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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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Moreira RS, Calomeno NA, das Neves GB, do Nascimento LFN, Filho VB, Wagner G, Miletti LC. Trypanosoma evansi secretome carries potential biomarkers for Surra diagnosis. J Proteomics 2023; 272:104789. [PMID: 36464092 DOI: 10.1016/j.jprot.2022.104789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Trypanosoma evansi is a parasite that is phylogenetically close to Trypanosoma brucei and is the causative agent of a disease known as surra. Surra is responsible for a high mortality rate in livestock and large economic losses in the Americas, Africa, and Asia. This work aimed to analyze in vitro secreted proteins from T. evansi and identify potential treatment and diagnostic biomarkers for surra diagnosis. Two groups were used. In one group the parasites were purified using a DEAE-Cellulose column and maintained in a secretion medium while in the other group the parasites were not purified. Each group was further divided to be maintained at either 37 °C or 27 °C. We identified 246 proteins through mass spectrometry and found that the temperature appears to modulate protein secretion. We found minimal variations in the protein pools from pure and non-purified sets. We observed an emphasis on proteins associated to vesicles, glycolysis, and cellular homeostasis through the enrichment of GO. Also, we found that most secretome proteins share homologous proteins with T. b. brucei, T. b. gambiense, T. vivax, T. equiperdum, and T. b. rhodesiense secretome but unique T. evansi epitopes with potential biomarkers for surra diagnosis were detected. SIGNIFICANCE: Trypanosoma evansi is a parasite of African origin that is phylogenetically close to Trypanosoma brucei. As with other trypanosomatids and blood parasites, its infection causes non-pathognomonic symptoms, which makes its diagnosis difficult. One great problem is the fact that no diagnostic test differentiates between Trypanosoma equiperdum and T. evansi, which is a problem in South America and Asia, and Africa. Thus, it is urgent to study the biochemistry of the parasite to discover proteins that can be used for differential diagnosis or be possible therapeutic targets. In addition, the study of the secretome can point out proteins that are used by the parasite in its interactions with the host, helping to understand the progression of the disease.
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Affiliation(s)
- Renato Simões Moreira
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil; Instituto Federal de Santa Catarina (IFSC), Campus Gaspar, R. Adriano Kormann, 510 - Bela Vista, Gaspar, SC 89111-009, Brazil
| | - Nathália Anderson Calomeno
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Gabriella Bassi das Neves
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Luiz Flávio Nepomuceno do Nascimento
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil
| | - Vilmar Benetti Filho
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Glauber Wagner
- Laboratório de Bioinformática, Universidade Federal de Santa Catarina, Campus João David Ferreira Lima, Setor F, Bloco A, Sala 318, Caixa postal 476, Trindade, Florianópolis, SC 88040-970, Brazil
| | - Luiz Claudio Miletti
- Laboratório de Hemoparasitas e Vetores, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Av. Luís de Camões, 2090, Conta Dinheiro, Lages, SC 88520-000, Brazil.
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3
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Jung Y, Noda N, Takaya J, Abo M, Toh K, Tajiri K, Cui C, Zhou L, Sato SI, Uesugi M. Discovery of Non-Cysteine-Targeting Covalent Inhibitors by Activity-Based Proteomic Screening with a Cysteine-Reactive Probe. ACS Chem Biol 2022; 17:340-347. [PMID: 35076225 DOI: 10.1021/acschembio.1c00824] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covalent inhibitors of enzymes are increasingly appreciated as pharmaceutical seeds, yet discovering non-cysteine-targeting inhibitors remains challenging. Herein, we report an intriguing experience during our activity-based proteomic screening of 1601 reactive small molecules, in which we monitored the ability of library molecules to compete with a cysteine-reactive iodoacetamide probe. One epoxide molecule, F8, exhibited unexpected enhancement of the probe reactivity for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a rate-limiting glycolysis enzyme. In-depth mechanistic analysis suggests that F8 forms a covalent adduct with an aspartic acid in the active site to displace NAD+, a cofactor of the enzyme, with concomitant enhancement of the probe reaction with the catalytic cysteine. The mechanistic underpinning permitted the identification of an optimized aspartate-reactive GAPDH inhibitor. Our findings exemplify that activity-based proteomic screening with a cysteine-reactive probe can be used for discovering covalent inhibitors that react with non-cysteine residues.
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Affiliation(s)
- Yejin Jung
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Naotaka Noda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Junichiro Takaya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiro Abo
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kohei Toh
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Tajiri
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Changyi Cui
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shin-ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
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Nogueira WG, Jaiswal AK, Tiwari S, Ramos RTJ, Ghosh P, Barh D, Azevedo V, Soares SC. Computational identification of putative common genomic drug and vaccine targets in Mycoplasma genitalium. Genomics 2021; 113:2730-2743. [PMID: 34118385 DOI: 10.1016/j.ygeno.2021.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Mycoplasma genitalium is an obligate intracellular bacterium that is responsible for several sexually transmitted infections, including non-gonococcal urethritis in men and several inflammatory reproductive tract syndromes in women. Here, we applied subtractive genomics and reverse vaccinology approaches for in silico prediction of potential vaccine and drug targets against five strains of M. genitalium. We identified 403 genes shared by all five strains, from which 104 non-host homologous proteins were selected, comprising of 44 exposed/secreted/membrane proteins and 60 cytoplasmic proteins. Based on the essentiality, functionality, and structure-based binding affinity, we finally predicted 19 (14 novel) putative vaccine and 7 (2 novel) candidate drug targets. The docking analysis showed six molecules from the ZINC database as promising drug candidates against the identified targets. Altogether, both vaccine candidates and drug targets identified here may contribute to the future development of therapeutic strategies to control the spread of M. genitalium worldwide.
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Affiliation(s)
- Wylerson G Nogueira
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Arun Kumar Jaiswal
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.; Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil..
| | - Rommel T J Ramos
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond VA-23284, USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C Soares
- Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
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5
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Schormann N, Campos J, Motamed R, Hayden KL, Gould JR, Green TJ, Senkovich O, Banerjee S, Ulett GC, Chattopadhyay D. Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding. Protein Sci 2020; 29:2446-2458. [PMID: 33058314 DOI: 10.1002/pro.3975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/27/2022]
Abstract
Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is an evolutionarily conserved essential enzyme in the glycolytic pathway. GAPDH is also involved in a wide spectrum of non-catalytic cellular 'moonlighting' functions. Bacterial surface-associated GAPDHs engage in many host interactions that aid in colonization, pathogenesis, and virulence. We have structurally and functionally characterized the recombinant GAPDH of the obligate intracellular bacteria Chlamydia trachomatis, the leading cause of sexually transmitted bacterial and ocular infections. Contrary to earlier speculations, recent data confirm the presence of glucose-catabolizing enzymes including GAPDH in both stages of the biphasic life cycle of the bacterium. The high-resolution crystal structure described here provides a close-up view of the enzyme's active site and surface topology and reveals two chemically modified cysteine residues. Moreover, we show for the first time that purified C. trachomatis GAPDH binds to human plasminogen and plasmin. Based on the versatility of GAPDH's functions, data presented here emphasize the need for investigating the Chlamydiae GAPDH's involvement in biological functions beyond energy metabolism.
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Affiliation(s)
- Norbert Schormann
- Department of Biochemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Juan Campos
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Rachael Motamed
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Katherine L Hayden
- Department of Chemistry and Physics, Birmingham-Southern College, Birmingham, Alabama, USA
| | - Joseph R Gould
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga Senkovich
- Department of Biochemistry and Molecular Genetics, Midwestern University, Glendale, Arizona, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois, USA
| | - Glen C Ulett
- School of Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Parklands, Australia
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6
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Muronetz VI, Melnikova AK, Barinova KV, Schmalhausen EV. Inhibitors of Glyceraldehyde 3-Phosphate Dehydrogenase and Unexpected Effects of Its Reduced Activity. BIOCHEMISTRY (MOSCOW) 2019; 84:1268-1279. [PMID: 31760917 DOI: 10.1134/s0006297919110051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The review describes the use of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) inhibitors to study the enzyme and to suppress its activity in various cell types. The main problem of selective GAPDH inhibition is a highly conserved nature of the enzyme active site and, especially, Cys150 environment important for the catalytic action of cysteine sulfhydryl group. Numerous attempts to find specific inhibitors of sperm GAPDH and enzymes from Trypanosoma sp. and Mycobacterium tuberculosis that would not inhibit GAPDH of somatic mammalian cells have failed, which has pushed researchers to search for new ways to solve this problem. The sections of the review are devoted to the studies of GAPDH inactivation by reactive oxygen species, glutathione, and glycating agents. The final section discusses possible effects of GAPDH inhibition and inactivation on glycolysis and related metabolic pathways (pentose phosphate pathway, uncoupling of the glycolytic oxidation and phosphorylation, etc.).
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Affiliation(s)
- V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia
| | - A K Melnikova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia
| | - K V Barinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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7
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Roca C, Sebastián-Pérez V, Campillo NE. In silico Tools for Target Identification and Drug Molecular Docking in Leishmania. DRUG DISCOVERY FOR LEISHMANIASIS 2017. [DOI: 10.1039/9781788010177-00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neglected tropical diseases represent a significant health burden in large parts of the world. Drug discovery is currently a key bottleneck in the pipeline of these diseases. In this chapter, the in silico approaches used for the processes involved in drug discovery, identification and validation of druggable Leishmania targets, and design and optimisation of new anti-leishmanial drugs are discussed. We also provide a general view of the different computational tools that can be employed in pursuit of this aim, along with the most interesting cases found in the literature.
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Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
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8
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Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LDJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo VAC. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 2017; 12:e0186401. [PMID: 29049350 PMCID: PMC5648181 DOI: 10.1371/journal.pone.0186401] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 09/29/2017] [Indexed: 01/03/2023] Open
Abstract
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms.
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Affiliation(s)
- Syed Babar Jamal
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Syed Shah Hassan
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Sandeep Tiwari
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcus V. Viana
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leandro de Jesus Benevides
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Asad Ullah
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, Argentina
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Daniela Arruda Costa
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Artur Silva
- Institute of Biologic Sciences, Federal University of Para, Belém, PA, Brazil
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Vasco A. C. Azevedo
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of General Biology (LGCM), Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
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9
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An In Silico Identification of Common Putative Vaccine Candidates against Treponema pallidum: A Reverse Vaccinology and Subtractive Genomics Based Approach. Int J Mol Sci 2017; 18:ijms18020402. [PMID: 28216574 PMCID: PMC5343936 DOI: 10.3390/ijms18020402] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/22/2017] [Accepted: 01/27/2017] [Indexed: 01/28/2023] Open
Abstract
Sexually transmitted infections (STIs) are caused by a wide variety of bacteria, viruses, and parasites that are transmitted from one person to another primarily by vaginal, anal, or oral sexual contact. Syphilis is a serious disease caused by a sexually transmitted infection. Syphilis is caused by the bacterium Treponema pallidum subspecies pallidum. Treponema pallidum (T. pallidum) is a motile, gram-negative spirochete, which can be transmitted both sexually and from mother to child, and can invade virtually any organ or structure in the human body. The current worldwide prevalence of syphilis emphasizes the need for continued preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine targets and putative drugs against syphilis disease using reverse vaccinology and subtractive genomics. We compared 13 strains of T. pallidum using T. pallidum Nichols as the reference genome. Using an in silicoapproach, four pathogenic islands were detected in the genome of T. pallidum Nichols. We identified 15 putative antigenic proteins and sixdrug targets through reverse vaccinology and subtractive genomics, respectively, which can be used as candidate therapeutic targets in the future.
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Novel concept of enzyme selective nicotinamide adenine dinucleotide (NAD)-modified inhibitors based on enzyme taxonomy from the diphosphate conformation of NAD. Bioorg Med Chem Lett 2015; 25:5133-6. [PMID: 26463132 DOI: 10.1016/j.bmcl.2015.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/29/2015] [Accepted: 10/03/2015] [Indexed: 11/23/2022]
Abstract
The dihedral angle θ of the diphosphate part of NAD(P) were investigated to distinguish the differences in the binding-conformation of NAD(P) to enzymes and to create an enzyme taxonomy. Furthermore, new inhibitors with fixed dihedral angles showed that enzymes could recognize the differences in the dihedral angle θ. We suggest the taxonomy and the dihedral angle θ are important values for chemists to consider when designing inhibitors and drugs that target enzymes.
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11
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Merritt C, Silva L, Tanner AL, Stuart K, Pollastri MP. Kinases as druggable targets in trypanosomatid protozoan parasites. Chem Rev 2014; 114:11280-304. [PMID: 26443079 PMCID: PMC4254031 DOI: 10.1021/cr500197d] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/21/2022]
Affiliation(s)
- Christopher Merritt
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Lisseth
E. Silva
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Angela L. Tanner
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kenneth Stuart
- Seattle
Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109-5219, United States
| | - Michael P. Pollastri
- Department
of Chemistry & Chemical Biology, Northeastern
University, 417 Egan
Research Center, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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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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13
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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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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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15
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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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16
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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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17
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Dixit SS, Upadhayaya RS, Chattopadhyaya J. New parasite inhibitors encompassing novel conformationally-locked 5′-acyl sulfamoyl adenosines. Org Biomol Chem 2012; 10:6121-9. [DOI: 10.1039/c2ob25879j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Structure and kinetic characterization of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase, GAPDS. Biochem J 2011; 435:401-9. [DOI: 10.1042/bj20101442] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
hGAPDS (human sperm-specific glyceraldehyde-3-phosphate dehydrogenase) is a glycolytic enzyme essential for the survival of spermatozoa, and constitutes a potential target for non-hormonal contraception. However, enzyme characterization of GAPDS has been hampered by the difficulty in producing soluble recombinant protein. In the present study, we have overexpressed in Escherichia coli a highly soluble form of hGAPDS truncated at the N-terminus (hGAPDSΔN), and crystallized the homotetrameric enzyme in two ligand complexes. The hGAPDSΔN–NAD+–phosphate structure maps the two anion-recognition sites within the catalytic pocket that correspond to the conserved Ps site and the newly recognized Pi site identified in other organisms. The hGAPDSΔN–NAD+–glycerol structure shows serendipitous binding of glycerol at the Ps and new Pi sites, demonstrating the propensity of these anion-recognition sites to bind non-physiologically relevant ligands. A comparison of kinetic profiles between hGAPDSΔN and its somatic equivalent reveals a 3-fold increase in catalytic efficiency for hGAPDSΔN. This may be attributable to subtle amino acid substitutions peripheral to the active centre that influence the charge properties and protonation states of catalytic residues. Our data therefore elucidate structural and kinetic features of hGAPDS that might provide insightful information towards inhibitor development.
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Butterfield DA, Hardas SS, Lange MLB. Oxidatively modified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Alzheimer's disease: many pathways to neurodegeneration. J Alzheimers Dis 2010; 20:369-93. [PMID: 20164570 DOI: 10.3233/jad-2010-1375] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recently, the oxidoreductase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has become a subject of interest as more and more studies reveal a surfeit of diverse GAPDH functions, extending beyond traditional aerobic metabolism of glucose. As a result of multiple isoforms and cellular locales, GAPDH is able to come in contact with a variety of small molecules, proteins, membranes, etc., that play important roles in normal and pathologic cell function. Specifically, GAPDH has been shown to interact with neurodegenerative disease-associated proteins, including the amyloid-beta protein precursor (AbetaPP). Studies from our laboratory have shown significant inhibition of GAPDH dehydrogenase activity in Alzheimer's disease (AD) brain due to oxidative modification. Although oxidative stress and damage is a common phenomenon in the AD brain, it would seem that inhibition of glycolytic enzyme activity is merely one avenue in which AD pathology affects neuronal cell development and survival, as oxidative modification can also impart a toxic gain-of-function to many proteins, including GAPDH. In this review, we examine the many functions of GAPDH with respect to AD brain; in particular, the apparent role(s) of GAPDH in AD-related apoptotic cell death is emphasized.
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Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, University of Kentucky, Center of Membrane Sciences, Lexington, KY40506-0055, USA.
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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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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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23
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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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25
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Quan J, Xu JM, Liu BK, Zheng CZ, Lin XF. Synthesis and characterization of drug–saccharide conjugates by enzymatic strategy in organic media. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Dolezal K, Popa I, Hauserová E, Spíchal L, Chakrabarty K, Novák O, Krystof V, Voller J, Holub J, Strnad M. Preparation, biological activity and endogenous occurrence of N6-benzyladenosines. Bioorg Med Chem 2007; 15:3737-47. [PMID: 17418578 DOI: 10.1016/j.bmc.2007.03.038] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 03/06/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Cytokinin activity of forty-eight 6-benzyladenosine derivatives at both the receptor and cellular levels as well as their anticancer properties were compared in various in vitro assays. The compounds were prepared by the condensation of 6-chloropurine riboside with corresponding substituted benzylamines and characterized by standard collection of physico-chemical methods. The majority of synthesized derivatives exhibited high activity in all three of the cytokinin bioassays used (tobacco callus, wheat leaf senescence and Amaranthus bioassay). The highest activities were observed in the senescence bioassay. For several of the compounds tested, significant differences in activity were found between the bioassays used, indicating that diverse recognition systems may operate. This suggests that it may be possible to modulate particular cytokinin-dependent processes with specific compounds. In contrast to their high activity in bioassays, the tested compounds were recognized with only very low sensitivity in both Arabidopsis thaliana AHK3 and AHK4 receptor assays. The prepared derivatives were also investigated for their antiproliferative properties on cancer and normal cell lines. Several of them showed very strong cytotoxic activity against various cancer cell lines. On the other hand, they were not cytotoxic for normal murine fibroblast (NIH/3T3) cell line. This anticancer activity of cytokinin ribosides may be important, given that several of them occur as endogenous compounds in different organisms.
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Affiliation(s)
- Karel Dolezal
- Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany AS CR, Slechtitelů 11, 783 71 Olomouc, Czech Republic.
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Rejman D, Olesiak M, Chen L, Patterson SE, Wilson D, Jayaram HN, Hedstrom L, Pankiewicz KW. Novel methylenephosphophosphonate analogues of mycophenolic adenine dinucleotide. Inhibition of inosine monophosphate dehydrogenase. J Med Chem 2006; 49:5018-22. [PMID: 16884314 DOI: 10.1021/jm060479r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Novel methylenephosphophosphonate analogues of mycophenolic adenine dinucleotide (MAD) have been prepared as potential inhibitors of IMP dehydrogenase. A coupling of the mycophenolic (hydroxymethyl)phosphonate 6 with the phosphitylated adenosine analogue 11 followed by oxidation and deprotection afforded the phosphophosphonate 8. A similar coupling between adenosine (hydroxymethyl)phosphonate 10 and phosphitylated mycophenolic alcohol 5 gave the corresponding phosphophosphonate 13. Both 8 and 13 (Ki = 20-87 nM) were found to be the most potent cofactor type inhibitors of IMP dehydrogenase.
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Affiliation(s)
- Dominik Rejman
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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28
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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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29
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Laezza C, Notarnicola M, Caruso MG, Messa C, Macchia M, Bertini S, Minutolo F, Portella G, Fiorentino L, Stingo S, Bifulco M. N6‐isopentenyladenosine arrests tumor cell proliferation by inhibiting farnesyl diphosphate synthase and protein prenylation. FASEB J 2006; 20:412-8. [PMID: 16507758 DOI: 10.1096/fj.05-4044lsf] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The physiological effects of a variety of N6-substituted adenine and adenosine derivatives called cytokinins have been documented in plants, but information on their occurrence and function in other biological system is limited. Here we investigated the anti-proliferative effect of N6-isopentenyladenosine (i6A), an adenosine and isoprenoid derivative, in a thyroid cell system, FRTL-5 wild-type, and K-ras transformed KiMol cells. Addition of i6A to FRTL-5 cells caused a dose-dependent arrest of the G0-G1 cell phase transition associated with a reduction of cells in the S phase that was much more evident in KiMol cells. I6A arrested tumor cell proliferation by inhibiting farnesyl diphosphate synthase (FPPS) and protein prenylation. Indeed the addition of farnesol reversed these effects and i6A affected protein prenylation, in particular lamin B processing. I6A effect was not mediated by the adenosine receptor but was due to a direct modulation of FPPS enzyme activity as a result of its uptake inside the cells. I6A inhibited FPPS activity more efficaciously in KiMol cells than in normal FRTL-5. Moreover, the i6A anti-proliferative effect was evaluated in vivo in a nude mouse xenograft model, where KiMol cells were implanted subcutaneously. Mice treated with i6A showed a drastic reduction in tumor volume. Our findings indicate that this isoprenoid end product might be used for antineoplastic therapy, an application emulating that of the lovastatin and/or farnesyl-transferase inhibitors
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Affiliation(s)
- Chiara Laezza
- Istituto di Endocrinologia e Oncologia Sperimentale. I.E.O.S., CNR, Bari, Italy.
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30
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Moyersoen J, Choe J, Fan E, Hol WGJ, Michels PAM. Biogenesis of peroxisomes and glycosomes: trypanosomatid glycosome assembly is a promising new drug target. FEMS Microbiol Rev 2005; 28:603-43. [PMID: 15539076 DOI: 10.1016/j.femsre.2004.06.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 06/14/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022] Open
Abstract
In trypanosomatids (Trypanosoma and Leishmania), protozoa responsible for serious diseases of mankind in tropical and subtropical countries, core carbohydrate metabolism including glycolysis is compartmentalized in peculiar peroxisomes called glycosomes. Proper biogenesis of these organelles and the correct sequestering of glycolytic enzymes are essential to these parasites. Biogenesis of glycosomes in trypanosomatids and that of peroxisomes in other eukaryotes, including the human host, occur via homologous processes involving proteins called peroxins, which exert their function through multiple, transient interactions with each other. Decreased expression of peroxins leads to death of trypanosomes. Peroxins show only a low level of sequence conservation. Therefore, it seems feasible to design compounds that will prevent interactions of proteins involved in biogenesis of trypanosomatid glycosomes without interfering with peroxisome formation in the human host cells. Such compounds would be suitable as lead drugs against trypanosomatid-borne diseases.
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Affiliation(s)
- Juliette Moyersoen
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, ICP-TROP 74.39, Avenue Hippocrate 74, B-1200 Brussels, Belgium
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31
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Ladame S, Fauré R, Denier C, Lakhdar-Ghazal F, Willson M. Selective inhibition of Trypanosoma cruzi GAPDH by “bi-substrate” analogues. Org Biomol Chem 2005; 3:2070-2. [PMID: 15917890 DOI: 10.1039/b504703j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new series of "bi-substrate" analogues have been synthesized as potential inhibitors of the glyceraldehyde-3-phosphate dehydrogenase and one lead compound has been identified that inhibits the enzyme from Trypanosoma cruzi with good affinity and very high (50-fold) specificity.
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Affiliation(s)
- Sylvain Ladame
- University Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, UK.
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32
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Menezes IRA, Lopes JCD, Montanari CA, Oliva G, Pavão F, Castilho MS, Vieira PC, Pupo MT. 3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi. J Comput Aided Mol Des 2004; 17:277-90. [PMID: 14635721 DOI: 10.1023/a:1026171723068] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Drug design strategies based on Comparative Molecular Field Analysis (CoMFA) have been used to predict the activity of new compounds. The major advantage of this approach is that it permits the analysis of a large number of quantitative descriptors and uses chemometric methods such as partial least squares (PLS) to correlate changes in bioactivity with changes in chemical structure. Because it is often difficult to rationalize all variables affecting the binding affinity of compounds using CoMFA solely, the program GRID was used to describe ligands in terms of their molecular interaction fields, MIFs. The program VolSurf that is able to compress the relevant information present in 3D maps into a few descriptors can treat these GRID fields. The binding affinities of a new set of compounds consisting of 13 coumarins, for one of which the three-dimensional ligand-enzyme bound structure is known, were studied. A final model based on the mentioned programs was independently validated by synthesizing and testing new coumarin derivatives. By relying on our knowledge of the real physical data (i.e., combining crystallographic and binding affinity results), it is also shown that ligand-based design agrees with structure-based design. The compound with the highest binding affinity was the coumarin chalepin, isolated from Rutaceae species, with an IC50 value of 55.5 microM towards the enzyme glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) from glycosomes of the parasite Trypanosoma cruzi, the causative agent of Chagas' disease. The proposed models from GRID MIFs have revealed the importance of lipophilic interactions in modulating the inhibition, but without excluding the dependence on stereo-electronic properties as found from CoMFA fields.
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Affiliation(s)
- Irwin R A Menezes
- Núcleo de Estudos em Química Medicinal, NEQUIM, Chemistry Department, University of Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
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33
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Leitão A, Andricopulo AD, Oliva G, Pupo MT, de Marchi AA, Vieira PC, da Silva MFGF, Ferreira VF, de Souza MCBV, Sá MM, Moraes VRS, Montanari CA. Structure–activity relationships of novel inhibitors of glyceraldehyde-3-phosphate dehydrogenase. Bioorg Med Chem Lett 2004; 14:2199-204. [PMID: 15081008 DOI: 10.1016/j.bmcl.2004.02.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2003] [Revised: 02/05/2004] [Accepted: 02/05/2004] [Indexed: 11/17/2022]
Abstract
3D QSAR studies were performed on a library of 120 GAPDH inhibitors, including a series of coumarins, flavonoids, and nucleosides. The VolSurf method was successfully used to calculate surface descriptors for protein-ligand affinity and binding site of the enzyme. PCA/PLS analyses have permitted the evaluation of the structural features crucial for potency, selectivity, and favorable pharmacokinetic properties, and are important for the design of new ligands.
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Affiliation(s)
- Andrei Leitão
- Departamento de Química, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte-MG, Brazil
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34
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Abstract
The discovery and optimization of antiparasitic compounds has profited by information-based methods newly emerged in the modern drug development process. The generation of computer models enables the cost-efficient and fast computational screening of virtual compound libraries for biologically active molecules. Two sources of information are available: structure-based drug design utilizes information about the disease target. We describe two different computational approaches, realized as the fast, flexible docking program FlexX and as the de novo design program LUDI. Ligand-based drug design, on the other hand, requires the structures and experimental data from biologically active compounds. Parasitic targets and antiparasitic compounds studied by various information-based methods include trypanosomal trypanothione reductase, antiprotozoal bisphosphonates, and trypanosomal glycosomal glyceraldehyde-3-phosphate dehydrogenase.
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Affiliation(s)
- Kristina Wolf
- 4SC AG, Am Klopferspitz 19a, 82152 Martinsried, Germany
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35
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Choe J, Suresh S, Wisedchaisri G, Kennedy KJ, Gelb MH, Hol WGJ. Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase. CHEMISTRY & BIOLOGY 2002; 9:1189-97. [PMID: 12445769 DOI: 10.1016/s1074-5521(02)00243-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. Using the adenine part of NAD as a lead compound, several 2,6-disubstituted purines were synthesized as inhibitors of Leishmania mexicana GPDH (LmGPDH). The electron densities for the inhibitor 2-bromo-6-chloro-purine bound to LmGPDH using a "conventional" wavelength around 1 A displayed a quasisymmetric shape. The anomalous signals from data collected at 1.77 A clearly indicated the positions of the halogen atoms and revealed the multiple binding modes of this inhibitor. Intriguing differences in the observed binding modes of the inhibitor between very similarly prepared crystals illustrate the possibility of crystal-to-crystal variations in protein-ligand complex structures.
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Affiliation(s)
- Jungwoo Choe
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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36
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Bottoms CA, Smith PE, Tanner JJ. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Protein Sci 2002; 11:2125-37. [PMID: 12192068 PMCID: PMC2373605 DOI: 10.1110/ps.0213502] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A computational comparison of 102 high-resolution (</=1.90 A) enzyme-dinucleotide (NAD, NADP, FAD) complexes was performed to investigate the role of solvent in dinucleotide recognition by Rossmann fold domains. The typical binding site contains about 9-12 water molecules, and about 30% of the hydrogen bonds between the protein and the dinucleotide are water mediated. Detailed inspection of the structures reveals a structurally conserved water molecule bridging dinucleotides with the well-known glycine-rich phosphate-binding loop. This water molecule displays a conserved hydrogen-bonding pattern. It forms hydrogen bonds to the dinucleotide pyrophosphate, two of the three conserved glycine residues of the phosphate-binding loop, and a residue at the C-terminus of strand four of the Rossmann fold. The conserved water molecule is also present in high-resolution structures of apo enzymes. However, the water molecule is not present in structures displaying significant deviations from the classic Rossmann fold motif, such as having nonstandard topology, containing a very short phosphate-binding loop, or having alpha-helix "A" oriented perpendicular to the beta-sheet. Thus, the conserved water molecule appears to be an inherent structural feature of the classic Rossmann dinucleotide-binding domain.
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37
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Pavão F, Castilho MS, Pupo MT, Dias RLA, Correa AG, Fernandes JB, da Silva MFGF, Mafezoli J, Vieira PC, Oliva G. Structure of Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 A resolution. FEBS Lett 2002; 520:13-7. [PMID: 12044862 DOI: 10.1016/s0014-5793(02)02700-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The structure of the glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) from Trypanosoma cruzi complexed with chalepin, a natural product from Pilocarpus spicatus, has been determined by X-ray crystallography to 1.95 A resolution. The structure is in the apo form without cofactors in the subunits of the tetrameric gGAPDH in the asymmetric unit. Unequivocal density corresponding to the inhibitor was clearly identified in one monomer. The final refined model of the complex shows extensive conformational changes when compared with the native structure. The mode of binding of chalepin to gGAPDH and its implications for inhibitor design are discussed.
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Affiliation(s)
- F Pavão
- Instituto de Química de São Carlos, USP, São Carlos, SP, Brazil
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38
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Zubrzycki IZ. Homology modeling and molecular dynamics study of NAD-dependent glycerol-3-phosphate dehydrogenase from Trypanosoma brucei rhodesiense, a potential target enzyme for anti-sleeping sickness drug development. Biophys J 2002; 82:2906-15. [PMID: 12023213 PMCID: PMC1302078 DOI: 10.1016/s0006-3495(02)75631-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sleeping sickness and Chagas disease are among the most severe diseases in Africa as well as Latin America. These two diseases are caused by Trypanosoma spp. Recently, an enzyme of a glycolytic pathway, NAD-dependent glycerol-3-phosphate dehydrogenase, of Leishmania mexicana was crystallized and its structure determined by x-ray crystallography. This structure has offered an excellent template for modeling of the homologous enzymes from another Trypanosoma species. Here, a homology model of the T. brucei enzyme based on the x-ray structure of LmGPDH has been generated. This model was used as the starting point for molecular dynamics simulation in a water box. The analysis of the molecular dynamics trajectory indicates that the functionally important motifs have both a very stable secondary structure and tertiary arrangement.
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Affiliation(s)
- Igor Z Zubrzycki
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
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39
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Golisade A, Herforth C, Quirijnen L, Maes L, Link A. Improving an antitrypanosomal lead applying nucleophilic substitution on a safety catch linker. Bioorg Med Chem 2002; 10:159-65. [PMID: 11738617 DOI: 10.1016/s0968-0896(01)00253-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In a joint effort with various laboratories we have been aiming at the structure-based design of glycolysis inhibitors as anti-trypanosomal drugs. 2'-Deoxy-2'-(3-methoxybenzamido)-N(6)-(1-naphtylmethyl)adenosine (1a) was thus revealed as a promising lead structure for the development of selective agents against protozoan parasites. Here we describe the polymer-assisted synthesis of novel amido derivatives of the scaffold 2'-amino-2'-deoxy-N(6)-(1-naphtylmethyl)adenosine (5a) we reported recently. This building block synthesized in solution was treated with an excess of polymer-supported carboxylic acids leading to chemoselective, practically quantitative conversion of the amine to the desired analogous amides. The best compound (1h) from this series was obtained after on-bead nucleophilic substitution of the carboxylic acid equivalent attached to the Kenner safety catch linker and exhibited an improved inhibitory effect on T. b. brucei blood stream forms with an IC(50) of 0.85 microM in vitro
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Affiliation(s)
- Abolfasl Golisade
- Institut für Pharmazie, Abteilung für Pharmazeutische Chemie, Universität Hamburg, Bundesstrasse 45, D-20146, Hamburg, Germany
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40
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Bressi JC, Verlinde CLMJ, Aronov AM, Shaw ML, Shin SS, Nguyen LN, Suresh S, Buckner FS, Van Voorhis WC, Kuntz ID, Hol WGJ, Gelb MH. Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of Trypanosomatidae via structure-based drug design. J Med Chem 2001; 44:2080-93. [PMID: 11405646 PMCID: PMC2957370 DOI: 10.1021/jm000472o] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In our continuation of the structure-based design of anti-trypanosomatid drugs, parasite-selective adenosine analogues were identified as low micromolar inhibitors of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana, and human GAPDH's provided details of how the adenosyl moiety of NAD(+) interacts with the proteins, and this facilitated the understanding of the relative affinities of a series of adenosine analogues for the various GAPDH's. From exploration of modifications of the naphthalenemethyl and benzamide substituents of a lead compound, N(6)-(1-naphthalenemethyl)-2'-deoxy-2'-(3-methoxybenzamido)adenosine (6e), N(6)-(substituted-naphthalenemethyl)-2'-deoxy-2'-(substituted-benzamido)adenosine analogues were investigated. N(6)-(1-Naphthalenemethyl)-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (6m), N(6)-[1-(3-hydroxynaphthalene)methyl]-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (7m), N(6)-[1-(3-methoxynaphthalene)methyl]-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (9m), N(6)-(2-naphthalenemethyl)-2'-deoxy-2'-(3-methoxybenzamido)adenosine (11e), and N(6)-(2-naphthalenemethyl)-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (11m) demonstrated a 2- to 3-fold improvement over 6e and a 7100- to 25000-fold improvement over the adenosine template. IC(50)'s of these compounds were in the range 2-12 microM for T. brucei, T. cruzi, and L. mexicana GAPDH's, and these compounds did not inhibit mammalian GAPDH when tested at their solubility limit. To explore more thoroughly the structure-activity relationships of this class of compounds, a library of 240 N(6)-(substituted)-2'-deoxy-2'-(amido)adenosine analogues was generated using parallel solution-phase synthesis with N(6) and C2' substituents chosen on the basis of computational docking scores. This resulted in the identification of 40 additional compounds that inhibit parasite GAPDH's in the low micromolar range. We also explored adenosine analogues containing 5'-amido substituents and found that 2',5'-dideoxy-2'-(3,5-dimethoxybenzamido)-5'-(diphenylacetamido)adenosine (49) displays an IC(50) of 60-100 microM against the three parasite GAPDH's.
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Affiliation(s)
- Jerome C. Bressi
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | | | - Alex M. Aronov
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - My Le Shaw
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Sam S. Shin
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Lisa N. Nguyen
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Stephen Suresh
- Department of Biological Structure, University of Washington, Seattle, Washington 98195
- Biomolecular Structure Center and Howard Hughes Medical Institute, Seattle, Washington 98195
| | | | | | - Irwin D. Kuntz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Wim G. J. Hol
- Department of Biological Structure, University of Washington, Seattle, Washington 98195
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- Biomolecular Structure Center and Howard Hughes Medical Institute, Seattle, Washington 98195
| | - Michael H. Gelb
- Department of Chemistry, University of Washington, Seattle, Washington 98195
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- To whom correspondence should be addressed. Phone: 206-543-7142. Fax: 206-685-8665.
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41
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Suresh S, Bressi JC, Kennedy KJ, Verlinde CL, Gelb MH, Hol WG. Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors. J Mol Biol 2001; 309:423-35. [PMID: 11371162 DOI: 10.1006/jmbi.2001.4588] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The glycolytic enzymes of trypanosomes are attractive drug targets, since the blood-stream form of Trypanosoma brucei lacks a functional citric acid cycle and is dependent solely on glycolysis for its energy requirements. Glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from the pathogenic trypanosomatids T. brucei, Trypanosoma cruzi and Leishmania mexicana are quite similar to each other, and yet have sufficient structural differences compared to the human enzyme to enable the structure-based design of compounds that selectively inhibit all three trypanosomatid enzymes but not the human homologue. Adenosine analogs with substitutions on N-6 of the adenine ring and on the 2' position of the ribose moiety were designed, synthesized and tested for inhibition. Two crystal structures of L. mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with high-affinity inhibitors that also block parasite growth were solved at a resolution of 2.6 A and 3.0 A. The complexes crystallized in the same crystal form, with one and a half tetramers in the crystallographic asymmetric unit. There is clear electron density for the inhibitor in all six copies of the binding site in each of the two structures. The L. mexicana GAPDH subunit exhibits substantial structural plasticity upon binding the inhibitor. Movements of the protein backbone, in response to inhibitor binding, enlarge a cavity at the binding site to accommodate the inhibitor in a classic example of induced fit. The extensive hydrophobic interactions between the protein and the two substituents on the adenine scaffold of the inhibitor provide a plausible explanation for the high affinity of these inhibitors for trypanosomatid GAPDHs.
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Affiliation(s)
- S Suresh
- Departments of Biological Structure, Biomolecular Structure Center, Howard Hughes Medical Institute, Seattle, WA 98915, USA
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42
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Verlinde CL, Hannaert V, Blonski C, Willson M, Périé JJ, Fothergill-Gilmore LA, Opperdoes FR, Gelb MH, Hol WG, Michels PA. Glycolysis as a target for the design of new anti-trypanosome drugs. Drug Resist Updat 2001; 4:50-65. [PMID: 11512153 DOI: 10.1054/drup.2000.0177] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Glycolysis is perceived as a promising target for new drugs against parasitic trypanosomatid protozoa because this pathway plays an essential role in their ATP supply. Trypanosomatid glycolysis is unique in that it is compartmentalized, and many of its enzymes display unique structural and kinetic features. Structure- and catalytic mechanism-based approaches are applied to design compounds that inhibit the glycolytic enzymes of the parasites without affecting the corresponding proteins of the human host. For some trypanosomatid enzymes, potent and selective inhibitors have already been developed that affect only the growth of cultured trypanosomatids, and not mammalian cells.
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Affiliation(s)
- C L Verlinde
- Department of Biological Structure, Biomolecular Structure Center, University of Washington, Seattle, USA
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43
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Chapter 10. New therapies for parasitic infection. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2001. [DOI: 10.1016/s0065-7743(01)36050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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44
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Bressi JC, Choe J, Hough MT, Buckner FS, Van Voorhis WC, Verlinde CL, Hol WG, Gelb MH. Adenosine analogues as inhibitors of Trypanosoma brucei phosphoglycerate kinase: elucidation of a novel binding mode for a 2-amino-N(6)-substituted adenosine. J Med Chem 2000; 43:4135-50. [PMID: 11063610 DOI: 10.1021/jm000287a] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As part of a project aimed at structure-based design of adenosine analogues as drugs against African trypanosomiasis, N(6)-, 2-amino-N(6)-, and N(2)-substituted adenosine analogues were synthesized and tested to establish structure-activity relationships for inhibiting Trypanosoma brucei glycosomal phosphoglycerate kinase (PGK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and glycerol-3-phosphate dehydrogenase (GPDH). Evaluation of X-ray structures of parasite PGK, GAPDH, and GPDH complexed with their adenosyl-bearing substrates led us to generate a series of adenosine analogues which would target all three enzymes simultaneously. There was a modest preference by PGK for N(6)-substituted analogues bearing the 2-amino group. The best compound in this series, 2-amino-N(6)- [2''(p-hydroxyphenyl)ethyl]adenosine (46b), displayed a 23-fold improvement over adenosine with an IC(50) of 130 microM. 2-[[2''-(p-Hydroxyphenyl)ethyl]amino]adenosine (46c) was a weak inhibitor of T. brucei PGK with an IC(50) of 500 microM. To explore the potential of an additive effect that having the N(6) and N(2) substitutions in one molecule might provide, the best ligands from the two series were incorporated into N(6),N(2)-disubstituted adenosine analogues to yield N(6)-(2''-phenylethyl)-2-[(2'' -phenylethyl)amino]adenosine (69) as a 30 microM inhibitor of T. brucei PGK which is 100-fold more potent than the adenosine template. In contrast, these series gave no compounds that inhibited parasitic GAPDH or GPDH more than 10-20% when tested at 1.0 mM. A 3.0 A X-ray structure of a T. brucei PGK/46b complex revealed a binding mode in which the nucleoside analogue was flipped and the ribosyl moiety adopted a syn conformation as compared with the previously determined binding mode of ADP. Molecular docking experiments using QXP and SAS program suites reproduced this "flipped and rotated" binding mode.
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Affiliation(s)
- J C Bressi
- Department of Chemistry, University of Washington, Seattle, 98195, USA
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45
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Golisade A, Bressi JC, Van Calenbergh S, Gelb MH, Link A. Polymer-assisted solution-phase synthesis of 2'-amido-2'-deoxyadenosine derivatives targeted at the NAD(+)-binding sites of parasite enzymes. JOURNAL OF COMBINATORIAL CHEMISTRY 2000; 2:537-44. [PMID: 11029179 DOI: 10.1021/cc0000343] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A polymer-assisted solution-phase (PASP) synthesis of lead structure analogues ready for biological testing without the demand for chromatographic purification is described. Carboxylic acids are coupled to the Kenner or Ellman safety catch linker, respectively, activated by methylation or cyanomethylation and subsequently transferred to the 2'-amino group of the 2'-amino-2'-deoxyadenosine scaffold (5). The chemoselective attack of weakly nucleophilic amino groups on the N-alkylated N-acyl sulfonamide linker allows for the synthesis of amides 6 in high yields without the need for protection of primary and secondary hydroxyl functions. Thus, the use of 4-sulfamylbenzoylaminomethyl polystyrene is reported for the construction of chemoselective polymer-supported acylating reagents instead of its known use as linker in solid-phase peptide or organic synthesis. This approach is demonstrated to be well suited to obtain 2'-amido-2'-deoxyadenosine derivatives 6 in parallel format. Biological evaluation of all compounds reported revealed no improvement over known lead structures.
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Affiliation(s)
- A Golisade
- Institut für Pharmazie, Fachbereich Chemie, Universität Hamburg, Bundesstrasse 45, D-20146 Hamburg, Germany
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46
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Szajnman SH, Yan W, Bailey BN, Docampo R, Elhalem E, Rodriguez JB. Design and synthesis of aryloxyethyl thiocyanate derivatives as potent inhibitors of Trypanosoma cruzi proliferation. J Med Chem 2000; 43:1826-40. [PMID: 10794699 DOI: 10.1021/jm9905007] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a part of our project directed at the search of new chemotherapeutic agents against American trypanosomiasis (Chagas' disease), several drugs possessing the 4-phenoxyphenoxy skeleton and other closely related structures employing the thiocyanate moiety as polar end group were designed, synthesized, and evaluated as antiproliferative agents against Trypanosoma cruzi, the parasite responsible for this disease. These thiocyanate analogues were envisioned bearing in mind the potent activity shown by 4-phenoxyphenoxyethyl thiocyanate (compound 8) taken as lead drug. This compound had previously proved to be an extremely active growth inhibitor against T. cruzi with IC(50) values ranging from the very low micromolar level in epimastigotes to the low nanomolar level in the intracellular form of the parasite. Of the designed compounds, the ethyl thiocyanate drugs connected to nonpolar skeletons, namely, arylthio, 2,4-dichlorophenoxy, ortho-substituted aryloxy, and 2-methyl-4-phenoxyphenoxy (compounds 15, 34, 47, 52, 72, respectively), were shown to be very potent antireplicative agents against T. cruzi. On the other hand, conformationally restricted analogues as well as branched derivatives at the aliphatic side chain were shown to be moderately active against T. cruzi growth. The biological activity of drugs bearing the thiocyanate group correlated quite well with the activity exhibited by their normal precursors, the tetrahydropyranyl ether derivatives, when bonded to the same nonpolar skeleton. Compounds having the tetrahydropyranyl moeity as polar end were proportionally much less active than sulfur-containing derivatives in all cases. Drugs 47 and 72 also resulted to be very active against the amastigote form of the parasite growing in myoblasts; however, they were slightly less active than the lead drug 8. On the other hand, compounds 34 and 52 were almost devoid of activity against myoblasts. Surprisingly, the dithio derivative 15 was toxic for myoblasts.
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Affiliation(s)
- S H Szajnman
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria, RA-1428 Buenos Aires, Argentina
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47
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Golisade A, Van Calenbergh S, Link A. 2′-Amino-2′-deoxy-N6-(1-naphthylmethyl)adenosine as Novel Scaffold for a Polymer-Assisted Amidation Protocol. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00228-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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48
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Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA. Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Mol Biochem Parasitol 2000; 106:1-10. [PMID: 10743606 DOI: 10.1016/s0166-6851(99)00197-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Glycolysis is the only ATP-generating process in bloodstream form trypanosomes and is therefore a promising drug target. Inhibitors which decrease significantly the glycolytic flux will kill the parasites. Both computer simulation and experimental studies of glycolysis in bloodstream form Trypanosoma brucei indicated that the control of the glycolytic flux is shared by several steps in the pathway. The results of these analyses provide quantitative information about the prospects of decreasing the flux by inhibition of any individual enzyme. The plasma membrane glucose transporter appears the most promising target from this perspective, followed by aldolase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and glycerol-3-phosphate dehydrogenase. Non-competitive or irreversible inhibitors would be most effective, but it is argued that potent competitive inhibitors can be suitable, provided that the concentration of the competing substrate cannot increase unrestrictedly. Such is the case for inhibitors that compete with coenzymes or with blood glucose.
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Affiliation(s)
- B M Bakker
- Kluyver Institute of Biotechnology, Delft University of Technology, The Netherlands
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49
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Marché S, Michels PA, Opperdoes FR. Comparative study of Leishmania mexicana and Trypanosoma brucei NAD-dependent glycerol-3-phosphate dehydrogenase. Mol Biochem Parasitol 2000; 106:83-91. [PMID: 10743613 DOI: 10.1016/s0166-6851(99)00204-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NAD-dependent glycerol-3-phosphate dehydrogenases (G3PDH, EC 1.1.1.8) of Trypanosoma brucei and Leishmania mexicana are thought to have different roles in carbohydrate metabolism. Here the physicochemical and kinetic properties of natural G3PDH from T. brucei with the recombinant homologue of L. mexicana which share 63% positional identity are compared. Despite their supposed different functions in energy metabolism of the parasites the two G3PDHs have remarkably similar properties, including pH optima and K(m) value for dihydroxyacetone phosphate (DHAP) and NADH in the formation of glycerol 3-phosphate (G3P) and for NAD+ and G3P in the reverse reaction. Both enzymes are subject inhibition by dihydroxyacetone phosphate at concentrations above 0.2 mM and are inhibited by the trypanocidal drugs suramin and melarsen oxide at sub-micromolar concentrations.
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Affiliation(s)
- S Marché
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology, Brussels, Belgium
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50
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Abstract
Enzymes bind NAD(+) in extended conformations and yet NAD(+) exists in aqueous solution as a compact, folded molecule. Thus, NAD(+) conformation is environment dependent. In an attempt to investigate the effects of environmental changes on the conformation of NAD(+), a series of molecular dynamics simulations in different solvents was performed. The solvents investigated (water, DMSO, methanol and chloroform) represented changes in relative permittivity and hydrophobic character. The simulations predicted folded conformations of NAD(+) to be more stable in water, DMSO and methanol. In contrast, extended conformations of NAD(+) were observed to be more stable in chloroform. Furthermore, the extended conformations observed in chloroform were similar to conformations of NAD(+) bound to enzymes. In particular, a large separation between the aromatic rings and a strong interaction between the pyrophosphate and nicotinamide groups were observed. The implications of these observations for the recognition of NAD(+) by enzymes is discussed. It is argued that a hydrophobic environment is important for stabilizing unfolded conformations of NAD(+).
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Affiliation(s)
- P E Smith
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506-3702, USA
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