest content of shikimic acid are shown. The existing isolation methods are analyzed and the most optimal approaches to extracting this acid from natural sources (plants and microorganisms) are considered.
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Affiliation(s)
- Denis V. Bochkov
- Institute for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), ul. Socialisticheskaya, 1, Biysk, 659322 Russia
| | - Sergey V. Sysolyatin
- Institute for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), ul. Socialisticheskaya, 1, Biysk, 659322 Russia
| | - Alexander I. Kalashnikov
- Institute for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), ul. Socialisticheskaya, 1, Biysk, 659322 Russia
| | - Irina A. Surmacheva
- Institute for Problems of Chemical and Energetic Technologies, Siberian Branch of the Russian Academy of Sciences (IPCET SB RAS), ul. Socialisticheskaya, 1, Biysk, 659322 Russia
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Frayne J, Taylor A, Cameron G, Hadfield AT. Structure of insoluble rat sperm glyceraldehyde-3-phosphate dehydrogenase (GAPDH) via heterotetramer formation with Escherichia coli GAPDH reveals target for contraceptive design. J Biol Chem 2009; 284:22703-12. [PMID: 19542219 PMCID: PMC2755679 DOI: 10.1074/jbc.m109.004648] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/21/2009] [Indexed: 11/06/2022] Open
Abstract
Sperm glyceraldehyde-3-phosphate dehydrogenase has been shown to be a successful target for a non-hormonal contraceptive approach, but the agents tested to date have had unacceptable side effects. Obtaining the structure of the sperm-specific isoform to allow rational inhibitor design has therefore been a goal for a number of years but has proved intractable because of the insoluble nature of both native and recombinant protein. We have obtained soluble recombinant sperm glyceraldehyde-3-phosphate dehydrogenase as a heterotetramer with the Escherichia coli glyceraldehyde-3-phosphate dehydrogenase in a ratio of 1:3 and have solved the structure of the heterotetramer which we believe represents a novel strategy for structure determination of an insoluble protein. A structure was also obtained where glyceraldehyde 3-phosphate binds in the P(s) pocket in the active site of the sperm enzyme subunit in the presence of NAD. Modeling and comparison of the structures of human somatic and sperm-specific glyceraldehyde-3-phosphate dehydrogenase revealed few differences at the active site and hence rebut the long presumed structural specificity of 3-chlorolactaldehyde for the sperm isoform. The contraceptive activity of alpha-chlorohydrin and its apparent specificity for the sperm isoform in vivo are likely to be due to differences in metabolism to 3-chlorolactaldehyde in spermatozoa and somatic cells. However, further detailed analysis of the sperm glyceraldehyde-3-phosphate dehydrogenase structure revealed sites in the enzyme that do show significant difference compared with published somatic glyceraldehyde-3-phosphate dehydrogenase structures that could be exploited by structure-based drug design to identify leads for novel male contraceptives.
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Affiliation(s)
- Jan Frayne
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Abby Taylor
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Gus Cameron
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
| | - Andrea T. Hadfield
- From the Department of Biochemistry, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom
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Link A, Heidler P, Kaiser M, Brun R. Parallel synthesis of a series of non-functional ATP/NAD analogs with activity against trypanosomatid parasites. Mol Divers 2009; 14:215-24. [PMID: 19484371 DOI: 10.1007/s11030-009-9160-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 05/09/2009] [Indexed: 11/29/2022]
Abstract
Non-functional analogs of the cofactors ATP and NAD are putative inhibitors of ATP- or NAD-dependant enzymes. Since pathogenic protozoa rely heavily on the salvage of purine nucleosides from the bloodstream of their host, such compounds are of interest as antiplasmodial and antitrypanosomal agents with a multitude of molecular targets. By replacing the negatively charged phosphate residues with a constrained unsaturated amide spacer and the nicotinamide moiety of NAD with various lipophilic substituents, 15 new ATP/NAD analogs were obtained in screening quantities. In these compounds, a 5'-desoxyadenosine moiety was conserved as key molecular recognition motif. The inhibition of P. falciparum and T. brucei ssp. in a whole parasite in vitro assay is reported.
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Affiliation(s)
- Andreas Link
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Strasse 17, 17487, Greifswald, Germany.
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Sharma P, Kumar A, Sahu V, Singh J. Calix[ n]arenes mediated phase-transfer catalytic synthesis of purine derivatives. INT J CHEM KINET 2009. [DOI: 10.1002/kin.20394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cook WJ, Senkovich O, Chattopadhyay D. An unexpected phosphate binding site in glyceraldehyde 3-phosphate dehydrogenase: crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme. BMC STRUCTURAL BIOLOGY 2009; 9:9. [PMID: 19243605 PMCID: PMC2662861 DOI: 10.1186/1472-6807-9-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022]
Abstract
Background The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate) and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips to the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate) proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. Results We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD) state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2Å resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate occupies an unexpected site not seen before and the phosphate binding loop remains in the substrate-free conformation. Orientation of the substrate with respect to the active site histidine and serine (in the mutant enzyme) also varies in different subunits. Conclusion The structures of the C. parvum GAPDH ternary complex and other GAPDH complexes demonstrate the plasticity of the substrate binding site. We propose that the active site of GAPDH can accommodate the substrate in multiple conformations at multiple locations during the initial encounter. However, the C-3 phosphate group clearly prefers the 'new Pi' site for initial binding in the active site.
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Affiliation(s)
- William J Cook
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Inhibitors of adenosine consuming parasites through polymer-assisted solution phase synthesis of lipophilic 5′-amido-5′-deoxyadenosine derivatives. Bioorg Med Chem 2009; 17:1428-36. [DOI: 10.1016/j.bmc.2009.01.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/12/2009] [Accepted: 01/13/2009] [Indexed: 11/19/2022]
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Soeiro MNC, de Castro SL. Trypanosoma cruzitargets for new chemotherapeutic approaches. Expert Opin Ther Targets 2008; 13:105-21. [DOI: 10.1517/14728220802623881] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Scatena R, Bottoni P, Pontoglio A, Mastrototaro L, Giardina B. Glycolytic enzyme inhibitors in cancer treatment. Expert Opin Investig Drugs 2008; 17:1533-45. [PMID: 18808312 DOI: 10.1517/13543784.17.10.1533] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND The radio- and chemotherapeutics currently used for the treatment of cancer are widely known to be characterized by a low therapeutic index. An interesting approach to overcoming some of the limits of these techniques is the exploitation of the so-called Warburg effect, which typically characterizes neoplastic cells. Interestingly, this feature has already been utilized with good results, but only for diagnostic purposes (PET and SPECT). From a pharmacological point of view, drugs able to perturb cancer cell metabolism, specifically at the level of glycolysis, may display interesting therapeutic activities in cancer. OBJECTIVE The pharmacological actions of these glycolytic enzyme inhibitors, based primarily on ATP depletion, could include: i) amelioration of drug selectivity by exploiting the particular glycolysis addiction of cancer cell; ii) inhibition of energetic and anabolic processes; iii) reduction of hypoxia-linked cancer-cell resistance; iv) reduction of ATP-dependent multi-drug resistance; and v) cytotoxic synergism with conventional cancer treatments. CONCLUSION Several glycolytic inhibitors are currently in preclinical and clinical development. Their clinical value as anticancer agents, above all in terms of therapeutic index, strictly depends on a careful reevaluation of the pathophyiological role of the unique metabolism of cancer cells in general and of Warburg effect in particular.
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Affiliation(s)
- Roberto Scatena
- Catholic University, Department of Laboratory Medicine, Largo A. Gemelli 8, 00168 Rome, Italy.
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O'Mahony G, Svensson S, Sundgren A, Grøtli M. Synthesis of 2'-([1,2,3]triazol-1-yl)-2'-deoxyadenosines. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:449-59. [PMID: 18569784 DOI: 10.1080/15257770802086880] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A reliable and efficient protocol for the synthesis of 2 '-([1,2,3]triazol-1-yl)-2 '-deoxyadenosine derivatives from vidarabine is presented. Vidarabine was converted to 2'-azido-2'-deoxy-3',5-O-(tetraisopropyldisiloxane-1,3-diyl)-adenosine. This azide was used as the starting material for the Cu(I)-catalyzed parallel synthesis of 1,2,3-triazoles using a variety of alkynes. The reactions proceeded in good yield and gave almost exclusively the 1,4-disubstituted 1,2,3-triazoles.
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Affiliation(s)
- Gavin O'Mahony
- Department of Chemistry, Medicinal Chemistry, Göteborg University, Göteborg, Sweden
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Bottoms CA, Xu D. Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate. BMC Bioinformatics 2008; 9 Suppl 9:S16. [PMID: 18793461 PMCID: PMC2537567 DOI: 10.1186/1471-2105-9-s9-s16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distinguish them from each other due to the lack of standardization. This issue has largely not been addressed by the protein structure community. RESULTS Of 472 diastereotopic atom pairs studied from the PDB, 118 were found to have names that are not uniquely assigned. Among the molecules identified with these inconsistencies were many cofactors of enzymatic processes such as mononucleotides (e.g. ADP, ATP, GTP), dinucleotide cofactors (e.g. FAD, NAD), and coenzyme A. There were no overall trends in naming conventions, though ligand-specific trends were prominent. CONCLUSION The lack of standardized naming conventions for diastereotopic atoms of small molecules has left the ad hoc names assigned to many of these atoms non-unique, which may create problems in data-mining of the PDB. We suggest a naming convention to resolve this issue. The in-house software used in this study is available upon request.A version of the software used for the analyses described in this paper is available at our web site: http://digbio.missouri.edu/ddan/DDAN.htm.
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Affiliation(s)
- Christopher A Bottoms
- Department of Computer Science and Christopher S, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Guido R, Castilho M, Mota S, Oliva G, Andricopulo A. Classical and Hologram QSAR Studies on a Series of Inhibitors of Trypanosomatid Glyceraldehyde‐3‐Phosphate Dehydrogenase. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200710139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Guido RVC, Oliva G, Montanari CA, Andricopulo AD. Structural Basis for Selective Inhibition of Trypanosomatid Glyceraldehyde-3-Phosphate Dehydrogenase: Molecular Docking and 3D QSAR Studies. J Chem Inf Model 2008; 48:918-29. [DOI: 10.1021/ci700453j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rafael V. C. Guido
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13560-970, São Carlos-SP, Brazil, and Grupo de Química Medicinal de Produtos Naturais, Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13566-970, São Carlos-SP, Brazil
| | - Glaucius Oliva
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13560-970, São Carlos-SP, Brazil, and Grupo de Química Medicinal de Produtos Naturais, Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13566-970, São Carlos-SP, Brazil
| | - Carlos A. Montanari
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13560-970, São Carlos-SP, Brazil, and Grupo de Química Medicinal de Produtos Naturais, Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13566-970, São Carlos-SP, Brazil
| | - Adriano D. Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13560-970, São Carlos-SP, Brazil, and Grupo de Química Medicinal de Produtos Naturais, Instituto de Química de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13566-970, São Carlos-SP, Brazil
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44
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Handman E, Kedzierski L, Uboldi AD, Goding JW. Fishing for anti-leishmania drugs: principles and problems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 625:48-60. [PMID: 18365658 DOI: 10.1007/978-0-387-77570-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
To date, there are no vaccines against any of the major parasitic diseases including leishmaniasis, and chemotherapy is the main weapon in our arsenal. Current drugs are toxic and expensive, and are losing their effectiveness due to parasite resistance. The availability of the genome sequence of two species of Leishmania, Leishmania major and Leishmania infantum, as well as that of Trypanosoma brucei and Trypanosoma cruzi should provide a cornucopia of potential new drug targets. Their exploitation will require a multi-disciplinary approach that includes protein structure and function and high throughput screening of random and directed chemical libraries, followed by in vivo testing in animals and humans. We outline the opportunities that are made possible by recent technologies, and potential problems that need to be overcome.
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Affiliation(s)
- Emanuela Handman
- Walter and Eliza Hall Institute of Medical Research, Victoria, Australia.
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45
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Chen L, Gao G, Felczak K, Bonnac L, Patterson SE, Wilson D, Bennett EM, Jayaram HN, Hedstrom L, Pankiewicz KW. Probing binding requirements of type I and type II isoforms of inosine monophosphate dehydrogenase with adenine-modified nicotinamide adenine dinucleotide analogues. J Med Chem 2007; 50:5743-51. [PMID: 17958343 DOI: 10.1021/jm070568j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel tiazofurin adenine dinucleotide (TAD) analogues 25-33 containing a substituent at C2 of the adenine ring have been synthesized as inhibitors of the two isoforms of human IMP-dehydrogenase. The 2-ethyl TAD analogue 33 [Ki = 1 nM (type I), Ki = 14 nM (type II)] was found to be the most potent. It did not inhibit three other cellular dehydrogenases up to 50 microM. Mycophenolic adenine bis(phosphonate)s containing a 2-phenyl (37) or 2-ethyl group (38), were prepared as metabolically stable compounds, both nanomolar inhibitors. Compound 38 [Ki = 16 nM (type I), Ki = 38 nM (type II)] inhibited proliferation of leukemic K562 cells (IC50 = 1.1 microM) more potently than tiazofurin (IC50 = 12.4 microM) or mycophenolic acid (IC50 = 7.7 microM).
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Affiliation(s)
- Liqiang Chen
- Center for Drug Design, University of Minnesota, Minneapolis, Minnesota 55455, USA
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46
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Rodenko B, van der Burg AM, Wanner MJ, Kaiser M, Brun R, Gould M, de Koning HP, Koomen GJ. 2,N6-disubstituted adenosine analogs with antitrypanosomal and antimalarial activities. Antimicrob Agents Chemother 2007; 51:3796-802. [PMID: 17698622 PMCID: PMC2151466 DOI: 10.1128/aac.00425-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A library of 2,N(6)-disubstituted adenosine analogs was synthesized and the analogs were tested for their antiprotozoal activities. It was found that 2-methoxy and 2-histamino and N(6)-m-iodobenzyl substitutions generally produced analogs with low levels of antiprotozoal activity. The best antiplasmodial activity was achieved with large aromatic substitutions, such as N(6)-2,2-diphenylethyl and naphthylmethyl, which could indicate a mechanism of action through aromatic stacking with heme in the digestive vacuole of Plasmodium spp. The activities against Trypanosoma cruzi trypomastigotes and Leishmania donovani amastigotes were generally low; but several analogs, particularly those with cyclopentylamino substitutions, displayed potent activities against Trypanosoma brucei rhodesiense and T. b. brucei bloodstream forms in vitro. The most active were 2-cyclopentylamino-N(6)-cyclopentyladenosine (compound NA42) and 2-cyclopentylamino-N(6)-cyclopentyladenine (compound NA134), with the nucleobase an order of magnitude more potent than the nucleoside, at 26 +/- 4 nM. It was determined that the mode of action of these purines was trypanostatic, with the compounds becoming trypanocidal only at much higher concentrations. Those 2,N(6)-disubstituted purines tested for their effects on purine transport in T. b. brucei displayed at best a moderate affinity for the transporters. It is highly probable that the large hydrophobic substitutions, which bestow high calculated octanol-water coefficient values on the analogs, allow them to diffuse across the membrane. Consistent with this view, the analogs were as effective against a T. b. brucei strain lacking the P2 nucleoside transporter as they were against the parental strain. As the analogs were not toxic to human cell lines, the purine analogs are likely to act on a trypanosome-specific target.
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Affiliation(s)
- Boris Rodenko
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, The Netherlands
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47
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Structure-Based Design and Synthesis of the First Weak Non-Phosphate Inhibitors for IspF, an Enzyme in the Non-Mevalonate Pathway of Isoprenoid Biosynthesis. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790105] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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48
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Laxman S, Riechers A, Sadilek M, Schwede F, Beavo JA. Hydrolysis products of cAMP analogs cause transformation of Trypanosoma brucei from slender to stumpy-like forms. Proc Natl Acad Sci U S A 2006; 103:19194-9. [PMID: 17142316 PMCID: PMC1748198 DOI: 10.1073/pnas.0608971103] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
African sleeping sickness is a disease caused by Trypanosoma brucei. T. brucei proliferate rapidly in the mammalian bloodstream as long, slender forms, but at higher population densities they transform into nondividing, short, stumpy forms. This is thought to be a mechanism adopted by T. brucei to establish a stable host-parasite relationship and to allow a transition into the insect stage of its life cycle. Earlier studies have suggested a role for cAMP in mediating this transformation. In this study, using membrane-permeable nucleotide analogs, we show that it is not the cAMP analogs themselves but rather the hydrolyzed products of membrane-permeable cAMP analogs that prevent proliferation of T. brucei. The metabolic products are more potent than the cAMP analogs, and hydrolysis-resistant cAMP analogs are not antiproliferative. We further show that the antiproliferative effect of these membrane-permeable adenosine analogs is caused by transformation into forms resembling short, stumpy bloodstream forms. These data suggest that the slender-to-stumpy transformation of T. brucei may not be mediated directly by cAMP and also raise the possibility of using such adenosine analogs as antitrypanosomal drugs.
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Affiliation(s)
| | | | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA 98195; and
| | - Frank Schwede
- BIOLOG Life Science Institute, Flughafendamm 9A, D-28199 Bremen, Germany
| | - Joseph A. Beavo
- *Department of Pharmacology
- To whom correspondence should be addressed. E-mail:
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49
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Marion N, Navarro O, Mei J, Stevens ED, Scott NM, Nolan SP. Modified (NHC)Pd(allyl)Cl (NHC = N-heterocyclic carbene) complexes for room-temperature Suzuki-Miyaura and Buchwald-Hartwig reactions. J Am Chem Soc 2006; 128:4101-11. [PMID: 16551119 DOI: 10.1021/ja057704z] [Citation(s) in RCA: 747] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of (NHC)Pd(R-allyl)Cl complexes [NHC: IPr = N,N'-bis(2,6-diisopropylphenyl)imidazol-2-ylidene, SIPr = N,N'-bis(2,6-diisopropylphenyl)-4,5-dihydroimidazol-2-ylidene; R = H, Me, gem-Me2, Ph] have been synthesized and fully characterized. When compared to (NHC)Pd(allyl)Cl, substitution at the terminal position of the allyl scaffold favors a more facile activation step. This translates into higher catalytic activity in the Suzuki-Miyaura and Buchwald-Hartwig reactions, allowing for the coupling of unactivated aryl chlorides at room temperature in minutes. In the Suzuki-Miyaura reaction, aryl triflates, bromides, and chlorides react with boronic acids using very low catalyst loading. In the N-aryl amination reaction, a wide range of substrates has been coupled efficiently; primary-, secondary-, alkyl-, or aryl-amines react in high yields with unactivated, neutral, and activated aryl chlorides and bromides. In both reactions, extremely hindered substrates such as tri-ortho-substituted biaryls and tetra-ortho-substituted diarylamines can be produced without loss of activity. Finally, the present catalytic system has proven to be efficient with as low as 10 parts-per-million (ppm) of precatalyst in the Buchwald-Hartwig reaction and 50 ppm in the Suzuki-Miyaura reaction.
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Affiliation(s)
- Nicolas Marion
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana 70148, USA
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50
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Robien MA, Bosch J, Buckner FS, Van Voorhis WCE, Worthey EA, Myler P, Mehlin C, Boni EE, Kalyuzhniy O, Anderson L, Lauricella A, Gulde S, Luft JR, DeTitta G, Caruthers JM, Hodgson KO, Soltis M, Zucker F, Verlinde CLMJ, Merritt EA, Schoenfeld LW, Hol WGJ. Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 A resolution reveals intriguing extra electron density in the active site. Proteins 2006; 62:570-7. [PMID: 16345073 DOI: 10.1002/prot.20801] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The crystal structure of D-glyceraldehyde-3-phosphate dehydrogenase (PfGAPDH) from the major malaria parasite Plasmodium falciparum is solved at 2.25 A resolution. The structure of PfGAPDH is of interest due to the dependence of the malaria parasite in infected human erythrocytes on the glycolytic pathway for its energy generation. Recent evidence suggests that PfGAPDH may also be required for other critical activities such as apical complex formation. The cofactor NAD(+) is bound to all four subunits of the tetrameric enzyme displaying excellent electron densities. In addition, in all four subunits a completely unexpected large island of extra electron density in the active site is observed, approaching closely the nicotinamide ribose of the NAD(+). This density is most likely the protease inhibitor AEBSF, found in maps from two different crystals. This putative AEBSF molecule is positioned in a crucial location and hence our structure, with expected and unexpected ligands bound, can be of assistance in lead development and design of novel antimalarials.
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Affiliation(s)
- Mark A Robien
- Structural Genomics of Pathogenic Protozoa (SGPP), Department of Biochemistry, University of Washington, Seattle 98195, USA
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