1
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Li B, Liang J, Phillips MA, Michael AJ. Neofunctionalization of S-adenosylmethionine decarboxylase into pyruvoyl-dependent L-ornithine and L-arginine decarboxylases is widespread in bacteria and archaea. J Biol Chem 2023; 299:105005. [PMID: 37399976 PMCID: PMC10407285 DOI: 10.1016/j.jbc.2023.105005] [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: 05/15/2023] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
S-adenosylmethionine decarboxylase (AdoMetDC/SpeD) is a key polyamine biosynthetic enzyme required for conversion of putrescine to spermidine. Autocatalytic self-processing of the AdoMetDC/SpeD proenzyme generates a pyruvoyl cofactor from an internal serine. Recently, we discovered that diverse bacteriophages encode AdoMetDC/SpeD homologs that lack AdoMetDC activity and instead decarboxylate L-ornithine or L-arginine. We reasoned that neofunctionalized AdoMetDC/SpeD homologs were unlikely to have emerged in bacteriophages and were probably acquired from ancestral bacterial hosts. To test this hypothesis, we sought to identify candidate AdoMetDC/SpeD homologs encoding L-ornithine and L-arginine decarboxylases in bacteria and archaea. We searched for the anomalous presence of AdoMetDC/SpeD homologs in the absence of its obligatory partner enzyme spermidine synthase, or the presence of two AdoMetDC/SpeD homologs encoded in the same genome. Biochemical characterization of candidate neofunctionalized genes confirmed lack of AdoMetDC activity, and functional presence of L-ornithine or L-arginine decarboxylase activity in proteins from phyla Actinomycetota, Armatimonadota, Planctomycetota, Melainabacteria, Perigrinibacteria, Atribacteria, Chloroflexota, Sumerlaeota, Omnitrophota, Lentisphaerota, and Euryarchaeota, the bacterial candidate phyla radiation and DPANN archaea, and the δ-Proteobacteria class. Phylogenetic analysis indicated that L-arginine decarboxylases emerged at least three times from AdoMetDC/SpeD, whereas L-ornithine decarboxylases arose only once, potentially from the AdoMetDC/SpeD-derived L-arginine decarboxylases, revealing unsuspected polyamine metabolic plasticity. Horizontal transfer of the neofunctionalized genes appears to be the more prevalent mode of dissemination. We identified fusion proteins of bona fide AdoMetDC/SpeD with homologous L-ornithine decarboxylases that possess two, unprecedented internal protein-derived pyruvoyl cofactors. These fusion proteins suggest a plausible model for the evolution of the eukaryotic AdoMetDC.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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2
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Maher SP, Vantaux A, Chaumeau V, Chua ACY, Cooper CA, Andolina C, Péneau J, Rouillier M, Rizopoulos Z, Phal S, Piv E, Vong C, Phen S, Chhin C, Tat B, Ouk S, Doeurk B, Kim S, Suriyakan S, Kittiphanakun P, Awuku NA, Conway AJ, Jiang RHY, Russell B, Bifani P, Campo B, Nosten F, Witkowski B, Kyle DE. Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro. Sci Rep 2021; 11:19905. [PMID: 34620901 PMCID: PMC8497498 DOI: 10.1038/s41598-021-99152-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 09/21/2021] [Indexed: 12/25/2022] Open
Abstract
Improved control of Plasmodium vivax malaria can be achieved with the discovery of new antimalarials with radical cure efficacy, including prevention of relapse caused by hypnozoites residing in the liver of patients. We screened several compound libraries against P. vivax liver stages, including 1565 compounds against mature hypnozoites, resulting in one drug-like and several probe-like hits useful for investigating hypnozoite biology. Primaquine and tafenoquine, administered in combination with chloroquine, are currently the only FDA-approved antimalarials for radical cure, yet their activity against mature P. vivax hypnozoites has not yet been demonstrated in vitro. By developing an extended assay, we show both drugs are individually hypnozonticidal and made more potent when partnered with chloroquine, similar to clinically relevant combinations. Post-hoc analyses of screening data revealed excellent performance of ionophore controls and the high quality of single point assays, demonstrating a platform able to support screening of greater compound numbers. A comparison of P. vivax liver stage activity data with that of the P. cynomolgi blood, P. falciparum blood, and P. berghei liver stages reveals overlap in schizonticidal but not hypnozonticidal activity, indicating that the delivery of new radical curative agents killing P. vivax hypnozoites requires an independent and focused drug development test cascade.
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Affiliation(s)
- Steven P Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA.
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Victor Chaumeau
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Adeline C Y Chua
- Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A*STAR), Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Caitlin A Cooper
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Chiara Andolina
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Julie Péneau
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Mélanie Rouillier
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Zaira Rizopoulos
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Sivchheng Phal
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Eakpor Piv
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Chantrea Vong
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sreyvouch Phen
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Chansophea Chhin
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Baura Tat
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sivkeng Ouk
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Bros Doeurk
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sangrawee Suriyakan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
| | - Praphan Kittiphanakun
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
| | - Nana Akua Awuku
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Amy J Conway
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Disease Research, University of South Florida, 3720 Spectrum Blvd Suite 402, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Disease Research, University of South Florida, 3720 Spectrum Blvd Suite 402, Tampa, FL, 33612, USA
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Pablo Bifani
- Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A*STAR), Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Brice Campo
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Benoît Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia.
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA.
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3
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Li B, Liang J, Hanfrey CC, Phillips MA, Michael AJ. Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis. J Biol Chem 2021; 297:101219. [PMID: 34560100 PMCID: PMC8503589 DOI: 10.1016/j.jbc.2021.101219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 11/15/2022] Open
Abstract
Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5'-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jue Liang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | | | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Anthony J Michael
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA.
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4
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Leifer BS, Doyle SK, Richters A, Evans HL, Koehler AN. An Array-Based Ligand Discovery Platform for Proteins With Short Half-Lives. Methods Enzymol 2018; 610:191-218. [PMID: 30390799 DOI: 10.1016/bs.mie.2018.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many promising therapeutic protein targets were previously considered "undruggable" due to a deficit in structural information to guide drug design and/or a lack of an obvious binding pocket. Fortunately, array-based methods for evaluating protein binding against large chemical libraries, such as small-molecule microarray screening, have provided one of several emerging inroads to ligand discovery for these elusive targets. Despite the advance in the area of ligand discovery for poorly structured and intrinsically disordered proteins provided by array-based technologies involving cell lysates, the extension of this technology for screening proteins with short half-lives in physiologically relevant conformations has been technically challenging. In this chapter we present a protocol for leveraging in vitro translation strategies to enable array-based screening of short-lived proteins against large small-molecule libraries for ligand discovery.
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Affiliation(s)
- Becky S Leifer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Shelby K Doyle
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - André Richters
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Helen L Evans
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.
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5
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Choi JY, Surovtseva YV, Van Sickle SM, Kumpf J, Bunz UHF, Ben Mamoun C, Voelker DR. A novel fluorescence assay for measuring phosphatidylserine decarboxylase catalysis. J Biol Chem 2017; 293:1493-1503. [PMID: 29247006 DOI: 10.1074/jbc.ra117.000525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/07/2017] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylserine decarboxylases (PSDs) are central enzymes in phospholipid metabolism that produce phosphatidylethanolamine (PE) in bacteria, protists, plants, and animals. We developed a fluorescence-based assay for selectively monitoring production of PE in reactions using a maltose-binding protein fusion with Plasmodium knowlesi PSD (MBP-His6-Δ34PkPSD) as the enzyme. The PE detection by fluorescence (λex = 403 nm, λem = 508 nm) occurred after the lipid reacted with a water-soluble distyrylbenzene-bis-aldehyde (DSB-3), and provided strong discrimination against the phosphatidylserine substrate. The reaction conditions were optimized for enzyme, substrate, product, and DSB-3 concentrations with the purified enzyme and also tested with crude extracts and membrane fractions from bacteria and yeast. The assay is readily amenable to application in 96- and 384-well microtiter plates and should prove useful for high-throughput screening for inhibitors of PSD enzymes across diverse phyla.
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Affiliation(s)
- Jae-Yeon Choi
- From the Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | | | - Sam M Van Sickle
- From the Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Jan Kumpf
- the Organisch-Chemisches Institut, Ruprecht-Karls-Universitat, Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Uwe H F Bunz
- the Organisch-Chemisches Institut, Ruprecht-Karls-Universitat, Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Choukri Ben Mamoun
- the Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut 06520, and
| | - Dennis R Voelker
- From the Basic Science Section, Department of Medicine, National Jewish Health, Denver, Colorado 80206,
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6
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Volkov OA, Cosner CC, Brockway AJ, Kramer M, Booker M, Zhong S, Ketcherside A, Wei S, Longgood J, McCoy M, Richardson TE, Wring SA, Peel M, Klinger JD, Posner BA, De Brabander JK, Phillips MA. Identification of Trypanosoma brucei AdoMetDC Inhibitors Using a High-Throughput Mass Spectrometry-Based Assay. ACS Infect Dis 2017; 3:512-526. [PMID: 28350440 DOI: 10.1021/acsinfecdis.7b00022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human African trypanosomiasis (HAT) is a fatal infectious disease caused by the eukaryotic pathogen Trypanosoma brucei (Tb). Available treatments are difficult to administer and have significant safety issues. S-Adenosylmethionine decarboxylase (AdoMetDC) is an essential enzyme in the parasite polyamine biosynthetic pathway. Previous attempts to develop TbAdoMetDC inhibitors into anti-HAT therapies failed due to poor brain exposure. Here, we describe a large screening campaign of two small-molecule libraries (∼400,000 compounds) employing a new high-throughput (∼7 s per sample) mass spectrometry-based assay for AdoMetDC activity. As a result of primary screening, followed by hit confirmation and validation, we identified 13 new classes of reversible TbAdoMetDC inhibitors with low-micromolar potency (IC50) against both TbAdoMetDC and T. brucei parasite cells. The majority of these compounds were >10-fold selective against the human enzyme. Importantly, compounds from four classes demonstrated high propensity to cross the blood-brain barrier in a cell monolayer assay. Biochemical analysis demonstrated that compounds from eight classes inhibited intracellular TbAdoMetDC in the parasite, although evidence for a secondary off-target component was also present. The discovery of several new TbAdoMetDC inhibitor chemotypes provides new hits for lead optimization programs aimed to deliver a novel treatment for HAT.
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Affiliation(s)
| | | | | | - Martin Kramer
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
| | - Michael Booker
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
| | | | | | | | | | | | - Thomas E. Richardson
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Stephen A. Wring
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Michael Peel
- Scynexis, Inc. (now Avista Pharma Solutions), 3501 Tricenter Boulevard, Suite
C, Durham, North Carolina 27713, United States
| | - Jeffrey D. Klinger
- Genzyme Corp. (now Sanofi Genzyme), 153 Second Avenue, Waltham, Massachusetts 02451-1122, United States
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7
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Liao C, Wang Y, Tan X, Sun L, Liu S. Discovery of novel inhibitors of human S-adenosylmethionine decarboxylase based on in silico high-throughput screening and a non-radioactive enzymatic assay. Sci Rep 2015; 5:10754. [PMID: 26030749 PMCID: PMC5377238 DOI: 10.1038/srep10754] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
Natural polyamines are small polycationic molecules essential for cell growth and development, and elevated level of polyamines is positively correlated with various cancers. As a rate-limiting enzyme of the polyamine biosynthetic pathway, S-adenosylmethionine decarboxylase (AdoMetDC) has been an attractive drug target. In this report, we present the discovery of novel human AdoMetDC (hAdoMetDC) inhibitors by coupling computational and experimental tools. We constructed a reasonable computational structure model of hAdoMetDC that is compatible with general protocols for high-throughput drug screening, and used this model in in silico screening of hAdoMetDC inhibitors against a large compound library using a battery of computational tools. We also established and validated a simple, economic, and non-radioactive enzymatic assay, which can be adapted for experimental high-throughput screening of hAdoMetDC inhibitors. Finally, we obtained an hAdoMetDC inhibitor lead with a novel scaffold. This study provides both new tools and a new lead for the developing of novel hAdoMetDC inhibitors.
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Affiliation(s)
- Chenzeng Liao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yanlin Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Xiao Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Lidan Sun
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
| | - Sen Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Medical Science, China Three Gorges University, Yichang 443002, China
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8
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Sharma LK, Leonardi R, Lin W, Boyd VA, Goktug A, Shelat AA, Chen T, Jackowski S, Rock CO. A high-throughput screen reveals new small-molecule activators and inhibitors of pantothenate kinases. J Med Chem 2015; 58:1563-8. [PMID: 25569308 PMCID: PMC4357395 DOI: 10.1021/jm501585q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Pantothenate
kinase (PanK) is a regulatory enzyme that controls
coenzyme A (CoA) biosynthesis. The association of PanK with neurodegeneration
and diabetes suggests that chemical modifiers of PanK activity may
be useful therapeutics. We performed a high throughput screen of >520000
compounds from the St. Jude compound library and identified new potent
PanK inhibitors and activators with chemically tractable scaffolds.
The HTS identified PanK inhibitors exemplified by the detailed characterization
of a tricyclic compound (7) and a preliminary SAR. Biophysical
studies reveal that the PanK inhibitor acts by binding to the ATP–enzyme
complex.
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Affiliation(s)
- Lalit Kumar Sharma
- Department of Chemical Biology and Therapeutics, ‡Department of Infectious Diseases, St. Jude Children's Research Hospital , 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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9
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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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10
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Ren J, Zhang Y, Jin H, Yu J, Zhou Y, Wu F, Zhang W. Novel inhibitors of human DOPA decarboxylase extracted from Euonymus glabra Roxb. ACS Chem Biol 2014; 9:897-903. [PMID: 24471650 DOI: 10.1021/cb500009r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Dopamine, a biogenic amine with important biological functions, is produced from l-DOPA by DOPA decarboxylase (DDC). DDC is a potential target to modulate the production of dopamine in several pathological states. Known inhibitors of DDC have been used for treatment of Parkinson's disease but suffered low specificity and diverse side effects. In the present study, we identified and characterized a novel class of natural-product-based selective inhibitors for DDC from the extract of Euonymus glabra Roxb. by a newly developed high-throughput enzyme assay. The structures of these inhibitors are dimeric diarylpropane, a unique chemical structure containing a divalent dopamine motif. The most effective inhibitors 5 and 6 have an IC50 of 11.5 ± 1.6 and 21.6 ± 2.7 μM in an in vitro purified enzyme assay, respectively, but did not inhibit other homologous enzymes. Compound 5 but not 6 dose-dependently suppressed the activity of hDDC and dopamine levels at low micromolar concentrations in cells. Furthermore, structure-activity relationship analyses revealed that p-benzoquinone might be a crucial moiety of these inhibitors for inhibiting hDDC. The natural-product-based selective inhibitors of hDDC could serve as a chemical lead for developing improved drugs for dopamine-related disease states.
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Affiliation(s)
| | - Yuanyuan Zhang
- Key
Laboratory of Exploration and Utilization of Aquatic Genetic Resources,
Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
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Willert E, Phillips MA. Regulation and function of polyamines in African trypanosomes. Trends Parasitol 2011; 28:66-72. [PMID: 22192816 DOI: 10.1016/j.pt.2011.11.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 02/03/2023]
Abstract
The polyamine biosynthetic pathway is an important drug target for the treatment of human African trypanosomiasis (HAT), raising interest in understanding polyamine function and their mechanism of regulation. Polyamine levels are tightly controlled in mammalian cells, but similar regulatory mechanisms appear absent in trypanosomes. Instead trypanosomatid S-adenosylmethionine decarboxylase (AdoMetDC), which catalyzes a key step in the biosynthesis of the polyamine spermidine, is activated by dimerization with an inducible protein termed prozyme. Prozyme is an inactive paralog of the active AdoMetDC enzyme that evolved by gene duplication and is found only in the trypanosomatids. In Trypanosoma brucei, AdoMetDC activity appears to be controlled by regulation of prozyme protein levels, potentially at the translational level.
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Affiliation(s)
- Erin Willert
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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Smithson DC, Lee J, Shelat AA, Phillips MA, Guy RK. Discovery of potent and selective inhibitors of Trypanosoma brucei ornithine decarboxylase. J Biol Chem 2010; 285:16771-81. [PMID: 20220141 PMCID: PMC2878083 DOI: 10.1074/jbc.m109.081588] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/03/2010] [Indexed: 11/06/2022] Open
Abstract
Human African trypanosomiasis, caused by the eukaryotic parasite Trypanosoma brucei, is a serious health problem in much of central Africa. The only validated molecular target for treatment of human African trypanosomiasis is ornithine decarboxylase (ODC), which catalyzes the first step in polyamine metabolism. Here, we describe the use of an enzymatic high throughput screen of 316,114 unique molecules to identify potent and selective inhibitors of ODC. This screen identified four novel families of ODC inhibitors, including the first inhibitors selective for the parasitic enzyme. These compounds display unique binding modes, suggesting the presence of allosteric regulatory sites on the enzyme. Docking of a subset of these inhibitors, coupled with mutagenesis, also supports the existence of these allosteric sites.
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Affiliation(s)
- David C. Smithson
- From the Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
- the Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143-2280, and
| | - Jeongmi Lee
- the Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
| | - Anang A. Shelat
- From the Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Margaret A. Phillips
- the Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
| | - R. Kiplin Guy
- From the Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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