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Barritt SA, DuBois-Coyne SE, Dibble CC. Coenzyme A biosynthesis: mechanisms of regulation, function and disease. Nat Metab 2024; 6:1008-1023. [PMID: 38871981 DOI: 10.1038/s42255-024-01059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/30/2024] [Indexed: 06/15/2024]
Abstract
The tricarboxylic acid cycle, nutrient oxidation, histone acetylation and synthesis of lipids, glycans and haem all require the cofactor coenzyme A (CoA). Although the sources and regulation of the acyl groups carried by CoA for these processes are heavily studied, a key underlying question is less often considered: how is production of CoA itself controlled? Here, we discuss the many cellular roles of CoA and the regulatory mechanisms that govern its biosynthesis from cysteine, ATP and the essential nutrient pantothenate (vitamin B5), or from salvaged precursors in mammals. Metabolite feedback and signalling mechanisms involving acetyl-CoA, other acyl-CoAs, acyl-carnitines, MYC, p53, PPARα, PINK1 and insulin- and growth factor-stimulated PI3K-AKT signalling regulate the vitamin B5 transporter SLC5A6/SMVT and CoA biosynthesis enzymes PANK1, PANK2, PANK3, PANK4 and COASY. We also discuss methods for measuring CoA-related metabolites, compounds that target CoA biosynthesis and diseases caused by mutations in pathway enzymes including types of cataracts, cardiomyopathy and neurodegeneration (PKAN and COPAN).
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Affiliation(s)
- Samuel A Barritt
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Department of Medicine, Department of Biological Chemistry and Molecular Pharmacology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian C Dibble
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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2
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Subramanian C, Frank MW, Sukhun R, Henry CE, Wade A, Harden ME, Rao S, Tangallapally R, Yun MK, White SW, Lee RE, Sinha U, Rock CO, Jackowski S. Pantothenate Kinase Activation Restores Brain Coenzyme A in a Mouse Model of Pantothenate Kinase-Associated Neurodegeneration. J Pharmacol Exp Ther 2024; 388:171-180. [PMID: 37875310 DOI: 10.1124/jpet.123.001919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Pantothenate kinase-associated neurodegeneration (PKAN) is characterized by a motor disorder with combinations of dystonia, parkinsonism, and spasticity, leading to premature death. PKAN is caused by mutations in the PANK2 gene that result in loss or reduction of PANK2 protein function. PANK2 is one of three kinases that initiate and regulate coenzyme A biosynthesis from vitamin B5, and the ability of BBP-671, an allosteric activator of pantothenate kinases, to enter the brain and elevate coenzyme A was investigated. The metabolic stability, protein binding, and membrane permeability of BBP-671 all suggest that it has the physical properties required to cross the blood-brain barrier. BBP-671 was detected in plasma, liver, cerebrospinal fluid, and brain following oral administration in rodents, demonstrating the ability of BBP-671 to penetrate the brain. The pharmacokinetic and pharmacodynamic properties of orally administered BBP-671 evaluated in cannulated rats showed that coenzyme A (CoA) concentrations were elevated in blood, liver, and brain. BBP-671 elevation of whole-blood acetyl-CoA served as a peripheral pharmacodynamic marker and provided a suitable method to assess target engagement. BBP-671 treatment elevated brain coenzyme A concentrations and improved movement and body weight in a PKAN mouse model. Thus, BBP-671 crosses the blood-brain barrier to correct the brain CoA deficiency in a PKAN mouse model, resulting in improved locomotion and survival and providing a preclinical foundation for the development of BBP-671 as a potential treatment of PKAN. SIGNIFICANCE STATEMENT: The blood-brain barrier represents a major hurdle for drugs targeting brain metabolism. This work describes the pharmacokinetic/pharmacodynamic properties of BBP-671, a pantothenate kinase activator. BBP-671 crosses the blood-brain barrier to correct the neuron-specific coenzyme A (CoA) deficiency and improve motor function in a mouse model of pantothenate kinase-associated neurodegeneration. The central role of CoA and acetyl-CoA in intermediary metabolism suggests that pantothenate kinase activators may be useful in modifying neurological metabolic disorders.
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Affiliation(s)
- Chitra Subramanian
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Matthew W Frank
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Rajaa Sukhun
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Christopher E Henry
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Anna Wade
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Mallory E Harden
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Satish Rao
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Rajendra Tangallapally
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Mi-Kyung Yun
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Stephen W White
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Richard E Lee
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Uma Sinha
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Charles O Rock
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Suzanne Jackowski
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
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3
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Bishop TR, Subramanian C, Bilotta EM, Garnar-Wortzel L, Ramos AR, Zhang Y, Asiaban JN, Ott CJ, Rock CO, Erb MA. Acetyl-CoA biosynthesis drives resistance to histone acetyltransferase inhibition. Nat Chem Biol 2023; 19:1215-1222. [PMID: 37127754 PMCID: PMC10538425 DOI: 10.1038/s41589-023-01320-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Histone acetyltransferases (HATs) are implicated as both oncogene and nononcogene dependencies in diverse human cancers. Acetyl-CoA-competitive HAT inhibitors have emerged as potential cancer therapeutics and the first clinical trial for this class of drugs is ongoing (NCT04606446). Despite these developments, the potential mechanisms of therapeutic response and evolved drug resistance remain poorly understood. Having discovered that multiple regulators of de novo coenzyme A (CoA) biosynthesis can modulate sensitivity to CBP/p300 HAT inhibition (PANK3, PANK4 and SLC5A6), we determined that elevated acetyl-CoA concentrations can outcompete drug-target engagement to elicit acquired drug resistance. This not only affects structurally diverse CBP/p300 HAT inhibitors, but also agents related to an investigational KAT6A/B HAT inhibitor that is currently in Phase 1 clinical trials. Altogether, this work uncovers CoA metabolism as an unexpected liability of anticancer HAT inhibitors and will therefore buoy future efforts to optimize the efficacy of this new form of targeted therapy.
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Affiliation(s)
- Timothy R Bishop
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Eric M Bilotta
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Anissa R Ramos
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yuxiang Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua N Asiaban
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher J Ott
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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4
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Álvarez-Córdoba M, Talaverón-Rey M, Povea-Cabello S, Cilleros-Holgado P, Gómez-Fernández D, Piñero-Pérez R, Reche-López D, Munuera-Cabeza M, Suárez-Carrillo A, Romero-González A, Romero-Domínguez JM, López-Cabrera A, Armengol JÁ, Sánchez-Alcázar JA. Patient-Derived Cellular Models for Polytarget Precision Medicine in Pantothenate Kinase-Associated Neurodegeneration. Pharmaceuticals (Basel) 2023; 16:1359. [PMID: 37895830 PMCID: PMC10609847 DOI: 10.3390/ph16101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The term neurodegeneration with brain iron accumulation (NBIA) brings together a broad set of progressive and disabling neurological genetic disorders in which iron is deposited preferentially in certain areas of the brain. Among NBIA disorders, the most frequent subtype is pantothenate kinase-associated neurodegeneration (PKAN) caused by pathologic variants in the PANK2 gene codifying the enzyme pantothenate kinase 2 (PANK2). To date, there are no effective treatments to stop the progression of these diseases. This review discusses the utility of patient-derived cell models as a valuable tool for the identification of pharmacological or natural compounds for implementing polytarget precision medicine in PKAN. Recently, several studies have described that PKAN patient-derived fibroblasts present the main pathological features associated with the disease including intracellular iron overload. Interestingly, treatment of mutant cell cultures with various supplements such as pantothenate, pantethine, vitamin E, omega 3, α-lipoic acid L-carnitine or thiamine, improved all pathophysiological alterations in PKAN fibroblasts with residual expression of the PANK2 enzyme. The information provided by pharmacological screenings in patient-derived cellular models can help optimize therapeutic strategies in individual PKAN patients.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Marta Talaverón-Rey
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Suleva Povea-Cabello
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Paula Cilleros-Holgado
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - David Gómez-Fernández
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Rocío Piñero-Pérez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Diana Reche-López
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Manuel Munuera-Cabeza
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra Suárez-Carrillo
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Ana Romero-González
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Jose Manuel Romero-Domínguez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra López-Cabrera
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - José Ángel Armengol
- Department of Physiology, Anatomy and Cellular Biology, Pablo de Olavide University, 41013 Seville, Spain;
| | - José Antonio Sánchez-Alcázar
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
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5
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Fan S, Yuan P, Li S, Li H, Zhai B, Li Y, Zhang H, Gu J, Li H, Tian Y, Kang X, Zhang Y, Li G. Genetic architecture and key regulatory genes of fatty acid composition in Gushi chicken breast muscle determined by GWAS and WGCNA. BMC Genomics 2023; 24:434. [PMID: 37537524 PMCID: PMC10398928 DOI: 10.1186/s12864-023-09503-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/03/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Fatty acids composition in poultry muscle is directly related to its tenderness, flavour, and juiciness, whereas its genetic mechanisms have not been elucidated. In this study, the genetic structure and key regulatory genes of the breast muscle fatty acid composition of local Chinese chicken, Gushi-Anka F2 resource population by integrating genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) strategies. GWAS was performed based on 323,306 single nucleotide polymorphisms (SNPs) obtained by genotyping by sequencing (GBS) method and 721 chickens from the Gushi-Anka F2 resource population with highly variable fatty acid composition traits in the breast muscle. And then, according to the transcriptome data of the candidate genes that were obtained and phenotypic data of fatty acid composition traits in breast muscle of Gushi chickens at 14, 22, and 30 weeks of age, we conducted a WGCNA. RESULTS A total of 128 suggestive significantly associated SNPs for 11 fatty acid composition traits were identified and mapped on chromosomes (Chr) 2, 3, 4, 5, 13, 17, 21, and 27. Of these, the two most significant SNPs were Chr13:5,100,140 (P = 4.56423e-10) and Chr13:5,100,173 (P = 4.56423e-10), which explained 5.6% of the phenotypic variation in polyunsaturated fatty acids (PUFA). In addition, six fatty acid composition traits, including C20:1, C22:6, saturated fatty acid (SFA), unsaturated fatty acids (UFA), PUFA, and average chain length (ACL), were located in the same QTL intervals on Chr13. We obtained 505 genes by scanning the linkage disequilibrium (LD) regions of all significant SNPs and performed a WGCNA based on the transcriptome data of the above 505 genes. Combining two strategies, 9 hub genes (ENO1, ADH1, ASAH1, ADH1C, PIK3CD, WISP1, AKT1, PANK3, and C1QTNF2) were finally identified, which could be the potential candidate genes regulating fatty acid composition traits in chicken breast muscle. CONCLUSION The results of this study deepen our understanding of the genetic mechanisms underlying the regulation of fatty acid composition traits, which is helpful in the design of breeding strategies for the subsequent improvement of fatty acid composition in poultry muscle.
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Affiliation(s)
- Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Yuanfang Li
- School of Medicine and Health, Harbin Institute of Technology, Harbin, 150001, HeiLongJiang, China
- Zhengzhou Research Institute, Harbin Institute of Technology, Zhengzhou, 450000, Henan, China
| | - Hongyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Jinxin Gu
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China
- The Shennong Laboratory, Zhengzhou, 450002, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China.
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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6
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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7
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Xue L, Schnacke P, Frei MS, Koch B, Hiblot J, Wombacher R, Fabritz S, Johnsson K. Probing coenzyme A homeostasis with semisynthetic biosensors. Nat Chem Biol 2023; 19:346-355. [PMID: 36316571 PMCID: PMC9974488 DOI: 10.1038/s41589-022-01172-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/13/2022] [Indexed: 11/07/2022]
Abstract
Coenzyme A (CoA) is one of the central cofactors of metabolism, yet a method for measuring its concentration in living cells is missing. Here we introduce the first biosensor for measuring CoA levels in different organelles of mammalian cells. The semisynthetic biosensor is generated through the specific labeling of an engineered GFP-HaloTag fusion protein with a fluorescent ligand. Its readout is based on CoA-dependent changes in Förster resonance energy transfer efficiency between GFP and the fluorescent ligand. Using this biosensor, we probe the role of numerous proteins involved in CoA biosynthesis and transport in mammalian cells. On the basis of these studies, we propose a cellular map of CoA biosynthesis that suggests how pools of cytosolic and mitochondrial CoA are maintained.
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Affiliation(s)
- Lin Xue
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- MOE Key Laboratory for Cellular Dynamics, Hefei National Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China.
| | - Paul Schnacke
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Michelle S Frei
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Birgit Koch
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Richard Wombacher
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Sebastian Fabritz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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8
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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9
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Subramanian C, Frank MW, Tangallapally R, Yun MK, White SW, Lee RE, Rock CO, Jackowski S. Relief of CoA sequestration and restoration of mitochondrial function in a mouse model of propionic acidemia. J Inherit Metab Dis 2023; 46:28-42. [PMID: 36251252 PMCID: PMC10092110 DOI: 10.1002/jimd.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 01/19/2023]
Abstract
Propionic acidemia (PA, OMIM 606054) is a devastating inborn error of metabolism arising from mutations that reduce the activity of the mitochondrial enzyme propionyl-CoA carboxylase (PCC). The defects in PCC reduce the concentrations of nonesterified coenzyme A (CoASH), thus compromising mitochondrial function and disrupting intermediary metabolism. Here, we use a hypomorphic PA mouse model to test the effectiveness of BBP-671 in correcting the metabolic imbalances in PA. BBP-671 is a high-affinity allosteric pantothenate kinase activator that counteracts feedback inhibition of the enzyme to increase the intracellular concentration of CoA. Liver CoASH and acetyl-CoA are depressed in PA mice and BBP-671 treatment normalizes the cellular concentrations of these two key cofactors. Hepatic propionyl-CoA is also reduced by BBP-671 leading to an improved intracellular C3:C2-CoA ratio. Elevated plasma C3:C2-carnitine ratio and methylcitrate, hallmark biomarkers of PA, are significantly reduced by BBP-671. The large elevations of malate and α-ketoglutarate in the urine of PA mice are biomarkers for compromised tricarboxylic acid cycle activity and BBP-671 therapy reduces the amounts of both metabolites. Furthermore, the low survival of PA mice is restored to normal by BBP-671. These data show that BBP-671 relieves CoA sequestration, improves mitochondrial function, reduces plasma PA biomarkers, and extends the lifespan of PA mice, providing the preclinical foundation for the therapeutic potential of BBP-671.
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Affiliation(s)
- Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Matthew W Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States
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10
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Gihaz S, Gareiss P, Choi JY, Renard I, Pal AC, Surovsteva Y, Chiu JE, Thekkiniath J, Plummer M, Hungerford W, Montgomery ML, Hosford A, Adams EM, Lightfoot JD, Fox D, Ojo KK, Staker BL, Fuller K, Ben Mamoun C. High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development. Structure 2022; 30:1494-1507.e6. [PMID: 36167065 PMCID: PMC10042587 DOI: 10.1016/j.str.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/28/2022] [Accepted: 09/01/2022] [Indexed: 01/22/2023]
Abstract
Fungal infections are the leading cause of mortality by eukaryotic pathogens, with an estimated 150 million severe life-threatening cases and 1.7 million deaths reported annually. The rapid emergence of multidrug-resistant fungal isolates highlights the urgent need for new drugs with new mechanisms of action. In fungi, pantothenate phosphorylation, catalyzed by PanK enzyme, is the first step in the utilization of pantothenic acid and coenzyme A biosynthesis. In all fungi sequenced so far, this enzyme is encoded by a single PanK gene. Here, we report the crystal structure of a fungal PanK alone as well as with high-affinity inhibitors from a single chemotype identified through a high-throughput chemical screen. Structural, biochemical, and functional analyses revealed mechanisms governing substrate and ligand binding, dimerization, and catalysis and helped identify new compounds that inhibit the growth of several Candida species. The data validate PanK as a promising target for antifungal drug development.
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Affiliation(s)
- Shalev Gihaz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter Gareiss
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Jae-Yeon Choi
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Isaline Renard
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anasuya Chattopadhyay Pal
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yulia Surovsteva
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Joy E Chiu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jose Thekkiniath
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Plummer
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Micaela L Montgomery
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alanah Hosford
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Emily M Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jorge D Lightfoot
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David Fox
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Kayode K Ojo
- Center for Emerging & Re-emerging Infectious Disease, Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.
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11
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Álvarez-Córdoba M, Reche-López D, Cilleros-Holgado P, Talaverón-Rey M, Villalón-García I, Povea-Cabello S, Suárez-Rivero JM, Suárez-Carrillo A, Munuera-Cabeza M, Piñero-Pérez R, Sánchez-Alcázar JA. Therapeutic approach with commercial supplements for pantothenate kinase-associated neurodegeneration with residual PANK2 expression levels. Orphanet J Rare Dis 2022; 17:311. [PMID: 35945593 PMCID: PMC9364590 DOI: 10.1186/s13023-022-02465-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/24/2022] [Indexed: 12/24/2022] Open
Abstract
Background Neurodegeneration with brain iron accumulation (NBIA) is a group of rare neurogenetic disorders frequently associated with iron accumulation in the basal nuclei of the brain characterized by progressive spasticity, dystonia, muscle rigidity, neuropsychiatric symptoms, and retinal degeneration or optic nerve atrophy. Pantothenate kinase-associated neurodegeneration (PKAN) is one of the most widespread NBIA subtypes. It is caused by mutations in the gene of pantothenate kinase 2 (PANK2) that result in dysfunction in PANK2 enzyme activity, with consequent deficiency of coenzyme A (CoA) biosynthesis, as well as low levels of essential metabolic intermediates such as 4′-phosphopantetheine, a necessary cofactor for essential cytosolic and mitochondrial proteins. Methods In this manuscript, we examined the therapeutic effectiveness of pantothenate, panthetine, antioxidants (vitamin E and omega 3) and mitochondrial function boosting supplements (L-carnitine and thiamine) in mutant PANK2 cells with residual expression levels. Results Commercial supplements, pantothenate, pantethine, vitamin E, omega 3, carnitine and thiamine were able to eliminate iron accumulation, increase PANK2, mtACP, and NFS1 expression levels and improve pathological alterations in mutant cells with residual PANK2 expression levels. Conclusion Our results suggest that several commercial compounds are indeed able to significantly correct the mutant phenotype in cellular models of PKAN. These compounds alone or in combinations are of common use in clinical practice and may be useful for the treatment of PKAN patients with residual enzyme expression levels. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02465-9.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Diana Reche-López
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Paula Cilleros-Holgado
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Marta Talaverón-Rey
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Irene Villalón-García
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Suleva Povea-Cabello
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Juan M Suárez-Rivero
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Alejandra Suárez-Carrillo
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Manuel Munuera-Cabeza
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Rocío Piñero-Pérez
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - José A Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD-CSIC-Universidad Pablo de Olavide), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain.
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12
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A Potential Citrate Shunt in Erythrocytes of PKAN Patients Caused by Mutations in Pantothenate Kinase 2. Biomolecules 2022; 12:biom12020325. [PMID: 35204826 PMCID: PMC8869601 DOI: 10.3390/biom12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 02/04/2023] Open
Abstract
Pantothenate kinase-associated neurodegeneration (PKAN) is a progressive neurodegenerative disease caused by mutations in the pantothenate kinase 2 (PANK2) gene and associated with iron deposition in basal ganglia. Pantothenate kinase isoforms catalyze the first step in coenzyme A (CoA) biosynthesis. Since PANK2 is the only isoform in erythrocytes, these cells are an excellent ex vivo model to study the effect of PANK2 point mutations on expression/stability and activity of the protein as well as on the downstream molecular consequences. PKAN erythrocytes containing the T528M PANK2 mutant had residual enzyme activities but variable PANK2 abundances indicating an impaired regulation of the protein. Patients with G521R/G521R, G521R/G262R, and R264N/L275fs PANK2 mutants had no residual enzyme activity and strongly reduced PANK2 abundance. G521R inactivates the catalytic activity of the enzyme, whereas G262R and the R264N point mutations impair the switch from the inactive to the active conformation of the PANK2 dimer. Metabolites in cytosolic extracts were analyzed by gas chromatography–mass spectrometry and multivariate analytic methods revealing changes in the carboxylate metabolism of erythrocytes from PKAN patients as compared to that of the carrier and healthy control. Assuming low/absent CoA levels in PKAN erythrocytes, changes are consistent with a model of altered citrate channeling where citrate is preferentially converted to α-ketoglutarate and α-hydroxyglutarate instead of being used for de novo acetyl-CoA generation. This finding hints at the importance of carboxylate metabolism in PKAN pathology with potential links to reduced cytoplasmic acetyl-CoA levels in neurons and to aberrant brain iron regulation.
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13
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Sharma LK, Yun MK, Subramanian C, Tangallapally R, Jackowski S, Rock CO, White SW, Lee RE. LipE guided discovery of isopropylphenyl pyridazines as pantothenate kinase modulators. Bioorg Med Chem 2021; 52:116504. [PMID: 34814071 PMCID: PMC8693618 DOI: 10.1016/j.bmc.2021.116504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022]
Abstract
Pantothenate kinase (PANK) is the critical regulator of intracellular levels of coenzyme A and has emerged as an attractive target for treating neurological and metabolic disorders. This report describes the optimization, synthesis, and full structure–activity relationships of a new chemical series of pantothenate competitive PANK inhibitors. Potent drug-like molecules were obtained by optimizing a high throughput screening hit, using lipophilic ligand efficiency (LipE) derived from human PANK3 IC50 values to guide ligand development. X-ray crystal structures of PANK3 with index inhibitors from the optimization were determined to rationalize the emerging structure activity relationships. The analysis revealed a key bidentate hydrogen bonding interaction between pyridazine and R306′ as a major contributor to the LipE gain observed in the optimization. A tractable series of PANK3 modulators with nanomolar potency, excellent LipE values, desirable physicochemical properties, and a well-defined structural binding mode was produced from this study.
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Affiliation(s)
- Lalit Kumar Sharma
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas PI, MS1000, Memphis, TN 38105, United States; Department of Infectious Diseases, St. Jude Children's Research Hospital, United States
| | - Mi Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, United States
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, United States
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas PI, MS1000, Memphis, TN 38105, United States
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, United States
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, United States
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, United States
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas PI, MS1000, Memphis, TN 38105, United States.
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14
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Mostert KJ, Sharma N, van der Zwaag M, Staats R, Koekemoer L, Anand R, Sibon OCM, Strauss E. The Coenzyme A Level Modulator Hopantenate (HoPan) Inhibits Phosphopantotenoylcysteine Synthetase Activity. ACS Chem Biol 2021; 16:2401-2414. [PMID: 34582681 DOI: 10.1021/acschembio.1c00535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pantothenate analogue hopantenate (HoPan) is widely used as a modulator of coenzyme A (CoA) levels in cell biology and disease models─especially for pantothenate kinase associated neurodegeneration (PKAN), a genetic disease rooted in impaired CoA metabolism. This use of HoPan was based on reports that it inhibits pantothenate kinase (PanK), the first enzyme of CoA biosynthesis. Using a combination of in vitro enzyme kinetic studies, crystal structure analysis, and experiments in a typical PKAN cell biology model, we demonstrate that instead of inhibiting PanK, HoPan relies on it for metabolic activation. Once phosphorylated, HoPan inhibits the next enzyme in the CoA pathway─phosphopantothenoylcysteine synthetase (PPCS)─through formation of a nonproductive substrate complex. Moreover, the obtained structure of the human PPCS in complex with the inhibitor and activating nucleotide analogue provides new insights into the catalytic mechanism of PPCS enzymes─including the elusive binding mode for cysteine─and reveals the functional implications of mutations in the human PPCS that have been linked to severe dilated cardiomyopathy. Taken together, this study demonstrates that the molecular mechanism of action of HoPan is more complex than previously thought, suggesting that the results of studies in which it is used as a tool compound must be interpreted with care. Moreover, our findings provide a clear framework for evaluating the various factors that contribute to the potency of CoA-directed inhibitors, one that will prove useful in the future rational development of potential therapies of both human genetic and infectious diseases.
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Affiliation(s)
- Konrad J. Mostert
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Marianne van der Zwaag
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Roxine Staats
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Lizbé Koekemoer
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - Ody C. M. Sibon
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa
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15
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Subramanian C, Frank MW, Tangallapally R, Yun MK, Edwards A, White SW, Lee RE, Rock CO, Jackowski S. Pantothenate kinase activation relieves coenzyme A sequestration and improves mitochondrial function in mice with propionic acidemia. Sci Transl Med 2021; 13:eabf5965. [PMID: 34524863 DOI: 10.1126/scitranslmed.abf5965] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis TN, 38105, USA
| | - Anne Edwards
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis TN, 38105, USA.,St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Center for Pediatric Experimental Therapeutics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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16
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Tjhin ET, Howieson VM, Spry C, van Dooren GG, Saliba KJ. A novel heteromeric pantothenate kinase complex in apicomplexan parasites. PLoS Pathog 2021; 17:e1009797. [PMID: 34324601 PMCID: PMC8366970 DOI: 10.1371/journal.ppat.1009797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 08/16/2021] [Accepted: 07/13/2021] [Indexed: 11/19/2022] Open
Abstract
Coenzyme A is synthesised from pantothenate via five enzyme-mediated steps. The first step is catalysed by pantothenate kinase (PanK). All PanKs characterised to date form homodimers. Many organisms express multiple PanKs. In some cases, these PanKs are not functionally redundant, and some appear to be non-functional. Here, we investigate the PanKs in two pathogenic apicomplexan parasites, Plasmodium falciparum and Toxoplasma gondii. Each of these organisms express two PanK homologues (PanK1 and PanK2). We demonstrate that PfPanK1 and PfPanK2 associate, forming a single, functional PanK complex that includes the multi-functional protein, Pf14-3-3I. Similarly, we demonstrate that TgPanK1 and TgPanK2 form a single complex that possesses PanK activity. Both TgPanK1 and TgPanK2 are essential for T. gondii proliferation, specifically due to their PanK activity. Our study constitutes the first examples of heteromeric PanK complexes in nature and provides an explanation for the presence of multiple PanKs within certain organisms.
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Affiliation(s)
- Erick T. Tjhin
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Vanessa M. Howieson
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Giel G. van Dooren
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Kevin J. Saliba
- Research School of Biology, The Australian National University, Canberra, Australia
- Medical School, The Australian National University, Canberra, Australia
- * E-mail:
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17
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Simão-Gurge RM, Thakre N, Strickland J, Isoe J, Delacruz LR, Torrevillas BK, Rodriguez AM, Riehle MA, Luckhart S. Activation of Anopheles stephensi Pantothenate Kinase and Coenzyme A Biosynthesis Reduces Infection with Diverse Plasmodium Species in the Mosquito Host. Biomolecules 2021; 11:807. [PMID: 34072373 PMCID: PMC8228300 DOI: 10.3390/biom11060807] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria parasites require pantothenate from both human and mosquito hosts to synthesize coenzyme A (CoA). Specifically, mosquito-stage parasites cannot synthesize pantothenate de novo or take up preformed CoA from the mosquito host, making it essential for the parasite to obtain pantothenate from mosquito stores. This makes pantothenate utilization an attractive target for controlling sexual stage malaria parasites in the mosquito. CoA is synthesized from pantothenate in a multi-step pathway initiated by the enzyme pantothenate kinase (PanK). In this work, we manipulated A. stephensi PanK activity and assessed the impact of mosquito PanK activity on the development of two malaria parasite species with distinct genetics and life cycles: the human parasite Plasmodium falciparum and the mouse parasite Plasmodium yoelii yoelii 17XNL. We identified two putative A. stephensi PanK isoforms encoded by a single gene and expressed in the mosquito midgut. Using both RNAi and small molecules with reported activity against human PanK, we confirmed that A. stephensi PanK manipulation was associated with corresponding changes in midgut CoA levels. Based on these findings, we used two small molecule modulators of human PanK activity (PZ-2891, compound 7) at reported and ten-fold EC50 doses to examine the effects of manipulating A. stephensi PanK on malaria parasite infection success. Our data showed that oral provisioning of 1.3 nM and 13 nM PZ-2891 increased midgut CoA levels and significantly decreased infection success for both Plasmodium species. In contrast, oral provisioning of 62 nM and 620 nM compound 7 decreased CoA levels and significantly increased infection success for both Plasmodium species. This work establishes the A. stephensi CoA biosynthesis pathway as a potential target for broadly blocking malaria parasite development in anopheline hosts. We envision this strategy, with small molecule PanK modulators delivered to mosquitoes via attractive bait stations, working in concert with deployment of parasite-directed novel pantothenamide drugs to block parasite infection in the human host. In mosquitoes, depletion of pantothenate through manipulation to increase CoA biosynthesis is expected to negatively impact Plasmodium survival by starving the parasite of this essential nutrient. This has the potential to kill both wild type parasites and pantothenamide-resistant parasites that could develop under pantothenamide drug pressure if these compounds are used as future therapeutics for human malaria.
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Affiliation(s)
- Raquel M. Simão-Gurge
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA; (R.M.S.-G.); (J.S.); (B.K.T.); (A.M.R.)
| | - Neha Thakre
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA; (N.T.); (J.I.); (L.R.D.); (M.A.R.)
| | - Jessica Strickland
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA; (R.M.S.-G.); (J.S.); (B.K.T.); (A.M.R.)
| | - Jun Isoe
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA; (N.T.); (J.I.); (L.R.D.); (M.A.R.)
| | - Lillian R. Delacruz
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA; (N.T.); (J.I.); (L.R.D.); (M.A.R.)
| | - Brandi K. Torrevillas
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA; (R.M.S.-G.); (J.S.); (B.K.T.); (A.M.R.)
| | - Anna M. Rodriguez
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA; (R.M.S.-G.); (J.S.); (B.K.T.); (A.M.R.)
| | - Michael A. Riehle
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA; (N.T.); (J.I.); (L.R.D.); (M.A.R.)
| | - Shirley Luckhart
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83843, USA; (R.M.S.-G.); (J.S.); (B.K.T.); (A.M.R.)
- Department of Biological Sciences, University of Idaho, Moscow, ID 83843, USA
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18
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Thakur N, Klopstock T, Jackowski S, Kuscer E, Tricta F, Videnovic A, Jinnah HA. Rational Design of Novel Therapies for Pantothenate Kinase-Associated Neurodegeneration. Mov Disord 2021; 36:2005-2016. [PMID: 34002881 DOI: 10.1002/mds.28642] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/09/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND This review highlights the recent scientific advances that have enabled rational design of novel clinical trials for pantothenate kinase-associated neurodegeneration (PKAN), a rare autosomal recessive neurogenetic disorder associated with progressive neurodegenerative changes and functional impairment. PKAN is caused by genetic variants in the PANK2 gene that result in dysfunction in pantothenate kinase 2 (PANK2) enzyme activity, with consequent disruption of coenzyme A (CoA) synthesis, and subsequent accumulation of brain iron. The clinical phenotype is varied and may include dystonia, rigidity, bradykinesia, postural instability, spasticity, loss of ambulation and ability to communicate, feeding difficulties, psychiatric issues, and cognitive and visual impairment. There are several symptom-targeted treatments, but these do not provide sustained benefit as the disorder progresses. OBJECTIVES A detailed understanding of the molecular and biochemical pathogenesis of PKAN has opened the door for the design of novel rationally designed therapeutics that target the underlying mechanisms. METHODS Two large double-blind phase 3 clinical trials have been completed for deferiprone (an iron chelation treatment) and fosmetpantotenate (precursor replacement therapy). A pilot open-label trial of pantethine as a potential precursor replacement strategy has also been completed, and a trial of 4-phosphopantetheine has begun enrollment. Several other compounds have been evaluated in pre-clinical studies, and additional clinical trials may be anticipated. CONCLUSIONS Experience with these trials has encouraged a critical evaluation of optimal trial designs, as well as the development of PKAN-specific measures to monitor outcomes. PKAN provides a valuable example for understanding targeted drug development and clinical trial design for rare disorders. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Nivedita Thakur
- Department of Pediatrics, Division of Child and Adolescent Neurology, University of Texas at Houston Medical School, Houston, Texas, USA
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, University Hospital LMU Munich, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Enej Kuscer
- Comet Therapeutics, Cambridge, Massachusetts, USA
| | - Fernando Tricta
- Rare Diseases, Chiesi Canada Corporation, Toronto, Ontario, Canada
| | - Aleksandar Videnovic
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Hyder A Jinnah
- Departments of Neurology and Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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19
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Kita A, Kishimoto A, Shimosaka T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K. Crystal structure of pantoate kinase from Thermococcus kodakarensis. Proteins 2019; 88:718-724. [PMID: 31697438 DOI: 10.1002/prot.25852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/29/2019] [Accepted: 11/03/2019] [Indexed: 11/09/2022]
Abstract
The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4'-phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.
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Affiliation(s)
- Akiko Kita
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
| | - Asako Kishimoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takahiro Shimosaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hiroya Tomita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Yuusuke Yokooji
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,JST, CREST, Tokyo, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,JST, CREST, Tokyo, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.,JST, CREST, Tokyo, Japan
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20
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Duncan D, Auclair K. The coenzyme A biosynthetic pathway: A new tool for prodrug bioactivation. Arch Biochem Biophys 2019; 672:108069. [PMID: 31404525 DOI: 10.1016/j.abb.2019.108069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/29/2022]
Abstract
Prodrugs account for more than 5% of pharmaceuticals approved worldwide. Over the past decades several prodrug design strategies have been firmly established; however, only a few functional groups remain amenable to this approach. The aim of this overview is to highlight the use of coenzyme A (CoA) biosynthetic enzymes as a recently explored bioactivation scheme and provide information about its scope of utility. This emerging tool is likely to have a strong impact on future medicinal and biological studies as it offers promiscuity, orthogonal selectivity, and the capability of assembling exceptionally large molecules.
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Affiliation(s)
- Dustin Duncan
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Sherbrooke Street West, Montreal, Quebec, H3A 0B8, Canada.
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21
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Yao J, Subramanian C, Rock CO, Jackowski S. Human pantothenate kinase 4 is a pseudo-pantothenate kinase. Protein Sci 2019; 28:1031-1047. [PMID: 30927326 DOI: 10.1002/pro.3611] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/28/2019] [Indexed: 11/07/2022]
Abstract
Pantothenate kinase generates 4'-phosphopantothenate in the first and rate-determining step of coenzyme A (CoA) biosynthesis. The human genome encodes three well-characterized and nearly identical pantothenate kinases (PANK1-3) plus a putative bifunctional protein (PANK4) with a predicted amino-terminal pantothenate kinase domain fused to a carboxy-terminal phosphatase domain. Structural and phylogenetic analyses show that all active, characterized PANKs contain the key catalytic residues Glu138 and Arg207 (HsPANK3 numbering). However, all amniote PANK4s, including human PANK4, encode Glu138Val and Arg207Trp substitutions which are predicted to inactivate kinase activity. Biochemical analysis corroborates bioinformatic predictions-human PANK4 lacks pantothenate kinase activity. Introducing Glu138Val and Arg207Trp substitutions to the human PANK3 and plant PANK4 abolished their robust pantothenate kinase activity. Introducing both catalytic residues back into human PANK4 restored kinase activity, but only to a low level. This result suggests that epistatic changes to the rest of the protein already reduced the kinase activity prior to mutation of the catalytic residues in the course of evolution. The PANK4 from frog, an anamniote living relative encoding the catalytically active residues, had only a low level of kinase activity, supporting the view that HsPANK4 had reduced kinase activity prior to the catalytic residue substitutions in amniotes. Together, our data show that human PANK4 is a pseudo-pantothenate kinase-a catalytically deficient variant of the catalytically active PANK4 found in plants and fungi. The Glu138Val and Arg207Trp substitutions in amniotes (HsPANK3 numbering) completely deactivated the pantothenate kinase activity that had already been reduced by prior epistatic mutations.
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Affiliation(s)
- Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105
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22
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Sharma LK, Subramanian C, Yun MK, Frank MW, White SW, Rock CO, Lee RE, Jackowski S. A therapeutic approach to pantothenate kinase associated neurodegeneration. Nat Commun 2018; 9:4399. [PMID: 30352999 PMCID: PMC6199309 DOI: 10.1038/s41467-018-06703-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/20/2018] [Indexed: 12/17/2022] Open
Abstract
Pantothenate kinase (PANK) is a metabolic enzyme that regulates cellular coenzyme A (CoA) levels. There are three human PANK genes, and inactivating mutations in PANK2 lead to pantothenate kinase associated neurodegeneration (PKAN). Here we performed a library screen followed by chemical optimization to produce PZ-2891, an allosteric PANK activator that crosses the blood brain barrier. PZ-2891 occupies the pantothenate pocket and engages the dimer interface to form a PANK•ATP•Mg2+•PZ-2891 complex. The binding of PZ-2891 to one protomer locks the opposite protomer in a catalytically active conformation that is refractory to acetyl-CoA inhibition. Oral administration of PZ-2891 increases CoA levels in mouse liver and brain. A knockout mouse model of brain CoA deficiency exhibited weight loss, severe locomotor impairment and early death. Knockout mice on PZ-2891 therapy gain weight, and have improved locomotor activity and life span establishing pantazines as novel therapeutics for the treatment of PKAN.
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Affiliation(s)
- Lalit Kumar Sharma
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Nurix, Inc, 1700 Owens Street, Suite 205, San Francisco, CA, 94158, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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23
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Giessner C, Millet V, Mostert KJ, Gensollen T, Vu Manh TP, Garibal M, Dieme B, Attaf-Bouabdallah N, Chasson L, Brouilly N, Laprie C, Lesluyes T, Blay JY, Shintu L, Martin JC, Strauss E, Galland F, Naquet P. Vnn1 pantetheinase limits the Warburg effect and sarcoma growth by rescuing mitochondrial activity. Life Sci Alliance 2018; 1:e201800073. [PMID: 30456364 PMCID: PMC6238586 DOI: 10.26508/lsa.201800073] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022] Open
Abstract
Expression of the Vnn1 pantetheinase by sarcomas is tumor suppressive by limiting the use of aerobic glycolysis for growth and rescuing mitochondrial activity through CoA regeneration. Like other tumors, aggressive soft tissue sarcomas (STS) use glycolysis rather than mitochondrial oxidative phosphorylation (OXPHOS) for growth. Given the importance of the cofactor coenzyme A (CoA) in energy metabolism, we investigated the impact of Vnn1 pantetheinase—an enzyme that degrades pantetheine into pantothenate (vitamin B5, the CoA biosynthetic precursor) and cysyteamine—on tumor growth. Using two models, we show that Vnn1+ STS remain differentiated and grow slowly, and that in patients a detectable level of VNN1 expression in STS is associated with an improved prognosis. Increasing pantetheinase activity in aggressive tumors limits their growth. Using combined approaches, we demonstrate that Vnn1 permits restoration of CoA pools, thereby maintaining OXPHOS. The simultaneous production of cysteamine limits glycolysis and release of lactate, resulting in a partial inhibition of STS growth in vitro and in vivo. We propose that the Warburg effect observed in aggressive STS is reversed by induction of Vnn1 pantetheinase and the rewiring of cellular energy metabolism by its products.
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Affiliation(s)
- Caroline Giessner
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Virginie Millet
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Konrad J Mostert
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Thomas Gensollen
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Thien-Phong Vu Manh
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Marc Garibal
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Institut National de la Recherche Agronomique, C2VN, Marseille, France
| | - Binta Dieme
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Institut National de la Recherche Agronomique, C2VN, Marseille, France
| | - Noudjoud Attaf-Bouabdallah
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Lionel Chasson
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Nicolas Brouilly
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de Développement de Marseille, Marseille, France
| | | | - Tom Lesluyes
- Centre Lyon Bérard, Université Claude Bernard, Lyon 1, Lyon Recherche Innovation contre le Cancer, Lyon, France
| | - Jean Yves Blay
- Centre Lyon Bérard, Université Claude Bernard, Lyon 1, Lyon Recherche Innovation contre le Cancer, Lyon, France
| | - Laetitia Shintu
- Aix Marseille Université, Centre National de la Recherche Scientifique, Centrale Marseille, ISM2, Marseille, France
| | - Jean Charles Martin
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Institut National de la Recherche Agronomique, C2VN, Marseille, France
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Franck Galland
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
| | - Philippe Naquet
- Aix Marseille Univ, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d'Immunologie de Marseille Luminy, Marseille, France
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24
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Tjhin ET, Spry C, Sewell AL, Hoegl A, Barnard L, Sexton AE, Siddiqui G, Howieson VM, Maier AG, Creek DJ, Strauss E, Marquez R, Auclair K, Saliba KJ. Mutations in the pantothenate kinase of Plasmodium falciparum confer diverse sensitivity profiles to antiplasmodial pantothenate analogues. PLoS Pathog 2018; 14:e1006918. [PMID: 29614109 PMCID: PMC5882169 DOI: 10.1371/journal.ppat.1006918] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
The malaria-causing blood stage of Plasmodium falciparum requires extracellular pantothenate for proliferation. The parasite converts pantothenate into coenzyme A (CoA) via five enzymes, the first being a pantothenate kinase (PfPanK). Multiple antiplasmodial pantothenate analogues, including pantothenol and CJ-15,801, kill the parasite by targeting CoA biosynthesis/utilisation. Their mechanism of action, however, remains unknown. Here, we show that parasites pressured with pantothenol or CJ-15,801 become resistant to these analogues. Whole-genome sequencing revealed mutations in one of two putative PanK genes (Pfpank1) in each resistant line. These mutations significantly alter PfPanK activity, with two conferring a fitness cost, consistent with Pfpank1 coding for a functional PanK that is essential for normal growth. The mutants exhibit a different sensitivity profile to recently-described, potent, antiplasmodial pantothenate analogues, with one line being hypersensitive. We provide evidence consistent with different pantothenate analogue classes having different mechanisms of action: some inhibit CoA biosynthesis while others inhibit CoA-utilising enzymes. The coenzyme A (CoA) biosynthetic pathway is under investigation as a target for the development of drugs aimed at several infectious agents, including malaria parasites. To synthesise CoA, the parasite scavenges the essential precursor pantothenate (vitamin B5). Several pantothenate analogues possess potent (nM) activity against the parasite, but their exact mechanism of action is unknown. We have generated mutant parasites that are resistant or hypersensitive to various pantothenate analogues. These parasites harbour mutations in a gene we now show codes for the first enzyme in the CoA biosynthesis pathway. This enzyme is not the target of the analogues, but instead converts them into antimetabolites that, depending on the analogue, either inhibit a CoA biosynthesis enzyme or downstream CoA-utilising enzymes.
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Affiliation(s)
- Erick T. Tjhin
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Christina Spry
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Alan L. Sewell
- Department of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | - Annabelle Hoegl
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Leanne Barnard
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Anna E. Sexton
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Ghizal Siddiqui
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Vanessa M. Howieson
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Alexander G. Maier
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Darren J. Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Rodolfo Marquez
- Department of Chemistry, University of Glasgow, Glasgow, United Kingdom
- Department of Chemistry, Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Kevin J. Saliba
- Research School of Biology, The Australian National University, Canberra, Australia
- Medical School, The Australian National University, Canberra, Australia
- * E-mail:
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25
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de Villiers M, Spry C, Macuamule CJ, Barnard L, Wells G, Saliba KJ, Strauss E. Antiplasmodial Mode of Action of Pantothenamides: Pantothenate Kinase Serves as a Metabolic Activator Not as a Target. ACS Infect Dis 2017; 3:527-541. [PMID: 28437604 DOI: 10.1021/acsinfecdis.7b00024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
N-Substituted pantothenamides (PanAms) are pantothenate analogues with up to nanomolar potency against blood-stage Plasmodium falciparum (the most virulent species responsible for malaria). Although these compounds are known to target coenzyme A (CoA) biosynthesis and/or utilization, their exact mode of action (MoA) is still unknown. Importantly, PanAms that retain the natural β-alanine moiety are more potent than other variants, consistent with the involvement of processes that are selective for pantothenate (the precursor of CoA) or its derivatives. The transport of pantothenate and its phosphorylation by P. falciparum pantothenate kinase (PfPanK, the first enzyme of CoA biosynthesis) are two such processes previously highlighted as potential targets for the PanAms' antiplasmodial action. In this study, we investigated the effect of PanAms on these processes using their radiolabeled versions (synthesized here for the first time), which made possible the direct measurement of PanAm uptake by isolated blood-stage parasites and PanAm phosphorylation by PfPanK present in parasite lysates. We found that the MoA of PanAms does not involve interference with pantothenate transport and that inhibition of PfPanK-mediated pantothenate phosphorylation does not correlate with PanAm antiplasmodial activity. Instead, PanAms that retain the β-alanine moiety were found to be metabolically activated by PfPanK in a selective manner, forming phosphorylated products that likely inhibit other steps in CoA biosynthesis or are transformed into CoA antimetabolites that can interfere with CoA utilization. These findings provide direction for the ongoing development of CoA-targeted inhibitors as antiplasmodial agents with clinical potential.
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Affiliation(s)
- Marianne de Villiers
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | | | | | - Leanne Barnard
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Gordon Wells
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
| | | | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa
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26
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Corbin DR, Rehg JE, Shepherd DL, Stoilov P, Percifield RJ, Horner L, Frase S, Zhang YM, Rock CO, Hollander JM, Jackowski S, Leonardi R. Excess coenzyme A reduces skeletal muscle performance and strength in mice overexpressing human PANK2. Mol Genet Metab 2017; 120:350-362. [PMID: 28189602 PMCID: PMC5382100 DOI: 10.1016/j.ymgme.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 11/23/2022]
Abstract
Coenzyme A (CoA) is a cofactor that is central to energy metabolism and CoA synthesis is controlled by the enzyme pantothenate kinase (PanK). A transgenic mouse strain expressing human PANK2 was derived to determine the physiological impact of PANK overexpression and elevated CoA levels. The Tg(PANK2) mice expressed high levels of the transgene in skeletal muscle and heart; however, CoA was substantially elevated only in skeletal muscle, possibly associated with the comparatively low endogenous levels of acetyl-CoA, a potent feedback inhibitor of PANK2. Tg(PANK2) mice were smaller, had less skeletal muscle mass and displayed significantly impaired exercise tolerance and grip strength. Skeletal myofibers were characterized by centralized nuclei and aberrant mitochondria. Both the content of fully assembled complex I of the electron transport chain and ATP levels were reduced, while markers of oxidative stress were elevated in Tg(PANK2) skeletal muscle. These abnormalities were not detected in the Tg(PANK2) heart muscle, with the exception of spotty loss of cristae organization in the mitochondria. The data demonstrate that excessively high CoA may be detrimental to skeletal muscle function.
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Affiliation(s)
- Deborah R Corbin
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Jerold E Rehg
- Department Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Danielle L Shepherd
- Department of Exercise Physiology, West Virginia University, Morgantown, WV 26506, USA
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Ryan J Percifield
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA
| | - Linda Horner
- Cell and Tissue Imaging-Electron Microscopy Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sharon Frase
- Cell and Tissue Imaging-Electron Microscopy Shared Resource, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yong-Mei Zhang
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John M Hollander
- Department of Exercise Physiology, West Virginia University, Morgantown, WV 26506, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Roberta Leonardi
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506, USA.
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