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Li B, Liang J, Baniasadi HR, Kurihara S, Phillips MA, Michael AJ. Functional identification of bacterial spermine, thermospermine, norspermine, norspermidine, spermidine, and N 1-aminopropylagmatine synthases. J Biol Chem 2024:107281. [PMID: 38588807 DOI: 10.1016/j.jbc.2024.107281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
Spermine synthase is an aminopropyltransferase that adds an aminopropyl group to the essential polyamine spermidine to form tetraamine spermine, needed for normal human neural development, plant salt and drought resistance, and yeast CoA biosynthesis. We functionally identify for the first time bacterial spermine synthases, derived from phyla Bacillota, Rhodothermota, Thermodesulfobacteriota, Nitrospirota, Deinococcota and Pseudomonadota. We also identify bacterial aminopropyltransferases that synthesize the spermine same mass isomer thermospermine, from phyla Cyanobacteriota, Thermodesulfobacteriota, Nitrospirota, Dictyoglomota, Armatimonadota and Pseudomonadota, including the human opportunistic pathogen Pseudomonas aeruginosa. Most of these bacterial synthases were capable of synthesizing spermine or thermospermine from the diamine putrescine, and so possess also spermidine synthase activity. We found that most thermospermine synthases could synthesize tetraamine norspermine from triamine norspermidine, i.e., they are potential norspermine synthases. This finding could explain the enigmatic source of norspermine in bacteria. Some of the thermospermine synthases could synthesize norspermidine from diamine 1,3-diaminopropane, demonstrating that they are potential norspermidine synthases. Of 18 bacterial spermidine synthases identified, 17 were able to aminopropylate agmatine to form N1-aminopropylagmatine, including the spermidine synthase of Bacillus subtilis, a species known to be devoid of putrescine. This suggests that the N1-aminopropylagmatine pathway for spermidine biosynthesis, which bypasses putrescine, may be far more widespread than realized and may be the default pathway for spermidine biosynthesis in species encoding L-arginine decarboxylase for agmatine production. Some thermospermine synthases were able to aminopropylate N1-aminopropylagmatine to form N12-guanidinothermospermine. Our study reveals an unsuspected diversification of bacterial polyamine biosynthesis, and suggests a more prominent role for agmatine.
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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
| | - Hamid R Baniasadi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Shin Kurihara
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Imlay LS, Lawong AK, Gahalawat S, Kumar A, Xing C, Mittal N, Wittlin S, Churchyard A, Niederstrasser H, Crespo-Fernandez B, Posner BA, Gamo FJ, Baum J, Winzeler EA, LALEU B, Ready JM, Phillips MA. Fast-Killing Tyrosine Amide (( S)-SW228703) with Blood- and Liver-Stage Antimalarial Activity Associated with the Cyclic Amine Resistance Locus ( PfCARL). ACS Infect Dis 2023; 9:527-539. [PMID: 36763526 PMCID: PMC10053980 DOI: 10.1021/acsinfecdis.2c00527] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Current malaria treatments are threatened by drug resistance, and new drugs are urgently needed. In a phenotypic screen for new antimalarials, we identified (S)-SW228703 ((S)-SW703), a tyrosine amide with asexual blood and liver stage activity and a fast-killing profile. Resistance to (S)-SW703 is associated with mutations in the Plasmodium falciparum cyclic amine resistance locus (PfCARL) and P. falciparum acetyl CoA transporter (PfACT), similarly to several other compounds that share features such as fast activity and liver-stage activity. Compounds with these resistance mechanisms are thought to act in the ER, though their targets are unknown. The tyramine of (S)-SW703 is shared with some reported PfCARL-associated compounds; however, we observed that strict S-stereochemistry was required for the activity of (S)-SW703, suggesting differences in the mechanism of action or binding mode. (S)-SW703 provides a new chemical series with broad activity for multiple life-cycle stages and a fast-killing mechanism of action, available for lead optimization to generate new treatments for malaria.
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Affiliation(s)
- Leah S. Imlay
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Aloysus K. Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nimisha Mittal
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4002, Basel, Switzerland
- University of Basel, 4002, Basel, Switzerland
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Hanspeter Niederstrasser
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Bruce A. Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Jake Baum
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- School of Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Elizabeth A. Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Benoît LALEU
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - Joseph M. Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
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4
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Russo TA, Umland TC, Deng X, El Mazouni F, Kokkonda S, Olson R, Carlino-MacDonald U, Beanan J, Alvarado CL, Tomchick DR, Hutson A, Chen H, Posner B, Rathod PK, Charman SA, Phillips MA. Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii. Proc Natl Acad Sci U S A 2022; 119:e2213116119. [PMID: 36512492 PMCID: PMC9907071 DOI: 10.1073/pnas.2213116119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
New antimicrobials are needed for the treatment of extensively drug-resistant Acinetobacter baumannii. The de novo pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated drug target for malaria and human autoimmune diseases. We provide genetic evidence that A. baumannii DHODH (AbDHODH) is essential for bacterial survival in rodent infection models. We chemically validate the target by repurposing a unique library of ~450 triazolopyrimidine/imidazopyrimidine analogs developed for our malaria DHODH program to identify 21 compounds with submicromolar activity on AbDHODH. The most potent (DSM186, DHODH IC50 28 nM) had a minimal inhibitory concentration of ≤1 µg/ml against geographically diverse A. baumannii strains, including meropenem-resistant isolates. A structurally related analog (DSM161) with a long in vivo half-life conferred significant protection in the neutropenic mouse thigh infection model. Encouragingly, the development of resistance to these compounds was not identified in vitro or in vivo. Lastly, the X-ray structure of AbDHODH bound to DSM186 was solved to 1.4 Å resolution. These data support the potential of AbDHODH as a drug target for the development of antimicrobials for the treatment of A. baumannii and potentially other high-risk bacterial infections.
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Affiliation(s)
- Thomas A. Russo
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
- Department of Microbiology and Immunology, University at Buffalo-State University of New York, Buffalo, NY14203
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Timothy C. Umland
- Department of Structural Biology, University at Buffalo State University of New York, Buffalo, NY14203
- Hauptman Woodward Medical Research Institute, Buffalo, NY14203
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Sreekanth Kokkonda
- Department of Chemistry, University of Washington, Seattle, WA98195
- Department of Global Health, University of Washington, Seattle, WA98195
| | - Ruth Olson
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Ulrike Carlino-MacDonald
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Janet Beanan
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Cassandra L. Alvarado
- Department of Medicine, Veterans Administration Western New York Healthcare System, Buffalo, NY14215
- The Department of Medicine, University at Buffalo-State University of New York, Buffalo, NY14203
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY14203
| | - Hong Chen
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, WA98195
- Department of Global Health, University of Washington, Seattle, WA98195
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC3052Australia
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX75390
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Pontikos MA, Leija C, Zhao Z, Wang X, Kilgore J, Tornesi B, Adenmatten N, Phillips MA, Williams NS. Development of a biomarker to monitor target engagement after treatment with dihydroorotate dehydrogenase inhibitors. Biochem Pharmacol 2022; 204:115237. [PMID: 36055381 PMCID: PMC9547971 DOI: 10.1016/j.bcp.2022.115237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
Dihydroorotate dehydrogenase (DHODH) catalyzes a key step in pyrimidine biosynthesis and has recently been validated as a therapeutic target for malaria through clinical studies on the triazolopyrimidine-based Plasmodium DHODH inhibitor DSM265. Selective toxicity towards Plasmodium species could be achieved because malaria parasites lack pyrimidine salvage pathways, and DSM265 selectively inhibits Plasmodium DHODH over the human enzyme. However, while DSM265 does not inhibit human DHODH, it inhibits DHODH from several preclinical species, including mice, suggesting that toxicity could result from on-target DHODH inhibition in those species. We describe here the use of dihydroorotate (DHO) as a biomarker of DHODH inhibition. Treatment of mammalian cells with DSM265 or the mammalian DHODH inhibitor teriflunomide led to increases in DHO where the extent of biomarker buildup correlated with both dose and inhibitor potency on DHODH. Treatment of mice with leflunomide (teriflunomide prodrug) caused a large dose-dependent buildup of DHO in blood (up to 16-fold) and urine (up to 5,400-fold) that was not observed for mice treated with DSM265. Unbound plasma teriflunomide levels reached 20-85-fold above the mouse DHODH IC50, while free DSM265 levels were only 1.6-4.2-fold above, barely achieving ∼ IC90 concentrations, suggesting that unbound DSM265 plasma levels are not sufficient to block the pathway in vivo. Thus, any toxicity associated with DSM265 treatment in mice is likely caused by off-target mechanisms. The identification of a robust biomarker for mammalian DHODH inhibition represents an important advance to generally monitor for on-target effects in preclinical and clinical applications of DHODH inhibitors used to treat human disease.
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Affiliation(s)
- Michael A Pontikos
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Christopher Leija
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Zhiyu Zhao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Xiaoyu Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Jessica Kilgore
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States
| | - Belen Tornesi
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States.
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9135, United States.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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Zhang Z, Ray S, Imlay L, Callaghan LT, Niederstrasser H, Mallipeddi PL, Posner BA, Wetzel DM, Phillips MA, Smith MW. Total synthesis of (+)-spiroindimicin A and congeners unveils their antiparasitic activity. Chem Sci 2021; 12:10388-10394. [PMID: 34377425 PMCID: PMC8336461 DOI: 10.1039/d1sc02838c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/02/2022] Open
Abstract
The spiroindimicins are a unique class of chlorinated indole alkaloids characterized by three heteroaromatic rings structured around a congested spirocyclic stereocenter. Here, we report the first total synthesis of (+)-spiroindimicin A, which bears a challenging C-3′/C-5′′-linked spiroindolenine. We detail our initial efforts to effect a biomimetic oxidative spirocyclization from its proposed natural precursor, lynamicin D, and describe how these studies shaped our final abiotic 9-step solution to this complex alkaloid built around a key Pd-catalyzed asymmetric spirocyclization. Scalable access to spiroindimicins A, H, and their congeners has enabled discovery of their activity against several parasites relevant to human health, providing potential starting points for new therapeutics for the neglected tropical diseases leishmaniasis and African sleeping sickness. Spiroindimicins A and H have been synthesized for the first time via a key palladium-catalyzed spirocyclization. Access to these alkaloids and several congeners has allowed the discovery of their antiparasitic properties.![]()
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Affiliation(s)
- Zhen Zhang
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Sneha Ray
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Leah Imlay
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Lauren T Callaghan
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Hanspeter Niederstrasser
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Prema Latha Mallipeddi
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Bruce A Posner
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Dawn M Wetzel
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA .,Department of Pediatrics, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Margaret A Phillips
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390 USA
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8
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Palmer MJ, Deng X, Watts S, Krilov G, Gerasyuto A, Kokkonda S, El Mazouni F, White J, White KL, Striepen J, Bath J, Schindler KA, Yeo T, Shackleford DM, Mok S, Deni I, Lawong A, Huang A, Chen G, Wang W, Jayaseelan J, Katneni K, Patil R, Saunders J, Shahi SP, Chittimalla R, Angulo-Barturen I, Jiménez-Díaz MB, Wittlin S, Tumwebaze PK, Rosenthal PJ, Cooper RA, Aguiar ACC, Guido RVC, Pereira DB, Mittal N, Winzeler EA, Tomchick DR, Laleu B, Burrows JN, Rathod PK, Fidock DA, Charman SA, Phillips MA. Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series. J Med Chem 2021; 64:6085-6136. [PMID: 33876936 DOI: 10.1021/acs.jmedchem.1c00173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenase (DHODH) has been clinically validated as a target for the development of new antimalarials. Experience with clinical candidate triazolopyrimidine DSM265 (1) suggested that DHODH inhibitors have great potential for use in prophylaxis, which represents an unmet need in the malaria drug discovery portfolio for endemic countries, particularly in areas of high transmission in Africa. We describe a structure-based computationally driven lead optimization program of a pyrrole-based series of DHODH inhibitors, leading to the discovery of two candidates for potential advancement to preclinical development. These compounds have improved physicochemical properties over prior series frontrunners and they show no time-dependent CYP inhibition, characteristic of earlier compounds. Frontrunners have potent antimalarial activity in vitro against blood and liver schizont stages and show good efficacy in Plasmodium falciparum SCID mouse models. They are equally active against P. falciparum and Plasmodium vivax field isolates and are selective for Plasmodium DHODHs versus mammalian enzymes.
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Affiliation(s)
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Shawn Watts
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Aleksey Gerasyuto
- Schrodinger, Inc., 120 West 45th St, 17th Floor, New York, New York 100036-4041, United States
| | - Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kyra A Schindler
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Ann Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Wen Wang
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jaya Jayaseelan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jessica Saunders
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | | | - Iñigo Angulo-Barturen
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- TAD, Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Bd 612, Derio, 48160 Bizkaia, Basque Country, Spain
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, California 94143, United States
| | - Roland A Cooper
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California 94901, United States
| | | | - Rafael V C Guido
- University of Sao Paulo, Sao Carlos Institute of Physics, Sáo Carlos, SP 13560-970, Brazil
| | - Dhelio B Pereira
- Tropical Medicine Research Center of Rondonia, Av. Guaporé, 215, Porto Velho, RO 76812-329, Brazil
| | - Nimisha Mittal
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth A Winzeler
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, School of Medicine, University of California San Diego, La Jolla, California 92093, United States
| | - Diana R Tomchick
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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9
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Lawong A, Gahalawat S, Okombo J, Striepen J, Yeo T, Mok S, Deni I, Bridgford JL, Niederstrasser H, Zhou A, Posner B, Wittlin S, Gamo FJ, Crespo B, Churchyard A, Baum J, Mittal N, Winzeler E, Laleu B, Palmer MJ, Charman SA, Fidock DA, Ready JM, Phillips MA. Novel Antimalarial Tetrazoles and Amides Active against the Hemoglobin Degradation Pathway in Plasmodium falciparum. J Med Chem 2021; 64:2739-2761. [PMID: 33620219 DOI: 10.1021/acs.jmedchem.0c02022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Malaria control programs continue to be threatened by drug resistance. To identify new antimalarials, we conducted a phenotypic screen and identified a novel tetrazole-based series that shows fast-kill kinetics and a relatively low propensity to develop high-level resistance. Preliminary structure-activity relationships were established including identification of a subseries of related amides with antiplasmodial activity. Assaying parasites with resistance to antimalarials led us to test whether the series had a similar mechanism of action to chloroquine (CQ). Treatment of synchronized Plasmodium falciparum parasites with active analogues revealed a pattern of intracellular inhibition of hemozoin (Hz) formation reminiscent of CQ's action. Drug selections yielded only modest resistance that was associated with amplification of the multidrug resistance gene 1 (pfmdr1). Thus, we have identified a novel chemical series that targets the historically druggable heme polymerization pathway and that can form the basis of future optimization efforts to develop a new malaria treatment.
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Affiliation(s)
- Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Suraksha Gahalawat
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Ioanna Deni
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jessica L Bridgford
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Hanspeter Niederstrasser
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Anwu Zhou
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Bruce Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | - Benigno Crespo
- Medicines Development Campus, GlaxoSmithKline, Tres Cantos, 28760 Madrid, Spain
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Jake Baum
- Department of Life Sciences, Imperial College London, SW7 2AZ South Kensington, U.K
| | - Nimisha Mittal
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Elizabeth Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, California 92093, United States
| | - Benoît Laleu
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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10
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Li B, Deng X, Kim SH, Buhrow L, Tomchick DR, Phillips MA, Michael AJ. Alternative pathways utilize or circumvent putrescine for biosynthesis of putrescine-containing rhizoferrin. J Biol Chem 2020; 296:100146. [PMID: 33277357 PMCID: PMC7857480 DOI: 10.1074/jbc.ra120.016738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
The siderophore rhizoferrin (N1,N4-dicitrylputrescine) is produced in fungi and bacteria to scavenge iron. Putrescine-producing bacterium Ralstonia pickettii synthesizes rhizoferrin and encodes a single nonribosomal peptide synthetase-independent siderophore (NIS) synthetase. From biosynthetic logic, we hypothesized that this single enzyme is sufficient for rhizoferrin biosynthesis. We confirmed this by expression of R. pickettii NIS synthetase in Escherichia coli, resulting in rhizoferrin production. This was further confirmed in vitro using the recombinant NIS synthetase, synthesizing rhizoferrin from putrescine and citrate. Heterologous expression of homologous lbtA from Legionella pneumophila, required for rhizoferrin biosynthesis in that species, produced siderophore activity in E. coli. Rhizoferrin is also synthesized by Francisella tularensis and Francisella novicida, but unlike R. pickettii or L. pneumophila, Francisella species lack putrescine biosynthetic pathways because of genomic decay. Francisella encodes a NIS synthetase FslA/FigA and an ornithine decarboxylase homolog FslC/FigC, required for rhizoferrin biosynthesis. Ornithine decarboxylase produces putrescine from ornithine, but we show here in vitro that FigA synthesizes N-citrylornithine, and FigC is an N-citrylornithine decarboxylase that together synthesize rhizoferrin without using putrescine. We co-expressed F. novicida figA and figC in E. coli and produced rhizoferrin. A 2.1 Å X-ray crystal structure of the FigC N-citrylornithine decarboxylase reveals how the larger substrate is accommodated and how active site residues have changed to recognize N-citrylornithine. FigC belongs to a new subfamily of alanine racemase-fold PLP-dependent decarboxylases that are not involved in polyamine biosynthesis. These data reveal a natural product biosynthetic workaround that evolved to bypass a missing precursor and re-establish it in the final structure.
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Affiliation(s)
- Bin Li
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyi Deng
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Sok Ho Kim
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Leann Buhrow
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Diana R Tomchick
- Department of Biophysics, 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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11
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Kokkonda S, Deng X, White KL, El Mazouni F, White J, Shackleford DM, Katneni K, Chiu FCK, Barker H, McLaren J, Crighton E, Chen G, Angulo-Barturen I, Jimenez-Diaz MB, Ferrer S, Huertas-Valentin L, Martinez-Martinez MS, Lafuente-Monasterio MJ, Chittimalla R, Shahi SP, Wittlin S, Waterson D, Burrows JN, Matthews D, Tomchick D, Rathod PK, Palmer MJ, Charman SA, Phillips MA. Lead Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series for the Treatment of Malaria. J Med Chem 2020; 63:4929-4956. [PMID: 32248693 DOI: 10.1021/acs.jmedchem.0c00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Malaria puts at risk nearly half the world's population and causes high mortality in sub-Saharan Africa, while drug resistance threatens current therapies. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated target for malaria treatment based on our finding that triazolopyrimidine DSM265 (1) showed efficacy in clinical studies. Herein, we describe optimization of a pyrrole-based series identified using a target-based DHODH screen. Compounds with nanomolar potency versus Plasmodium DHODH and Plasmodium parasites were identified with good pharmacological properties. X-ray studies showed that the pyrroles bind an alternative enzyme conformation from 1 leading to improved species selectivity versus mammalian enzymes and equivalent activity on Plasmodium falciparum and Plasmodium vivax DHODH. The best lead DSM502 (37) showed in vivo efficacy at similar levels of blood exposure to 1, although metabolic stability was reduced. Overall, the pyrrole-based DHODH inhibitors provide an attractive alternative scaffold for the development of new antimalarial compounds.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Xiaoyi Deng
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Farah El Mazouni
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - David M Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Francis C K Chiu
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Helena Barker
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jenna McLaren
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | | | - Santiago Ferrer
- GSK, Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | | | | | | | | | | | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | | | | | - Dave Matthews
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Diana Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
| | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Margaret A Phillips
- Departments of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9135, United States
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12
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Affiliation(s)
- Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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13
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White J, Dhingra SK, Deng X, El Mazouni F, Lee MCS, Afanador GA, Lawong A, Tomchick DR, Ng CL, Bath J, Rathod PK, Fidock DA, Phillips MA. Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265. ACS Infect Dis 2019; 5:90-101. [PMID: 30375858 DOI: 10.1021/acsinfecdis.8b00211] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is one of the most challenging human infectious diseases, and both prevention and control have been hindered by the development of Plasmodium falciparum resistance to existing therapies. Several new compounds with novel mechanisms are in clinical development for the treatment of malaria, including DSM265, an inhibitor of Plasmodium dihydroorotate dehydrogenase. To explore the mechanisms by which resistance might develop to DSM265 in the field, we selected for DSM265-resistant P. falciparum parasites in vitro. Any of five different amino acid changes led to reduced efficacy on the parasite and to decreased DSM265 binding to P. falciparum DHODH. The DSM265-resistant parasites retained full sensitivity to atovaquone. All but one of the observed mutations were in the DSM265 binding site, and the remaining C276F was in the adjacent flavin cofactor site. The C276F mutation was previously identified in a recrudescent parasite during a Phase IIa clinical study. We confirmed that this mutation (and the related C276Y) accounted for the full level of observed DSM265 resistance by regenerating the mutation using CRISPR/Cas9 genome editing. X-ray structure analysis of the C276F mutant enzyme showed that conformational changes of nearby residues were required to accommodate the larger F276 residue, which in turn led to a restriction in the size of the DSM265 binding pocket. These findings underscore the importance of developing DSM265 as part of a combination therapy with other agents for successful use against malaria.
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Affiliation(s)
- John White
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - Satish K. Dhingra
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Xiaoyi Deng
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Farah El Mazouni
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Marcus C. S. Lee
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, U.K
| | - Gustavo A. Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Aloysus Lawong
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Diana R. Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
| | - Caroline L. Ng
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Jade Bath
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, 36 Bagley Hall, 400 15th Avenue NE, Seattle, Washington 98195, United States
| | - David A. Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, 701 West 168th Street, HHSC 1502, New York, New York 10032, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, PH8-W, 630 West 168th Street, PH 8-West, New York, New York 10032, United States
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390, United States
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14
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Patel MM, Volkov OA, Leija C, Lemoff A, Phillips MA. A dual regulatory circuit consisting of S-adenosylmethionine decarboxylase protein and its reaction product controls expression of the paralogous activator prozyme in Trypanosoma brucei. PLoS Pathog 2018; 14:e1007404. [PMID: 30365568 PMCID: PMC6221367 DOI: 10.1371/journal.ppat.1007404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/07/2018] [Accepted: 10/12/2018] [Indexed: 01/12/2023] Open
Abstract
Polyamines are essential for cell growth of eukaryotes including the etiologic agent of human African trypanosomiasis (HAT), Trypanosoma brucei. In trypanosomatids, a key enzyme in the polyamine biosynthetic pathway, S-adenosylmethionine decarboxylase (TbAdoMetDC) heterodimerizes with a unique catalytically-dead paralog called prozyme to form the active enzyme complex. In higher eukaryotes, polyamine metabolism is subject to tight feedback regulation by spermidine-dependent mechanisms that are absent in trypanosomatids. Instead, in T. brucei an alternative regulatory strategy based on TbAdoMetDC prozyme has evolved. We previously demonstrated that prozyme protein levels increase in response to loss of TbAdoMetDC activity. Herein, we show that prozyme levels are under translational control by monitoring incorporation of deuterated leucine into nascent prozyme protein. We furthermore identify pathway factors that regulate prozyme mRNA translation. We find evidence for a regulatory feedback mechanism in which TbAdoMetDC protein and decarboxylated AdoMet (dcAdoMet) act as suppressors of prozyme translation. In TbAdoMetDC null cells expressing the human AdoMetDC enzyme, prozyme levels are constitutively upregulated. Wild-type prozyme levels are restored by complementation with either TbAdoMetDC or an active site mutant, suggesting that TbAdoMetDC possesses an enzyme activity-independent function that inhibits prozyme translation. Depletion of dcAdoMet pools by three independent strategies: inhibition/knockdown of TbAdoMetDC, knockdown of AdoMet synthase, or methionine starvation, each cause prozyme upregulation, providing independent evidence that dcAdoMet functions as a metabolic signal for regulation of the polyamine pathway in T. brucei. These findings highlight a potential regulatory paradigm employing enzymes and pseudoenzymes that may have broad implications in biology. Trypanosoma brucei is a single-celled eukaryotic pathogen and the causative agent of human African trypanosomiasis (HAT). Polyamines are organic polycations that are essential for growth in T. brucei to facilitate protein translation and to maintain redox homeostasis. The pathway is the target of eflornithine, a current frontline therapy for treatment of HAT. Polyamine biosynthetic enzymes are regulated at multiple levels in mammals (e.g. transcription, translation and protein turnover), but in contrast, T. brucei lacks these mechanisms. Instead in T. brucei a central enzyme in polyamine metabolism called AdoMetDC must form a complex with a sister protein (termed a pseudoenzyme) to be active. Herein, we show that cellular levels of this sister protein we call prozyme are in turn feedback regulated by both AdoMetDC and by its reaction product in response to cell treatments that reduce pathway output. This regulatory paradigm highlights how pseudoenzymes can evolve to play an important role in metabolic pathway regulation and in organismal fitness.
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Affiliation(s)
- Manish M. Patel
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Oleg A. Volkov
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Christopher Leija
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
| | - Margaret A. Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Harry Hines Blvd, Dallas, TX, United States of America
- * E-mail:
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15
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Abstract
Polyamines are polycationic organic amines that are required for all eukaryotic life, exemplified by the polyamine spermidine, which plays an essential role in translation. They also play more specialized roles that differ across species, and their chemical versatility has been fully exploited during the evolution of protozoan pathogens. These eukaryotic pathogens, which cause some of the most globally widespread infectious diseases, have acquired species-specific polyamine-derived metabolites with essential cellular functions and have evolved unique mechanisms that regulate their core polyamine biosynthetic pathways. Many of these parasitic species have lost enzymes and or transporters from the polyamine metabolic pathway that are found in the human host. These pathway differences have prompted drug discovery efforts to target the parasite polyamine pathways, and indeed, the only clinically approved drug targeting the polyamine biosynthetic pathway is used to manage human African trypanosomiasis. This Minireview will primarily focus on polyamine metabolism and function in Trypanosoma, Leishmania, and Plasmodium species, which are the causative agents of human African trypanosomiasis (HAT) and Chagas disease, Leishmaniasis, and malaria, respectively. Aspects of polyamine metabolism across a diverse group of protozoan pathogens will also be explored.
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Affiliation(s)
- Margaret A Phillips
- From the Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9038
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16
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Afanador GA, Tomchick DR, Phillips MA. Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation between Pseudoenzyme Paralogs. Structure 2018; 26:1499-1512.e5. [PMID: 30197036 DOI: 10.1016/j.str.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
Trypanosoma brucei is a neglected tropical disease endemic to Africa. The polyamine spermidine is essential for post-translational hypusine modification of eukaryotic initiation factor 5A (eIF5A), which is catalyzed by deoxyhypusine synthase (TbDHS). In trypanosomatids, deoxyhypusine synthase (DHS) activity is dependent on heterotetramer formation between two paralogs, DHSc and DHSp, both with minimal activity on their own due to missing catalytic residues. We determined the X-ray structure of TbDHS showing a single functional shared active site is formed at the DHSc/DHSp heterodimer interface, with deficiencies in one subunit complemented by the other. Each heterodimer contains two NAD+ binding sites, one housed in the functional catalytic site and the second bound in a remnant dead site that lacks key catalytic residues. Functional analysis of these sites by site-directed mutagenesis identified long-range contributions to the catalytic site from the dead site. Differences between trypanosomatid and human DHS that could be exploited for drug discovery were identified.
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Affiliation(s)
- Gustavo A Afanador
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Kokkonda S, El Mazouni F, White KL, White J, Shackleford DM, Lafuente-Monasterio MJ, Rowland P, Manjalanagara K, Joseph JT, Garcia-Pérez A, Fernandez J, Gamo FJ, Waterson D, Burrows JN, Palmer MJ, Charman SA, Rathod PK, Phillips MA. Isoxazolopyrimidine-Based Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase with Antimalarial Activity. ACS Omega 2018; 3:9227-9240. [PMID: 30197997 PMCID: PMC6120730 DOI: 10.1021/acsomega.8b01573] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
Malaria kills nearly 0.5 million people yearly and impacts the lives of those living in over 90 countries where it is endemic. The current treatment programs are threatened by increasing drug resistance. Dihydroorotate dehydrogenase (DHODH) is now clinically validated as a target for antimalarial drug discovery as a triazolopyrimidine class inhibitor (DSM265) is currently undergoing clinical development. We discovered a related isoxazolopyrimidine series in a phenotypic screen, later determining that it targeted DHODH. To determine if the isoxazolopyrimidines could yield a drug candidate, we initiated hit-to-lead medicinal chemistry. Several potent analogues were identified, including a compound that showed in vivo antimalarial activity. The isoxazolopyrimidines were more rapidly metabolized than their triazolopyrimidine counterparts, and the pharmacokinetic data were not consistent with the goal of a single-dose treatment for malaria.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - Farah El Mazouni
- Department
of Biochemistry, University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9038, United States
| | - Karen L. White
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - John White
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - David M. Shackleford
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | | | - Paul Rowland
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | | | | | - Adolfo Garcia-Pérez
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | - Jorge Fernandez
- Tres
Cantos Medicines Development Campus, GSK, Severo Ochoa, Madrid 28760, Spain
| | | | - David Waterson
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Jeremy N. Burrows
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Michael J. Palmer
- Medicines
for Malaria Venture, 20, Route de Pré-Bois, 1215 Geneva, Switzerland
| | - Susan A. Charman
- Centre
for Drug Candidate Optimisation, Monash
Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Pradipsinh K. Rathod
- Departments
of Chemistry and Global Health, University
of Washington, Seattle, Washington 98195, United States
| | - Margaret A. Phillips
- Department
of Biochemistry, University of Texas Southwestern
Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, Texas 75390-9038, United States
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18
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Llanos-Cuentas A, Casapia M, Chuquiyauri R, Hinojosa JC, Kerr N, Rosario M, Toovey S, Arch RH, Phillips MA, Rozenberg FD, Bath J, Ng CL, Cowell AN, Winzeler EA, Fidock DA, Baker M, Möhrle JJ, Hooft van Huijsduijnen R, Gobeau N, Araeipour N, Andenmatten N, Rückle T, Duparc S. Antimalarial activity of single-dose DSM265, a novel plasmodium dihydroorotate dehydrogenase inhibitor, in patients with uncomplicated Plasmodium falciparum or Plasmodium vivax malaria infection: a proof-of-concept, open-label, phase 2a study. Lancet Infect Dis 2018; 18:874-883. [PMID: 29909069 PMCID: PMC6060173 DOI: 10.1016/s1473-3099(18)30309-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/27/2018] [Accepted: 05/09/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND DSM265 is a novel, long-duration inhibitor of plasmodium dihydroorotate dehydrogenase (DHODH) with excellent selectivity over human DHODH and activity against blood and liver stages of Plasmodium falciparum. This study aimed to assess the efficacy of DSM265 in patients with P falciparum or Plasmodium vivax malaria infection. METHODS This proof-of-concept, open-label, phase 2a study was conducted at the Asociación Civil Selva Amazónica in Iquitos, Peru. Patients aged 18-70 years, weighing 45-90 kg, who had clinical malaria (P falciparum or P vivax monoinfection) and fever within the previous 24 h were eligible. Exclusion criteria were clinical or laboratory signs of severe malaria, inability to take oral medicine, and use of other antimalarial treatment in the preceding 14 days. Patients were divided into cohorts of those with P falciparum (cohort a) or P vivax (cohort b) infection. Two initial cohorts received single oral doses of 400 mg DSM265. Patients were followed up for efficacy for 28 days and safety for 35 days. Further cohorts received escalated or de-escalated doses of DSM265, after safety and efficacy assessment of the initial dose. The primary endpoints were the proportion of patients achieving PCR-adjusted adequate clinical and parasitological response (ACPR) by day 14 for patients infected with P falciparum and the proportion of patients achieving a crude cure by day 14 for those infected with P vivax. Cohort success, the criteria for dose escalation, was defined as ACPR (P falciparum) or crude cure (P vivax) in at least 80% of patients in the cohort. The primary analysis was done in the intention-to-treat population (ITT) and the per-protocol population, and safety analyses were done in all patients who received the study drug. This study is registered at ClinicalTrials.gov (NCT02123290). FINDINGS Between Jan 12, 2015, and Dec 2, 2015, 45 Peruvian patients (24 with P falciparum [cohort a] and 21 with P vivax [cohort b] infection) were sequentially enrolled. For patients with P falciparum malaria in the per-protocol population, all 11 (100%) in the 400 mg group and eight (80%) of ten in the 250 mg group achieved ACPR on day 14. In the ITT analysis, 11 (85%) of 13 in the 400 mg group and eight (73%) of 11 in the 250 mg group achieved ACPR at day 14. For the patients with P vivax malaria, the primary endpoint was not met. In the per-protocol analysis, none of four patients who had 400 mg, three (50%) of six who had 600 mg, and one (25%) of four who had 800 mg DSM265 achieved crude cure at day 14. In the ITT analysis, none of five in the 400 mg group, three (33%) of nine in the 600 mg group, and one (14%) of seven in the 800 mg group achieved crude cure at day 14. During the 28-day extended observation of P falciparum patients, a resistance-associated mutation in the gene encoding the DSM265 target DHODH was observed in two of four recurring patients. DSM265 was well tolerated. The most common adverse events were pyrexia (20 [44%] of 45) and headache (18 [40%] of 45), which are both common symptoms of malaria, and no patients had any treatment-related serious adverse events or adverse events leading to study discontinuation. INTERPRETATION After a single dose of DSM265, P falciparum parasitaemia was rapidly cleared, whereas against P vivax, DSM265 showed less effective clearance kinetics. Its long duration of action provides the potential to prevent recurrence of P falciparum after treatment with a single dose, which should be further assessed in future combination studies. FUNDING The Global Health Innovative Technology Fund, the Bill & Melinda Gates Foundation, the National Institutes of Health (R01 AI103058), the Wellcome Trust, and the UK Department of International Development.
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Affiliation(s)
| | | | - Raúl Chuquiyauri
- Universidad Peruana Cayetano Heredia, Lima, Peru; Asociación Civil Selva Amazónica, Iquitos, Peru
| | | | - Nicola Kerr
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Maria Rosario
- Takeda Development Center Americas Inc, Cambridge, MA, USA
| | | | - Robert H Arch
- Takeda Development Center Americas Inc, Cambridge, MA, USA
| | - Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Centre, Dallas, TX, USA
| | - Felix D Rozenberg
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Jade Bath
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Caroline L Ng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
| | - Annie N Cowell
- School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- School of Medicine, University of California San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Mark Baker
- GlaxoSmithKline Consumer Healthcare Switzerland AG, Rotkreuz, Switzerland
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19
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Flannery EL, Foquet L, Chuenchob V, Fishbaugher M, Billman Z, Navarro MJ, Betz W, Olsen TM, Lee J, Camargo N, Nguyen T, Schafer C, Sack BK, Wilson EM, Saunders J, Bial J, Campo B, Charman SA, Murphy SC, Phillips MA, Kappe SH, Mikolajczak SA. Assessing drug efficacy against Plasmodium falciparum liver stages in vivo. JCI Insight 2018; 3:92587. [PMID: 29321371 PMCID: PMC5821200 DOI: 10.1172/jci.insight.92587] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022] Open
Abstract
Malaria eradication necessitates new tools to fight the evolving and complex Plasmodium pathogens. These tools include prophylactic drugs that eliminate Plasmodium liver stages and consequently prevent clinical disease, decrease transmission, and reduce the propensity for resistance development. Currently, the identification of these drugs relies on in vitro P. falciparum liver stage assays or in vivo causal prophylaxis assays using rodent malaria parasites; there is no method to directly test in vivo liver stage activity of candidate antimalarials against the human malaria-causing parasite P. falciparum. Here, we use a liver-chimeric humanized mouse (FRG huHep) to demonstrate in vivo P. falciparum liver stage development and describe the efficacy of clinically used and candidate antimalarials with prophylactic activity. We show that daily administration of atovaquone-proguanil (ATQ-PG; ATQ, 30 mg/kg, and PG, 10 mg/kg) protects 5 of 5 mice from liver stage infection, consistent with the use in humans as a causal prophylactic drug. Single-dose primaquine (60 mg/kg) has similar activity to that observed in humans, demonstrating the activity of this drug (and its active metabolites) in FRG huHep mice. We also show that DSM265, a selective Plasmodial dihydroorotate dehydrogenase inhibitor with causal prophylactic activity in humans, reduces liver stage burden in FRG huHep mice. Finally, we measured liver stage-to-blood stage transition of the parasite, the ultimate readout of prophylactic activity and measurement of infective capacity of parasites in the liver, to show that ATQ-PG reduces blood stage patency to below the limit of quantitation by quantitative PCR (qPCR). The FRG huHep model, thus, provides a platform for preclinical evaluation of drug candidates for liver stage causal prophylactic activity, pharmacokinetic/pharmacodynamics studies, and biological studies to investigate the mechanism of action of liver stage active antimalarials.
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Affiliation(s)
| | - Lander Foquet
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Vorada Chuenchob
- Center for Infectious Disease Research, Seattle, Washington, USA
| | | | - Zachary Billman
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | | | - William Betz
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Tayla M. Olsen
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | - Joshua Lee
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | - Nelly Camargo
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Thao Nguyen
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Carola Schafer
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Brandon K. Sack
- Center for Infectious Disease Research, Seattle, Washington, USA
| | | | - Jessica Saunders
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - John Bial
- Yecuris Corporation, Portland, Oregon, USA
| | - Brice Campo
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Sean C. Murphy
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, Washington, USA
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas Texas, USA
| | - Stefan H.I. Kappe
- Center for Infectious Disease Research, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle Washington, USA
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20
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Volkov OA, Brockway AJ, Wring SA, Peel M, Chen Z, Phillips MA, De Brabander JK. Species-Selective Pyrimidineamine Inhibitors of Trypanosoma brucei S-Adenosylmethionine Decarboxylase. J Med Chem 2018; 61:1182-1203. [PMID: 29271204 DOI: 10.1021/acs.jmedchem.7b01654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
New therapeutic options are needed for treatment of human African trypanosomiasis (HAT) caused by protozoan parasite Trypanosoma brucei. S-Adenosylmethionine decarboxylase (AdoMetDC) is an essential enzyme in the polyamine pathway of T. brucei. Previous attempts to target this enzyme were thwarted by the lack of brain penetration of the most advanced series. Herein, we describe a T. brucei AdoMetDC inhibitor series based on a pyrimidineamine pharmacophore that we identified by target-based high-throughput screening. The pyrimidineamines showed selectivity for T. brucei AdoMetDC over the human enzyme, inhibited parasite growth in whole-cell assay, and had good predicted blood-brain barrier penetration. The medicinal chemistry program elucidated structure-activity relationships within the series. Features of the series that were required for binding were revealed by determining the X-ray crystal structure of TbAdoMetDC bound to one analog. The pyrimidineamine series provides a novel starting point for an anti-HAT lead optimization.
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Affiliation(s)
| | | | - 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
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21
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Abstract
Malaria is caused in humans by five species of single-celled eukaryotic Plasmodium parasites (mainly Plasmodium falciparum and Plasmodium vivax) that are transmitted by the bite of Anopheles spp. mosquitoes. Malaria remains one of the most serious infectious diseases; it threatens nearly half of the world's population and led to hundreds of thousands of deaths in 2015, predominantly among children in Africa. Malaria is managed through a combination of vector control approaches (such as insecticide spraying and the use of insecticide-treated bed nets) and drugs for both treatment and prevention. The widespread use of artemisinin-based combination therapies has contributed to substantial declines in the number of malaria-related deaths; however, the emergence of drug resistance threatens to reverse this progress. Advances in our understanding of the underlying molecular basis of pathogenesis have fuelled the development of new diagnostics, drugs and insecticides. Several new combination therapies are in clinical development that have efficacy against drug-resistant parasites and the potential to be used in single-dose regimens to improve compliance. This ambitious programme to eliminate malaria also includes new approaches that could yield malaria vaccines or novel vector control strategies. However, despite these achievements, a well-coordinated global effort on multiple fronts is needed if malaria elimination is to be achieved.
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Affiliation(s)
- Margaret A Phillips
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, USA
| | | | | | | | - Wesley C Van Voorhis
- University of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Seattle, Washington, USA
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22
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Graves JL, Hertweck KL, Phillips MA, Han MV, Cabral LG, Barter TT, Greer LF, Burke MK, Mueller LD, Rose MR. Genomics of Parallel Experimental Evolution in Drosophila. Mol Biol Evol 2017; 34:831-842. [PMID: 28087779 PMCID: PMC5400383 DOI: 10.1093/molbev/msw282] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
What are the genomic foundations of adaptation in sexual populations? We address this question using fitness–character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.
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Affiliation(s)
- J L Graves
- Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC
| | - K L Hertweck
- Department of Biology, The University of Texas at Tyler, Tyler, TX
| | - M A Phillips
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV
| | - L G Cabral
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - T T Barter
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - L F Greer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - L D Mueller
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - M R Rose
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Allostery in motion: Trypanosoma brucei enzyme brought to life by a dead paralog. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317098038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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McCarthy JS, Lotharius J, Rückle T, Chalon S, Phillips MA, Elliott S, Sekuloski S, Griffin P, Ng CL, Fidock DA, Marquart L, Williams NS, Gobeau N, Bebrevska L, Rosario M, Marsh K, Möhrle JJ. Safety, tolerability, pharmacokinetics, and activity of the novel long-acting antimalarial DSM265: a two-part first-in-human phase 1a/1b randomised study. Lancet Infect Dis 2017; 17:626-635. [PMID: 28363636 PMCID: PMC5446412 DOI: 10.1016/s1473-3099(17)30171-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND DSM265 is a novel antimalarial that inhibits plasmodial dihydroorotate dehydrogenase, an enzyme essential for pyrimidine biosynthesis. We investigated the safety, tolerability, and pharmacokinetics of DSM265, and tested its antimalarial activity. METHODS Healthy participants aged 18-55 years were enrolled in a two-part study: part 1, a single ascending dose (25-1200 mg), double-blind, randomised, placebo-controlled study, and part 2, an open-label, randomised, active-comparator controlled study, in which participants were inoculated with Plasmodium falciparum induced blood-stage malaria (IBSM) and treated with DSM265 (150 mg) or mefloquine (10 mg/kg). Primary endpoints were DSM265 safety, tolerability, and pharmacokinetics. Randomisation lists were created using a validated, automated system. Both parts were registered with the Australian New Zealand Clinical Trials Registry, number ACTRN12613000522718 (part 1) and number ACTRN12613000527763 (part 2). FINDINGS In part 1, 73 participants were enrolled between April 12, 2013, and July 14, 2015 (DSM265, n=55; placebo, n=18). In part 2, nine participants were enrolled between Sept 30 and Nov 25, 2013 (150 mg DSM265, n=7; 10 mg/kg mefloquine, n=2). In part 1, 117 adverse events were reported; no drug-related serious or severe events were reported. The most common drug-related adverse event was headache. The mean DSM265 peak plasma concentration (Cmax) ranged between 1310 ng/mL and 34 800 ng/mL and was reached in a median time (tmax) between 1·5 h and 4 h, with a mean elimination half-life between 86 h and 118 h. In part 2, the log10 parasite reduction ratio at 48 h in the DSM265 (150 mg) group was 1·55 (95% CI 1·42-1·67) and in the mefloquine (10 mg/kg) group was 2·34 (2·17-2·52), corresponding to a parasite clearance half-life of 9·4 h (8·7-10·2) and 6·2 h (5·7-6·7), respectively. The median minimum inhibitory concentration of DSM265 in blood was estimated as 1040 ng/mL (range 552-1500), resulting in a predicted single efficacious dose of 340 mg. Parasite clearance was significantly faster in participants who received mefloquine than in participants who received DSM265 (p<0·0001). INTERPRETATION The good safety profile, long elimination half-life, and antimalarial effect of DSM265 supports its development as a partner drug in a single-dose antimalarial combination treatment. FUNDING Wellcome Trust, UK Department for International Development, Global Health Innovative Technology Fund, Bill & Melinda Gates Foundation.
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Affiliation(s)
- James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Q-Pharm Pty Ltd, Herston, QLD, Australia.
| | | | | | | | | | | | | | | | | | | | - Louise Marquart
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | - Maria Rosario
- Takeda Development Center Americas, Inc, Cambridge, MA, USA
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26
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Volkov OA, Kinch L, Ariagno C, Deng X, Zhong S, Grishin N, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. eLife 2016; 5. [PMID: 27977001 PMCID: PMC5201418 DOI: 10.7554/elife.20198] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 12/11/2016] [Indexed: 02/06/2023] Open
Abstract
Catalytically inactive enzyme paralogs occur in many genomes. Some regulate their active counterparts but the structural principles of this regulation remain largely unknown. We report X-ray structures of Trypanosoma brucei S-adenosylmethionine decarboxylase alone and in functional complex with its catalytically dead paralogous partner, prozyme. We show monomeric TbAdoMetDC is inactive because of autoinhibition by its N-terminal sequence. Heterodimerization with prozyme displaces this sequence from the active site through a complex mechanism involving a cis-to-trans proline isomerization, reorganization of a β-sheet, and insertion of the N-terminal α-helix into the heterodimer interface, leading to enzyme activation. We propose that the evolution of this intricate regulatory mechanism was facilitated by the acquisition of the dimerization domain, a single step that can in principle account for the divergence of regulatory schemes in the AdoMetDC enzyme family. These studies elucidate an allosteric mechanism in an enzyme and a plausible scheme by which such complex cooperativity evolved. DOI:http://dx.doi.org/10.7554/eLife.20198.001
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Affiliation(s)
- Oleg A Volkov
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Lisa Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Carson Ariagno
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shihua Zhong
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nick Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute,University of Texas Southwestern Medical Center, Dallas, United States
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
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27
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Phillips MA, White KL, Kokkonda S, Deng X, White J, El Mazouni F, Marsh K, Tomchick DR, Manjalanagara K, Rudra KR, Wirjanata G, Noviyanti R, Price RN, Marfurt J, Shackleford DM, Chiu FCK, Campbell M, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Martinez MS, Lafuente-Monasterio M, Kaminsky W, Silue K, Zeeman AM, Kocken C, Leroy D, Blasco B, Rossignol E, Rueckle T, Matthews D, Burrows JN, Waterson D, Palmer MJ, Rathod PK, Charman SA. A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-like Properties for Treatment and Prevention of Malaria. ACS Infect Dis 2016; 2:945-957. [PMID: 27641613 DOI: 10.1021/acsinfecdis.6b00144] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The emergence of drug-resistant malaria parasites continues to hamper efforts to control this lethal disease. Dihydroorotate dehydrogenase has recently been validated as a new target for the treatment of malaria, and a selective inhibitor (DSM265) of the Plasmodium enzyme is currently in clinical development. With the goal of identifying a backup compound to DSM265, we explored replacement of the SF5-aniline moiety of DSM265 with a series of CF3-pyridinyls while maintaining the core triazolopyrimidine scaffold. This effort led to the identification of DSM421, which has improved solubility, lower intrinsic clearance, and increased plasma exposure after oral dosing compared to DSM265, while maintaining a long predicted human half-life. Its improved physical and chemical properties will allow it to be formulated more readily than DSM265. DSM421 showed excellent efficacy in the SCID mouse model of P. falciparum malaria that supports the prediction of a low human dose (<200 mg). Importantly DSM421 showed equal activity against both P. falciparum and P. vivax field isolates, while DSM265 was more active on P. falciparum. DSM421 has the potential to be developed as a single-dose cure or once-weekly chemopreventative for both P. falciparum and P. vivax malaria, leading to its advancement as a preclinical development candidate.
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Affiliation(s)
| | - Karen L. White
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sreekanth Kokkonda
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - John White
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | | | - Kennan Marsh
- AbbVie Inc., 1 North Waukegan
Road, North Chicago, Illinois 60064-6104, United States
| | | | | | | | - Grennady Wirjanata
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
| | - Rintis Noviyanti
- Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430 Jakarta, Indonesia
| | - Ric N. Price
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
- Centre
for Tropical Medicine and Global Health, Nuffield Department of Clinical
Medicine, University of Oxford, Oxford OX3 7LJ, U.K
| | - Jutta Marfurt
- Global
and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, P.O. Box 41096, Casuarina, NT 0811, Australia
| | - David M. Shackleford
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Francis C. K. Chiu
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Michael Campbell
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | - Santiago Ferrer Bazaga
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | - Iñigo Angulo-Barturen
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Santos Martinez
- GlaxoSmithKline, Tres Cantos Medicines Development
Campus, Severo Ochoa, Madrid 28760, Spain
| | | | - Werner Kaminsky
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Kigbafori Silue
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Km17, Route de Dabou, Adiopodoumé, BP 1303 Abidjan, Ivory Coast
| | - Anne-Marie Zeeman
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - Clemens Kocken
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
| | - Didier Leroy
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | | | | | - Dave Matthews
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | | | | | - Pradipsinh K. Rathod
- Departments
of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Susan A. Charman
- Centre
for Drug Candidate Optimisation, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, VIC 3052, Australia
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Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PLoS Pathog 2016; 12:e1006010. [PMID: 27820863 PMCID: PMC5098729 DOI: 10.1371/journal.ppat.1006010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/18/2016] [Indexed: 01/17/2023] Open
Abstract
The human pathogenic parasite Trypanosoma brucei possess both de novo and salvage routes for the biosynthesis of pyrimidine nucleotides. Consequently, they do not require salvageable pyrimidines for growth. Thymidine kinase (TK) catalyzes the formation of dTMP and dUMP and is one of several salvage enzymes that appear redundant to the de novo pathway. Surprisingly, we show through analysis of TK conditional null and RNAi cells that TK is essential for growth and for infectivity in a mouse model, and that a catalytically active enzyme is required for its function. Unlike humans, T. brucei and all other kinetoplastids lack dCMP deaminase (DCTD), which provides an alternative route to dUMP formation. Ectopic expression of human DCTD resulted in full rescue of the RNAi growth phenotype and allowed for selection of viable TK null cells. Metabolite profiling by LC-MS/MS revealed a buildup of deoxypyrimidine nucleosides in TK depleted cells. Knockout of cytidine deaminase (CDA), which converts deoxycytidine to deoxyuridine led to thymidine/deoxyuridine auxotrophy. These unexpected results suggested that T. brucei encodes an unidentified 5'-nucleotidase that converts deoxypyrimidine nucleotides to their corresponding nucleosides, leading to their dead-end buildup in TK depleted cells at the expense of dTTP pools. Bioinformatics analysis identified several potential candidate genes that could encode 5'-nucleotidase activity including an HD-domain protein that we show catalyzes dephosphorylation of deoxyribonucleotide 5'-monophosphates. We conclude that TK is essential for synthesis of thymine nucleotides regardless of whether the nucleoside precursors originate from the de novo pathway or through salvage. Reliance on TK in the absence of DCTD may be a shared vulnerability among trypanosomatids and may provide a unique opportunity to selectively target a diverse group of pathogenic single-celled eukaryotes with a single drug.
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Affiliation(s)
- Christopher Leija
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Filipa Rijo-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Lisa N. Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nicole Nischan
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Jennifer J. Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zeping Hu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
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29
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Brockway AJ, Cosner CC, Volkov OA, Phillips MA, De Brabander JK. Improved Synthesis of MDL 73811 - a Potent AdoMetDC Inhibitor and Anti-Trypanosomal Compound. SYNTHESIS-STUTTGART 2016; 48:2065-2068. [PMID: 27482123 DOI: 10.1055/s-0035-1561608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An improved synthesis of MDL 73811 - a potent AdoMetDC (S-adenosylmethionine decarboxylease) inhibitor and anti-trypanosomal compound with in vivo activity has been completed in four steps from commercially available 2',3'-O-isopropylideneadenosine. Utilization of Mitsunobu chemistry was crucial for the reliable and scalable introduction of the 5'-methylamine moiety, which was problematic using traditional activation/displacement chemistry as previously reported. All reactions in this synthesis were run on gram-scale resulting in a five-fold increase in yield over the original synthesis.
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Affiliation(s)
- Anthony J Brockway
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Casey C Cosner
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
| | - Oleg A Volkov
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas,6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | - Margaret A Phillips
- Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas,6001 Forest Park Road, Dallas, Texas 75390-9041, United States
| | - Jef K De Brabander
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9038, United States
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30
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Kokkonda S, Deng X, White KL, Coteron JM, Marco M, de Las Heras L, White J, El Mazouni F, Tomchick DR, Manjalanagara K, Rudra KR, Chen G, Morizzi J, Ryan E, Kaminsky W, Leroy D, Martínez-Martínez MS, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Waterson D, Burrows JN, Matthews D, Charman SA, Phillips MA, Rathod PK. Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity. J Med Chem 2016; 59:5416-31. [PMID: 27127993 PMCID: PMC4904246 DOI: 10.1021/acs.jmedchem.6b00275] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Malaria persists as one of the most devastating global infectious diseases. The pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) has been identified as a new malaria drug target, and a triazolopyrimidine-based DHODH inhibitor 1 (DSM265) is in clinical development. We sought to identify compounds with higher potency against Plasmodium DHODH while showing greater selectivity toward animal DHODHs. Herein we describe a series of novel triazolopyrimidines wherein the p-SF5-aniline was replaced with substituted 1,2,3,4-tetrahydro-2-naphthyl or 2-indanyl amines. These compounds showed strong species selectivity, and several highly potent tetrahydro-2-naphthyl derivatives were identified. Compounds with halogen substitutions displayed sustained plasma levels after oral dosing in rodents leading to efficacy in the P. falciparum SCID mouse malaria model. These data suggest that tetrahydro-2-naphthyl derivatives have the potential to be efficacious for the treatment of malaria, but due to higher metabolic clearance than 1, they most likely would need to be part of a multidose regimen.
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Affiliation(s)
- Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | | | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Jose M Coteron
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - Maria Marco
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - Laura de Las Heras
- GSK , Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760 Spain
| | - John White
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | | | | | | | | | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Julia Morizzi
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Eileen Ryan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Werner Kaminsky
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
| | - Didier Leroy
- Medicines for Malaria Venture , 1215 Geneva, Switzerland
| | | | | | | | | | - David Waterson
- Medicines for Malaria Venture , 1215 Geneva, Switzerland
| | | | - Dave Matthews
- Medicines for Malaria Venture , 1215 Geneva, Switzerland
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington , Seattle, Washington 98195, United States
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31
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Phillips MA, Lotharius J, Marsh K, White J, Dayan A, White KL, Njoroge JW, El Mazouni F, Lao Y, Kokkonda S, Tomchick DR, Deng X, Laird T, Bhatia SN, March S, Ng CL, Fidock DA, Wittlin S, Lafuente-Monasterio M, Benito FJG, Alonso LMS, Martinez MS, Jimenez-Diaz MB, Bazaga SF, Angulo-Barturen I, Haselden JN, Louttit J, Cui Y, Sridhar A, Zeeman AM, Kocken C, Sauerwein R, Dechering K, Avery VM, Duffy S, Delves M, Sinden R, Ruecker A, Wickham KS, Rochford R, Gahagen J, Iyer L, Riccio E, Mirsalis J, Bathhurst I, Rueckle T, Ding X, Campo B, Leroy D, Rogers MJ, Rathod PK, Burrows JN, Charman SA. A long-duration dihydroorotate dehydrogenase inhibitor (DSM265) for prevention and treatment of malaria. Sci Transl Med 2016; 7:296ra111. [PMID: 26180101 DOI: 10.1126/scitranslmed.aaa6645] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Malaria is one of the most significant causes of childhood mortality, but disease control efforts are threatened by resistance of the Plasmodium parasite to current therapies. Continued progress in combating malaria requires development of new, easy to administer drug combinations with broad-ranging activity against all manifestations of the disease. DSM265, a triazolopyrimidine-based inhibitor of the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH), is the first DHODH inhibitor to reach clinical development for treatment of malaria. We describe studies profiling the biological activity, pharmacological and pharmacokinetic properties, and safety of DSM265, which supported its advancement to human trials. DSM265 is highly selective toward DHODH of the malaria parasite Plasmodium, efficacious against both blood and liver stages of P. falciparum, and active against drug-resistant parasite isolates. Favorable pharmacokinetic properties of DSM265 are predicted to provide therapeutic concentrations for more than 8 days after a single oral dose in the range of 200 to 400 mg. DSM265 was well tolerated in repeat-dose and cardiovascular safety studies in mice and dogs, was not mutagenic, and was inactive against panels of human enzymes/receptors. The excellent safety profile, blood- and liver-stage activity, and predicted long half-life in humans position DSM265 as a new potential drug combination partner for either single-dose treatment or once-weekly chemoprevention. DSM265 has advantages over current treatment options that are dosed daily or are inactive against the parasite liver stage.
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Affiliation(s)
- Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA.
| | | | - Kennan Marsh
- Abbvie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Anthony Dayan
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Karen L White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jacqueline W Njoroge
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Farah El Mazouni
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Yanbin Lao
- Abbvie, 1 North Waukegan Road, North Chicago, IL 60064-6104, USA
| | - Sreekanth Kokkonda
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Diana R Tomchick
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, TX 75390-9041, USA
| | - Trevor Laird
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Sangeeta N Bhatia
- Health Sciences and Technology/Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sandra March
- Health Sciences and Technology/Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Caroline L Ng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA. Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland. University of Basel, 4003 Basel, Switzerland
| | | | | | - Laura Maria Sanz Alonso
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Santos Martinez
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Maria Belen Jimenez-Diaz
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Santiago Ferrer Bazaga
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - Iñigo Angulo-Barturen
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | - John N Haselden
- GlaxoSmithKline (GSK), Tres Cantos Medicines Development Campus, Severo Ochoa, Madrid 28760, Spain
| | | | - Yi Cui
- GSK, Park Road, Ware, Hertfordshire SG12 0DP, UK
| | - Arun Sridhar
- GSK, Park Road, Ware, Hertfordshire SG12 0DP, UK
| | - Anna-Marie Zeeman
- Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, Netherlands
| | - Clemens Kocken
- Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH Rijswijk, Netherlands
| | | | | | - Vicky M Avery
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Sandra Duffy
- Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Michael Delves
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Robert Sinden
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Andrea Ruecker
- Imperial College of Science Technology and Medicine, London SW7 2AY, UK
| | - Kristina S Wickham
- State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Rosemary Rochford
- State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | | | | | - Ed Riccio
- SRI International, Menlo Park, CA 94025, USA
| | | | - Ian Bathhurst
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | | | - Xavier Ding
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - Didier Leroy
- Medicines for Malaria Venture, 1215 Geneva, Switzerland
| | - M John Rogers
- National Institutes for Allergy and Infectious Diseases, 6610 Rockledge Drive, Bethesda, MD 20892, USA
| | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | | | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
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Pavadai E, El Mazouni F, Wittlin S, de Kock C, Phillips MA, Chibale K. Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. J Chem Inf Model 2016; 56:548-62. [PMID: 26915022 DOI: 10.1021/acs.jcim.5b00680] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH), a key enzyme in the de novo pyrimidine biosynthesis pathway, which the Plasmodium falciparum relies on exclusively for survival, has emerged as a promising target for antimalarial drugs. In an effort to discover new and potent PfDHODH inhibitors, 3D-QSAR pharmacophore models were developed based on the structures of known PfDHODH inhibitors and the validated Hypo1 model was used as a 3D search query for virtual screening of the National Cancer Institute database. The virtual hit compounds were further filtered based on molecular docking and Molecular Mechanics/Generalized Born Surface Area binding energy calculations. The combination of the pharmacophore and structure-based virtual screening resulted in the identification of nine new compounds that showed >25% inhibition of PfDHODH at a concentration of 10 μM, three of which exhibited IC50 values in the range of 0.38-20 μM. The most active compound, NSC336047, displayed species-selectivity for PfDHODH over human DHODH and inhibited parasite growth with an IC50 of 26 μM. In addition to this, 13 compounds inhibited parasite growth with IC50 values of ≤ 50 μM, 4 of which showed IC50 values in the range of 5-12 μM. These compounds could be further explored in the identification and development of more potent PfDHODH and parasite growth inhibitors.
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Affiliation(s)
| | - Farah El Mazouni
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute , Socinstrasse 57, 4002 Basel, Switzerland.,University of Basel , 4002 Basel, Switzerland
| | - Carmen de Kock
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town , Observatory 7925, South Africa
| | - Margaret A Phillips
- Departments of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Blvd, Dallas, Texas 75390-9041, United States
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33
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Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. PLoS One 2015; 10:e0134697. [PMID: 26258606 PMCID: PMC4530941 DOI: 10.1371/journal.pone.0134697] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023] Open
Abstract
The 2012 Teach-Discover-Treat (TDT) community-wide experiment provided a unique opportunity to test prospective virtual screening protocols targeting the anti-malarial target dihydroorotate dehydrogenase (DHODH). Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted the bound structure of a non-triazolopyrimidine inhibitor, as well as an overall hit rate of 27% of tested active compounds from multiple novel chemical scaffolds. The general approach entailed exhaustively building and screening sparse pharmacophore models comprising of a minimum of three features for each bound ligand in all available DHODH co-crystals and iteratively adding features that increased the number of known binders returned by the query. Collectively, the TDT experiment provided a unique opportunity to teach computational methods of drug discovery, develop innovative methodologies and prospectively discover new compounds active against DHODH.
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Affiliation(s)
- David Ryan Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail: (DRK); (CJC)
| | - Nicolas A. Pabon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Blvd, Dallas, TX, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Blvd, Dallas, TX, United States of America
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States of America
- * E-mail: (DRK); (CJC)
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Nguyen S, Leija C, Kinch L, Regmi S, Li Q, Grishin NV, Phillips MA. Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins. J Biol Chem 2015; 290:19987-98. [PMID: 26082486 PMCID: PMC4528157 DOI: 10.1074/jbc.m115.656785] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/18/2015] [Indexed: 11/06/2022] Open
Abstract
The eukaryotic protozoan parasite Trypanosoma brucei is the causative agent of human African trypanosomiasis. Polyamine biosynthesis is essential in T. brucei, and the polyamine spermidine is required for synthesis of a novel cofactor called trypanothione and for deoxyhypusine modification of eukaryotic translation initiation factor 5A (eIF5A). eIF5A promotes translation of proteins containing polyprolyl tracts in mammals and yeast. To evaluate the function of eIF5A in T. brucei, we used RNA interference (RNAi) to knock down eIF5A levels and found that it is essential for T. brucei growth. The RNAi-induced growth defect was complemented by expression of wild-type human eIF5A but not by a Lys-50 mutant that blocks modification by deoxyhypusine. Bioinformatics analysis showed that 15% of the T. brucei proteome contains 3 or more consecutive prolines and that actin-related proteins and cysteine proteases were highly enriched in the group. Steady-state protein levels of representative proteins containing 9 consecutive prolines that are involved in actin assembly (formin and CAP/Srv2p) were significantly reduced by knockdown of eIF5A. Several T. brucei polyprolyl proteins are involved in flagellar assembly. Knockdown of TbeIF5A led to abnormal cell morphologies and detached flagella, suggesting that eIF5A is important for translation of proteins needed for these processes. Potential specialized functions for eIF5A in T. brucei in translation of variable surface glycoproteins were also uncovered. Inhibitors of deoxyhypusination would be expected to cause a pleomorphic effect on multiple cell processes, suggesting that deoxyhypusine/hypusine biosynthesis could be a promising drug target in not just T. brucei but in other eukaryotic pathogens.
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MESH Headings
- Amino Acid Sequence
- Animals
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Flagella/genetics
- Flagella/metabolism
- Flagella/ultrastructure
- Gene Knockdown Techniques
- Humans
- Lysine/analogs & derivatives
- Lysine/metabolism
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Molecular Sequence Data
- Peptide Initiation Factors/antagonists & inhibitors
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Peptides/metabolism
- Protein Processing, Post-Translational
- Proteome/genetics
- Proteome/metabolism
- Protozoan Proteins/antagonists & inhibitors
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/antagonists & inhibitors
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
- Trypanosoma brucei brucei/ultrastructure
- Eukaryotic Translation Initiation Factor 5A
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Affiliation(s)
| | | | | | | | - Qiong Li
- From the Departments of Pharmacology and
| | - Nick V Grishin
- Biophysics and Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
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35
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Li Q, Leija C, Rijo-Ferreira F, Chen J, Cestari I, Stuart K, Tu BP, Phillips MA. GMP synthase is essential for viability and infectivity of Trypanosoma brucei despite a redundant purine salvage pathway. Mol Microbiol 2015; 97:1006-20. [PMID: 26043892 DOI: 10.1111/mmi.13083] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2015] [Indexed: 12/28/2022]
Abstract
The causative agent of human African trypanosomiasis, Trypanosoma brucei, lacks de novo purine biosynthesis and depends on purine salvage from the host. The purine salvage pathway is redundant and contains two routes to guanosine-5'-monophosphate (GMP) formation: conversion from xanthosine-5'-monophosphate (XMP) by GMP synthase (GMPS) or direct salvage of guanine by hypoxanthine-guanine phosphoribosyltransferase (HGPRT). We show recombinant T. brucei GMPS efficiently catalyzes GMP formation. Genetic knockout of GMPS in bloodstream parasites led to depletion of guanine nucleotide pools and was lethal. Growth of gmps null cells was only rescued by supraphysiological guanine concentrations (100 μM) or by expression of an extrachromosomal copy of GMPS. Hypoxanthine was a competitive inhibitor of guanine rescue, consistent with a common uptake/metabolic conversion mechanism. In mice, gmps null parasites were unable to establish an infection demonstrating that GMPS is essential for virulence and that plasma guanine is insufficient to support parasite purine requirements. These data validate GMPS as a potential therapeutic target for treatment of human African trypanosomiasis. The ability to strategically inhibit key metabolic enzymes in the purine pathway unexpectedly bypasses its functional redundancy by exploiting both the nature of pathway flux and the limited nutrient environment of the parasite's extracellular niche.
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Affiliation(s)
- Qiong Li
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Christopher Leija
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jun Chen
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Igor Cestari
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA, 98109-5219, USA
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA, 98109-5219, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX, 75390-9041, USA
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36
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Lucas-Hourani M, Munier-Lehmann H, El Mazouni F, Malmquist NA, Harpon J, Coutant EP, Guillou S, Helynck O, Noel A, Scherf A, Phillips MA, Tangy F, Vidalain PO, Janin YL. Original 2-(3-Alkoxy-1H-pyrazol-1-yl)azines Inhibitors of Human Dihydroorotate Dehydrogenase (DHODH). J Med Chem 2015; 58:5579-98. [PMID: 26079043 PMCID: PMC4516315 DOI: 10.1021/acs.jmedchem.5b00606] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Following our discovery of human dihydroorotate dehydrogenase (DHODH) inhibition by 2-(3-alkoxy-1H-pyrazol-1-yl)pyrimidine derivatives as well as 2-(4-benzyl-3-ethoxy-5-methyl-1H-pyrazol-1-yl)-5-methylpyridine, we describe here the syntheses and evaluation of an array of azine-bearing analogues. As in our previous report, the structure-activity study of this series of human DHODH inhibitors was based on a phenotypic assay measuring measles virus replication. Among other inhibitors, this round of syntheses and biological evaluation iteration led to the highly active 5-cyclopropyl-2-(4-(2,6-difluorophenoxy)-3-isopropoxy-5-methyl-1H-pyrazol-1-yl)-3-fluoropyridine. Inhibition of DHODH by this compound was confirmed in an array of in vitro assays, including enzymatic tests and cell-based assays for viral replication and cellular growth. This molecule was found to be more active than the known inhibitors of DHODH, brequinar and teriflunomide, thus opening perspectives for its use as a tool or for the design of an original series of immunosuppressive agent. Moreover, because other series of inhibitors of human DHODH have been found to also affect Plasmodium falciparum DHODH, all the compounds were assayed for their effect on P. falciparum growth. However, the modest in vitro inhibition solely observed for two compounds did not correlate with their inhibition of P. falciparum DHODH.
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Affiliation(s)
- Marianne Lucas-Hourani
- †Unité de Génomique Virale et Vaccination, Département de Virologie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,‡Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Hélène Munier-Lehmann
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Farah El Mazouni
- ⊥Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, United States
| | - Nicholas A Malmquist
- #Unité de Biologie des Interactions Hôte-Parasite, Département de Parasitologie et Mycologie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.,^Unité 1201, Institut National de la Santé et de la Recherche Médicale, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,+Equipe de Recherche Labellisée 9195, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Jane Harpon
- #Unité de Biologie des Interactions Hôte-Parasite, Département de Parasitologie et Mycologie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.,^Unité 1201, Institut National de la Santé et de la Recherche Médicale, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,+Equipe de Recherche Labellisée 9195, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Eloi P Coutant
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Sandrine Guillou
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Olivier Helynck
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Anne Noel
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Artur Scherf
- #Unité de Biologie des Interactions Hôte-Parasite, Département de Parasitologie et Mycologie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.,^Unité 1201, Institut National de la Santé et de la Recherche Médicale, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,+Equipe de Recherche Labellisée 9195, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Margaret A Phillips
- ⊥Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, United States
| | - Frédéric Tangy
- †Unité de Génomique Virale et Vaccination, Département de Virologie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,‡Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Pierre-Olivier Vidalain
- †Unité de Génomique Virale et Vaccination, Département de Virologie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,‡Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, 25 Rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Yves L Janin
- §Unité Mixte de Recherche 3523, Centre National de la Recherche Scientifique, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France.,∥Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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37
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Deng X, Matthews D, Rathod PK, Phillips MA. The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions. Acta Crystallogr F Struct Biol Commun 2015; 71:553-9. [PMID: 25945708 DOI: 10.1107/s2053230x15000989] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/16/2015] [Indexed: 11/11/2022]
Abstract
Plasmodium species are protozoan parasites that are the causative agent of malaria. Malaria is a devastating disease, and its treatment and control have been hampered by the propensity of the parasite to become drug-resistant. Dihydroorotate dehydrogenase (DHODH) has been identified as a promising new target for the development of antimalarial agents. Here, the X-ray structure of P. falciparum DHODH bound to a potent and selective N-phenylbenzamide-based inhibitor (DSM59) is described at 2.3 Å resolution. The structure elucidates novel binding-site interactions and shows how conformational flexibility of the enzyme leads to the ability to bind diverse chemical structures with high affinity. This information provides new insight into the design of high-affinity DHODH inhibitors for the treatment of malaria.
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Affiliation(s)
- Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | | | - Pradipsinh K Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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38
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Deng X, Kokkonda S, El Mazouni F, White J, Burrows JN, Kaminsky W, Charman SA, Matthews D, Rathod PK, Phillips MA. Fluorine modulates species selectivity in the triazolopyrimidine class of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors. J Med Chem 2014; 57:5381-94. [PMID: 24801997 PMCID: PMC4079327 DOI: 10.1021/jm500481t] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Malaria is one of the most serious global infectious diseases. The pyrimidine biosynthetic enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) is an important target for antimalarial chemotherapy. We describe a detailed analysis of protein-ligand interactions between DHODH and a triazolopyrimidine-based inhibitor series to explore the effects of fluorine on affinity and species selectivity. We show that increasing fluorination dramatically increases binding to mammalian DHODHs, leading to a loss of species selectivity. Triazolopyrimidines bind Plasmodium and mammalian DHODHs in overlapping but distinct binding sites. Key hydrogen-bond and stacking interactions underlying strong binding to PfDHODH are absent in the mammalian enzymes. Increasing fluorine substitution leads to an increase in the entropic contribution to binding, suggesting that strong binding to mammalian DHODH is a consequence of an enhanced hydrophobic effect upon binding to an apolar pocket. We conclude that hydrophobic interactions between fluorine and hydrocarbons provide significant binding energy to protein-ligand interactions. Our studies define the requirements for species-selective binding to PfDHODH and show that the triazolopyrimidine scaffold can alternatively be tuned to inhibit human DHODH, an important target for autoimmune diseases.
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Affiliation(s)
- Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas , 6001 Forest Park Boulevard, Dallas, Texas 75390-9041, United States
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39
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Hooft van Huijsduijnen R, Guy RK, Chibale K, Haynes RK, Peitz I, Kelter G, Phillips MA, Vennerstrom JL, Yuthavong Y, Wells TNC. Anticancer properties of distinct antimalarial drug classes. PLoS One 2013; 8:e82962. [PMID: 24391728 PMCID: PMC3877007 DOI: 10.1371/journal.pone.0082962] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/22/2013] [Indexed: 12/31/2022] Open
Abstract
We have tested five distinct classes of established and experimental antimalarial drugs for their anticancer potential, using a panel of 91 human cancer lines. Three classes of drugs: artemisinins, synthetic peroxides and DHFR (dihydrofolate reductase) inhibitors effected potent inhibition of proliferation with IC50s in the nM- low µM range, whereas a DHODH (dihydroorotate dehydrogenase) and a putative kinase inhibitor displayed no activity. Furthermore, significant synergies were identified with erlotinib, imatinib, cisplatin, dasatinib and vincristine. Cluster analysis of the antimalarials based on their differential inhibition of the various cancer lines clearly segregated the synthetic peroxides OZ277 and OZ439 from the artemisinin cluster that included artesunate, dihydroartemisinin and artemisone, and from the DHFR inhibitors pyrimethamine and P218 (a parasite DHFR inhibitor), emphasizing their shared mode of action. In order to further understand the basis of the selectivity of these compounds against different cancers, microarray-based gene expression data for 85 of the used cell lines were generated. For each compound, distinct sets of genes were identified whose expression significantly correlated with compound sensitivity. Several of the antimalarials tested in this study have well-established and excellent safety profiles with a plasma exposure, when conservatively used in malaria, that is well above the IC50s that we identified in this study. Given their unique mode of action and potential for unique synergies with established anticancer drugs, our results provide a strong basis to further explore the potential application of these compounds in cancer in pre-clinical or and clinical settings.
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Affiliation(s)
| | - R. Kiplin Guy
- St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Kelly Chibale
- Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Richard K. Haynes
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | | | | | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jonathan L. Vennerstrom
- Department of Pharmaceutical Sciences, Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yongyuth Yuthavong
- BIOTEC, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
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40
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Das P, Deng X, Zhang L, Roth MG, Fontoura BMA, Phillips MA, De Brabander JK. SAR Based Optimization of a 4-Quinoline Carboxylic Acid Analog with Potent Anti-Viral Activity. ACS Med Chem Lett 2013; 4:517-521. [PMID: 23930152 DOI: 10.1021/ml300464h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
It is established that drugs targeting viral proteins are at risk of generating resistant strains. However, drugs targeting host factors can potentially avoid this problem. Herein we report structure-activity relationship studies leading to the discovery of a very potent lead compound 6-fluoro-2-(5-isopropyl-2-methyl-4-phenoxyphenyl)quinoline-4-carboxylic acid (C44) that inhibits human dihydroorotate dehydrogenase (DHODH) with an IC50 of 1 nM, and viral replication of VSV and WSN-Influenza with an EC50 of 2 nM and 41 nM. We also solved the X-ray structure of human DHODH bound to C44, providing structural insight into the potent inhibition of biaryl ether analogs of brequinar.
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Affiliation(s)
- Priyabrata Das
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Xiaoyi Deng
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Liang Zhang
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Michael G. Roth
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Beatriz M. A. Fontoura
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Margaret A. Phillips
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
| | - Jef K. De Brabander
- Department
of Biochemistry, ‡Department of Pharmacology, and §Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas,
Texas 75390, United States
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Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog 2013; 9:e1003375. [PMID: 23717205 PMCID: PMC3662640 DOI: 10.1371/journal.ppat.1003375] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH) inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes. Malaria parasites kill up to a million people around the world every year. Emergence of resistance to drugs remains a key obstacle against elimination of malaria. In the laboratory, parasites can efficiently acquire resistance to experimental antimalarials by changing DNA at the target locus. This happens efficiently even for an antimalarial that the parasite has never encountered in a clinical setting. In this study, we formally demonstrate how parasites achieve this feat: first, individual parasites in a population of millions randomly amplify large regions of DNA between short sequence repeats of adenines (A) or thymines (T) that are peppered throughout the malaria parasite genome. The rare lucky parasite that amplifies DNA coding for the target of the antimalarial, along with dozens of its neighboring genes, gains an evolutionary advantage and survives. In a second step, to withstand increasing drug pressure and to achieve higher levels of resistance, each parasite line makes additional copies of this region. This second expansion does not rely on the random A/T-based DNA rearrangements but, instead, a more precise amplification mechanism that retains the unique signature of co-amplified genes created earlier in each parasite. Generation of multiple copies of the target genes in the parasite genome may be the beginning of other beneficial changes for the parasite, including the future acquisition of mutations.
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Affiliation(s)
- Jennifer L. Guler
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Freeman
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Vida Ahyong
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Rapatbhorn Patrapuvich
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Ramesh Gujjar
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Joseph DeRisi
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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42
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Xiao Y, Nguyen S, Kim SH, Volkov OA, Tu BP, Phillips MA. Product feedback regulation implicated in translational control of the Trypanosoma brucei S-adenosylmethionine decarboxylase regulatory subunit prozyme. Mol Microbiol 2013; 88:846-61. [PMID: 23634831 DOI: 10.1111/mmi.12226] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 12/12/2022]
Abstract
Human African sleeping sickness (HAT) is caused by the parasitic protozoan Trypanosoma brucei. Polyamine biosynthesis is an important drug target in the treatment of HAT. Previously we showed that trypanosomatid S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme for biosynthesis of the polyamine spermidine, is activated by heterodimer formation with an inactive paralogue termed prozyme. Furthermore, prozyme protein levels were regulated in response to reduced AdoMetDC activity. Herein we show that T. brucei encodes three prozyme transcripts. The 3'UTRs of these transcripts were mapped and chloramphenicol acetyltransferase (CAT) reporter constructs were used to identify a 1.2 kb region that contained a 3'UTR prozyme regulatory element sufficient to upregulate CAT protein levels (but not RNA) upon AdoMetDC inhibition, supporting the hypothesis that prozyme expression is regulated translationally. To gain insight into trans-acting factors, genetic rescue of AdoMetDC RNAi knock-down lines with human AdoMetDC was performed leading to rescue of the cell growth block, and restoration of prozyme protein to wild-type levels. Metabolite analysis showed that prozyme protein levels were inversely proportional to intracellular levels of decarboxylated AdoMet (dcAdoMet). These data suggest that prozyme translation may be regulated by dcAdoMet, a metabolite not previously identified to play a regulatory role.
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Affiliation(s)
- Yanjing Xiao
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
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Nguyen S, Jones DC, Wyllie S, Fairlamb AH, Phillips MA. Allosteric activation of trypanosomatid deoxyhypusine synthase by a catalytically dead paralog. J Biol Chem 2013; 288:15256-67. [PMID: 23525104 PMCID: PMC3663545 DOI: 10.1074/jbc.m113.461137] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Polyamine biosynthesis is a key drug target in African trypanosomes. The “resurrection drug” eflornithine (difluoromethylornithine), which is used clinically to treat human African trypanosomiasis, inhibits the first step in polyamine (spermidine) biosynthesis, a highly regulated pathway in most eukaryotic cells. Previously, we showed that activity of a key trypanosomatid spermidine biosynthetic enzyme, S-adenosylmethionine decarboxylase, is regulated by heterodimer formation with a catalytically dead paralog (a prozyme). Here, we describe an expansion of this prozyme paradigm to the enzyme deoxyhypusine synthase, which is required for spermidine-dependent hypusine modification of a lysine residue in the essential translation factor eIF5A. Trypanosoma brucei encodes two deoxyhypusine synthase paralogs, one that is catalytically functional but grossly impaired, and the other is inactive. Co-expression in Escherichia coli results in heterotetramer formation with a 3000-fold increase in enzyme activity. This functional complex is also present in T. brucei, and conditional knock-out studies indicate that both DHS genes are essential for in vitro growth and infectivity in mice. The recurrent evolution of paralogous, catalytically dead enzyme-based activating mechanisms may be a consequence of the unusual gene expression in the parasites, which lack transcriptional regulation. Our results suggest that this mechanism may be more widely used by trypanosomatids to control enzyme activity and ultimately influence pathogenesis than currently appreciated.
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Affiliation(s)
- Suong Nguyen
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9041, USA
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Velez N, Brautigam CA, Phillips MA. Trypanosoma brucei S-adenosylmethionine decarboxylase N terminus is essential for allosteric activation by the regulatory subunit prozyme. J Biol Chem 2013; 288:5232-40. [PMID: 23288847 DOI: 10.1074/jbc.m112.442475] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human African trypanosomiasis is caused by a single-celled protozoan parasite, Trypanosoma brucei. Polyamine biosynthesis is a clinically validated target for the treatment of human African trypanosomiasis. Metabolic differences between the parasite and the human polyamine pathway are thought to contribute to species selectivity of pathway inhibitors. S-adenosylmethionine decarboxylase (AdoMetDC) catalyzes a key step in the production of the polyamine spermidine. We previously showed that trypanosomatid AdoMetDC differs from other eukaryotic enzymes in that it is regulated by heterodimer formation with a catalytically dead paralog, designated prozyme, which binds with high affinity to the enzyme and increases its activity by up to 10(3)-fold. Herein, we examine the role of specific residues involved in AdoMetDC activation by prozyme through deletion and site-directed mutagenesis. Results indicate that 12 key amino acids at the N terminus of AdoMetDC are essential for prozyme-mediated activation with Leu-8, Leu-10, Met-11, and Met-13 identified as the key residues. These N-terminal residues are fully conserved in the trypanosomatids but are absent from other eukaryotic homologs lacking the prozyme mechanism, suggesting co-evolution of these residues with the prozyme mechanism. Heterodimer formation between AdoMetDC and prozyme was not impaired by mutation of Leu-8 and Leu-10 to Ala, suggesting that these residues are involved in a conformational change that is essential for activation. Our findings provide the first insight into the mechanisms that influence catalytic regulation of AdoMetDC and may have potential implications for the development of new inhibitors against this enzyme.
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Affiliation(s)
- Nahir Velez
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041, USA
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Abstract
Trypanosoma brucei is the causative agent of African sleeping sickness, putting at risk up to 50 million people in sub-Saharan Africa. Current drug therapies are limited by toxicity and difficult treatment regimes and as the development of vaccines remains unlikely, the identification of better drugs to control this deadly disease is needed. Strategies for the identification of new lead compounds include phenotypic screening or target-based approaches. Implementation of the latter has been hampered by the lack of defined targets that are both essential and druggable. In this issue of Molecular Microbiology, Jones et al. (2012) report on the characterization of T. brucei pyridoxal kinase (PdxK), an enzyme required for the salvage of vitamin B6, an essential enzymatic cofactor. Genetic knock-down and small molecule inhibitor studies were used to demonstrate that PdxK is essential for parasite growth both in vitro and in a mouse model, providing both genetic and chemical validation of the target. An enzyme assay compatible with high-throughput screening (HTS) was developed and the X-ray crystal structure solved, showing the potential for species selective inhibition. These studies add a greatly needed additional target into the drug discovery pipeline for this deadly parasitic infection.
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Affiliation(s)
- Margaret A Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA.
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Marwaha A, White J, El Mazouni F, Creason SA, Kokkonda S, Buckner FS, Charman SA, Phillips MA, Rathod PK. Bioisosteric transformations and permutations in the triazolopyrimidine scaffold to identify the minimum pharmacophore required for inhibitory activity against Plasmodium falciparum dihydroorotate dehydrogenase. J Med Chem 2012; 55:7425-36. [PMID: 22877245 DOI: 10.1021/jm300351w] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum causes approximately 1 million deaths annually. However, increasing resistance imposes a continuous threat to existing drug therapies. We previously reported a number of potent and selective triazolopyrimidine-based inhibitors of P. falciparum dihydroorotate dehydrogenase that inhibit parasite in vitro growth with similar activity. Lead optimization of this series led to the recent identification of a preclinical candidate, showing good activity against P. falciparum in mice. As part of a backup program around this scaffold, we explored heteroatom rearrangement and substitution in the triazolopyrimidine ring and have identified several other ring configurations that are active as PfDHODH inhibitors. The imidazo[1,2-a]pyrimidines were shown to bind somewhat more potently than the triazolopyrimidines depending on the nature of the amino aniline substitution. DSM151, the best candidate in this series, binds with 4-fold better affinity (PfDHODH IC(50) = 0.077 μM) than the equivalent triazolopyrimidine and suppresses parasites in vivo in the Plasmodium berghei model.
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Affiliation(s)
- Alka Marwaha
- Department of Chemistry and Global Health, University of Washington, Seattle, Washington 98195, USA
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Zhang Y, Clark JA, Connelly MC, Zhu F, Min J, Guiguemde WA, Pradhan A, Iyer L, Furimsky A, Gow J, Parman T, El Mazouni F, Phillips MA, Kyle DE, Mirsalis J, Guy RK. Lead optimization of 3-carboxyl-4(1H)-quinolones to deliver orally bioavailable antimalarials. J Med Chem 2012; 55:4205-19. [PMID: 22435599 DOI: 10.1021/jm201642z] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria is a protozoal parasitic disease that is widespread in tropical and subtropical regions of Africa, Asia, and the Americas and causes more than 800,000 deaths per year. The continuing emergence of multidrug-resistant Plasmodium falciparum drives the ongoing need for the development of new and effective antimalarial drugs. Our previous work has explored the preliminary structural optimization of 4(1H)-quinolone ester derivatives, a new series of antimalarials related to the endochins. Herein, we report the lead optimization of 4(1H)-quinolones with a focus on improving both antimalarial potency and bioavailability. These studies led to the development of orally efficacious antimalarials including quinolone analogue 20g, a promising candidate for further optimization.
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Affiliation(s)
- Yiqun Zhang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
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Zhang L, Das P, Schmolke M, Manicassamy B, Wang Y, Deng X, Cai L, Tu BP, Forst CV, Roth MG, Levy DE, García-Sastre A, de Brabander J, Phillips MA, Fontoura BMA. Inhibition of pyrimidine synthesis reverses viral virulence factor-mediated block of mRNA nuclear export. ACTA ACUST UNITED AC 2012; 196:315-26. [PMID: 22312003 PMCID: PMC3275370 DOI: 10.1083/jcb.201107058] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The NS1 protein of influenza virus is a major virulence factor essential for virus replication, as it redirects the host cell to promote viral protein expression. NS1 inhibits cellular messenger ribonucleic acid (mRNA) processing and export, down-regulating host gene expression and enhancing viral gene expression. We report in this paper the identification of a nontoxic quinoline carboxylic acid that reverts the inhibition of mRNA nuclear export by NS1, in the absence or presence of the virus. This quinoline carboxylic acid directly inhibited dihydroorotate dehydrogenase (DHODH), a host enzyme required for de novo pyrimidine biosynthesis, and partially reduced pyrimidine levels. This effect induced NXF1 expression, which promoted mRNA nuclear export in the presence of NS1. The release of NS1-mediated mRNA export block by DHODH inhibition also occurred in the presence of vesicular stomatitis virus M (matrix) protein, another viral inhibitor of mRNA export. This reversal of mRNA export block allowed expression of antiviral factors. Thus, pyrimidines play a necessary role in the inhibition of mRNA nuclear export by virulence factors.
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Affiliation(s)
- Liang Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Phillips MA, Narayan R, Padath T, Rubinsky B. Irreversible electroporation on the small intestine. Br J Cancer 2012; 106:490-5. [PMID: 22223084 PMCID: PMC3273351 DOI: 10.1038/bjc.2011.582] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Non-thermal irreversible electroporation (NTIRE) has recently been conceived as a new minimally invasive ablation method, using microsecond electric fields to produce nanoscale defects in the cell membrane bilayer and induce cell death while keeping all other molecules, including the extracellular matrix, intact. Here, we present the first in vivo study that examines the effects of NTIRE on the small intestine, an organ whose collateral damage is of particular concern in the anticipated use of NTIRE for treatment of abdominal cancers. METHODS A typical NTIRE electrical protocol was applied directly to the rat small intestine and histological analysis was used to examine the effect of NTIRE over time. RESULTS The application of NTIRE led to complete cell ablation in the targeted tissue, but the animal did not show any physiological effects of the procedure and the intestine showed signs of recovery, developing an epithelial layer 3 days post treatment and regenerating its distinct layers within a week. CONCLUSION Our results indicate that this novel procedure can be used for abdominal cancer treatment while minimising collateral damage to adjacent tissues because of the unique ability of the NTIRE ablation method to target the cell membrane.
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Affiliation(s)
- M A Phillips
- Department of Mechanical Engineering, University of California-Berkeley, 6124 Etcheverry Hall, Berkeley, CA 94720, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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