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Burns D, Venditti V, Potoyan DA. Illuminating Protein Allostery by Chemically Accurate Contact Response Analysis (ChACRA). J Chem Theory Comput 2024. [PMID: 39038177 DOI: 10.1021/acs.jctc.4c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Decoding allostery at the atomic level is essential for understanding the relationship between a protein's sequence, structure, and dynamics. Recently, we have shown that decomposing temperature responses of inter-residue contacts can reveal allosteric couplings and provide useful insight into the functional dynamics of proteins. The details of this Chemically Accurate Contact Response Analysis (ChACRA) are presented here along with its application to two well-known allosteric proteins. The first protein, IGPS, is a model of ensemble allostery that lacks clear structural differences between the active and inactive states. We show that the application of ChACRA reveals the experimentally identified allosteric coupling between effector and active sites of IGPS. The second protein, ATCase, is a classic example of allostery with distinct active and inactive structural states. Using ChACRA, we directly identify the most significant residue level interactions underlying the enzyme's cooperative behavior. Both test cases demonstrate the utility of ChACRA's unsupervised machine learning approach for dissecting allostery at the residue level.
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Affiliation(s)
- Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Vincenzo Venditti
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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2
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Wang C, Zhang B, Cong Y, Du X, Chen S, Visser L, Ruiz-Moreno AJ, Zhang L, Reggiori F, Dömling ASS, Groves MR. Small-Molecule Allosteric Inhibitors of Human Aspartate Transcarbamoylase Suppress Proliferation of Bone Osteosarcoma Epithelial Cells. ChemMedChem 2024; 19:e202300688. [PMID: 38602859 DOI: 10.1002/cmdc.202300688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/13/2024]
Abstract
Aspartate transcarbamoylase (ATC) is the first committed step in de novo pyrimidine biosynthesis in eukaryotes and plants. A potent transition state analog of human ATCase (PALA) has previously been assessed in clinical trials for the treatment of cancer, but was ultimately unsuccessful. Additionally, inhibition of this pathway has been proposed to be a target to suppress cell proliferation in E. coli, the malarial parasite and tuberculosis. In this manuscript we screened a 70-member library of ATC inhibitors developed against the malarial and tubercular ATCases for inhibitors of the human ATC. Four compounds showed low nanomolar inhibition (IC50 30-120 nM) in an in vitro activity assay. These compounds significantly outperform PALA, which has a triphasic inhibition response under identical conditions, in which significant activity remains at PALA concentrations above 10 μM. Evidence for a druggable allosteric pocket in human ATC is provided by both in vitro enzyme kinetic, homology modeling and in silico docking. These compounds also suppress the proliferation of U2OS osteoblastoma cells by promoting cell cycle arrest in G0/G1 phase. This report provides the first evidence for an allosteric pocket in human ATC, which greatly enhances its druggability and demonstrates the potential of this series in cancer therapy.
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Affiliation(s)
- Chao Wang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Bidong Zhang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Yingying Cong
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
- Department of Biomedicine, Aarhus University, Ole Worms Alle' 4, 8000, Aarhus C, Denmark
| | - Xiaochen Du
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Siyao Chen
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Lidia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The, Netherlands
| | - Angel J Ruiz-Moreno
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Lili Zhang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Alle' 4, 8000, Aarhus C, Denmark
| | - Alexander S S Dömling
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
- CATRIN, Department of Innovative Chemistry, Palack University, 779 00, Olomouc - Holice, Czech Republic
| | - Matthew R Groves
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV, The, Netherlands
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3
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Dsouza L, Pant A, Pope B, Yang Z. Role of vaccinia virus growth factor in stimulating the mTORC1-CAD axis of the de novo pyrimidine pathway under different nutritional cues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601567. [PMID: 39005450 PMCID: PMC11245005 DOI: 10.1101/2024.07.02.601567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Vaccinia virus (VACV), the prototype poxvirus, actively reprograms host cell metabolism upon infection. However, the nature and molecular mechanisms remain largely elusive. Given the diverse nutritional exposures of cells in different physiological contexts, it is essential to understand how VACV may alter various metabolic pathways in different nutritional conditions. In this study, we established the importance of de novo pyrimidine biosynthesis in VACV infection. We elucidated the significance of vaccinia growth factor (VGF), a viral early protein and a homolog of cellular epidermal growth factor, in enabling VACV to phosphorylate the key enzyme CAD of the de novo pyrimidine pathway at serine 1859, a site known to positively regulate CAD activity. While nutrient-poor conditions typically inhibit mTORC1 activation, VACV activates CAD via mTORC1-S6K1 signaling axis, in conditions where glutamine and asparagine are absent. However, unlike its cellular homolog, epidermal growth factor (EGF), VGF peptide alone in the absence of VACV infection has minimal ability to activate CAD, suggestive of the involvement of other viral factor(s) and differential functions to EGF acquired during poxvirus evolution. Our research provides a foundation for understanding the regulation of a significant metabolic pathway, namely, de novo pyrimidine synthesis during VACV infection, shedding new light on viral regulation under distinct nutritional environments. This study not only has the potential to contribute to the advancement of antiviral treatments but also improve the development of VACV as an oncolytic agent and vaccine vector.
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Affiliation(s)
- Lara Dsouza
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Anil Pant
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Blake Pope
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Zhilong Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
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4
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Wan Q, Tavakoli L, Wang TY, Tucker AJ, Zhou R, Liu Q, Feng S, Choi D, He Z, Gack MU, Zhao J. Hijacking of nucleotide biosynthesis and deamidation-mediated glycolysis by an oncogenic herpesvirus. Nat Commun 2024; 15:1442. [PMID: 38365882 PMCID: PMC10873312 DOI: 10.1038/s41467-024-45852-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma (KS) and multiple types of B cell malignancies. Emerging evidence demonstrates that KSHV reprograms host-cell central carbon metabolic pathways, which contributes to viral persistence and tumorigenesis. However, the mechanisms underlying KSHV-mediated metabolic reprogramming remain poorly understood. Carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase (CAD) is a key enzyme of the de novo pyrimidine synthesis, and was recently identified to deamidate the NF-κB subunit RelA to promote aerobic glycolysis and cell proliferation. Here we report that KSHV infection exploits CAD for nucleotide synthesis and glycolysis. Mechanistically, KSHV vCyclin binds to and hijacks cyclin-dependent kinase CDK6 to phosphorylate Ser-1900 on CAD, thereby activating CAD-mediated pyrimidine synthesis and RelA-deamidation-mediated glycolytic reprogramming. Correspondingly, genetic depletion or pharmacological inhibition of CDK6 and CAD potently impeded KSHV lytic replication and thwarted tumorigenesis of primary effusion lymphoma (PEL) cells in vitro and in vivo. Altogether, our work defines a viral metabolic reprogramming mechanism underpinning KSHV oncogenesis, which may spur the development of new strategies to treat KSHV-associated malignancies and other diseases.
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Affiliation(s)
- Quanyuan Wan
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Leah Tavakoli
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Ting-Yu Wang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Andrew J Tucker
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Ruiting Zhou
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Qizhi Liu
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- State Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, Hunan, China
| | - Shu Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- Department of Diabetes & Cancer Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Dongwon Choi
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhiheng He
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA
| | - Jun Zhao
- Florida Research and Innovation Center, Cleveland Clinic, Port St. Lucie, FL, USA.
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5
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Du X, Sonawane V, Zhang B, Wang C, de Ruijter B, Dömling ASS, Reiling N, Groves MR. Inhibitors of Aspartate Transcarbamoylase Inhibit Mycobacterium tuberculosis Growth. ChemMedChem 2023; 18:e202300279. [PMID: 37294060 DOI: 10.1002/cmdc.202300279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023]
Abstract
Aspartate transcarbamoylase (ATCase) plays a key role in the second step of de novo pyrimidine biosynthesis in eukaryotes and has been proposed to be a target to suppress cell proliferation in E. coli, human cells and the malarial parasite. We hypothesized that a library of ATCase inhibitors developed for malarial ATCase (PfATCase) may also contain inhibitors of the tubercular ATCase and provide a similar inhibition of cellular proliferation. Of the 70 compounds screened, 10 showed single-digit micromolar inhibition in an in vitro activity assay and were tested for their effect on M. tuberculosis cell growth in culture. The most promising compound demonstrated a MIC90 of 4 μM. A model of MtbATCase was generated using the experimental coordinates of PfATCase. In silico docking experiments showed this compound can occupy a similar allosteric pocket on MtbATCase to that seen on PfATCase, explaining the observed species selectivity seen for this compound series.
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Affiliation(s)
- Xiaochen Du
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Vidhisha Sonawane
- CATRIN, Department of Innovative Chemistry, PalackȳUniversity, 779 00, Olomouc - Holice, Czech Republic
| | - Bidong Zhang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Chao Wang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Bram de Ruijter
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
| | - Alexander S S Dömling
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
- CATRIN, Department of Innovative Chemistry, PalackȳUniversity, 779 00, Olomouc - Holice, Czech Republic
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel Leibniz Lung Center, Parkallee 1-40, Borstel, 23845, Sülfeld, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems Borstel, 23845, Greifswald, Germany
| | - Matthew R Groves
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, Groningen, 9700AV (The, Netherlands
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6
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Mahen KK, Markley L, Bogart J, Klatka H, Krishna V, Maytin EV, Stark GR, McDonald C. Topical N-phosphonacetyl-l-aspartate is a dual action candidate for treating non-melanoma skin cancer. Exp Dermatol 2023; 32:1485-1497. [PMID: 37309615 PMCID: PMC10527533 DOI: 10.1111/exd.14853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 05/08/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
Each year, 3.3 million Americans are diagnosed with non-melanoma skin cancers (NMSC) and an additional 40 million individuals undergo treatment of precancerous actinic keratosis lesions. The most effective treatments of NMSC (surgical excision and Mohs surgery) are invasive, expensive and require specialised training. More readily accessible topical therapies currently are 5-fluorouracil (a chemotherapeutic agent) and imiquimod (an immune modulator), but these can have significant side effects which limit their efficacy. Therefore, more effective and accessible treatments are needed for non-melanoma cancers and precancers. Our previous work demonstrated that the small molecule N-phosphonacetyl-L-aspartate (PALA) both inhibits pyrimidine nucleotide synthesis and activates pattern recognition receptor nucleotide-binding oligomerization domain 2. We propose that topical application of PALA would be an effective NMSC therapy, by combining the chemotherapeutic and immune modulatory features of 5-fluorouracil and imiquimod. Daily topical application of PALA to mouse skin was well tolerated and resulted in less irritation, fewer histopathological changes, and less inflammation than caused by either 5-fluorouracil or imiquimod. In an ultraviolet light-induced NMSC mouse model, topical PALA treatment substantially reduced the numbers, areas and grades of tumours, compared to vehicle controls. This anti-neoplastic activity was associated with increased expression of the antimicrobial peptide cathelicidin and increased recruitment of CD8+ T cells and F4/80+ macrophages to the tumours, demonstrating both immunomodulatory and anti-proliferative effects. These findings indicate that topical PALA is an excellent candidate as an effective alternative to current standard-of-care NMSC therapies.
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Affiliation(s)
- Kala K. Mahen
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Lilian Markley
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Jolie Bogart
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Hope Klatka
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Vijay Krishna
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Edward V. Maytin
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Dermatology, Dermatology and Plastic Surgery Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - George R. Stark
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
| | - Christine McDonald
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
- Department of Inflammation & Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, Ohio 44195, USA
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7
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del Caño-Ochoa F, Rubio-del-Campo A, Ramón-Maiques S. A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020660. [PMID: 36677714 PMCID: PMC9863657 DOI: 10.3390/molecules28020660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
CAD is a 1.5 MDa hexameric protein with four enzymatic domains responsible for initiating de novo biosynthesis of pyrimidines nucleotides: glutaminase, carbamoyl phosphate synthetase, aspartate transcarbamoylase (ATC), and dihydroorotase. Despite its central metabolic role and implication in cancer and other diseases, our understanding of CAD is poor, and structural characterization has been frustrated by its large size and sensitivity to proteolytic cleavage. Recently, we succeeded in isolating intact CAD-like particles from the fungus Chaetomium thermophilum with high yield and purity, but their study by cryo-electron microscopy is hampered by the dissociation of the complex during sample grid preparation. Here we devised a specific crosslinking strategy to enhance the stability of this mega-enzyme. Based on the structure of the isolated C. thermophilum ATC domain, we inserted by site-directed mutagenesis two cysteines at specific locations that favored the formation of disulfide bridges and covalent oligomers. We further proved that this covalent linkage increases the stability of the ATC domain without damaging the structure or enzymatic activity. Thus, we propose that this cysteine crosslinking is a suitable strategy to strengthen the contacts between subunits in the CAD particle and facilitate its structural characterization.
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Affiliation(s)
| | | | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV), CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Group CB06/07/0077 at the Instituto de Biomedicina de Valencia (IBV-CSIC) of CIBERER-ISCIII, Centro de Investigación Biomédica en Red de Enfermedades Raras, Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Correspondence:
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Wang C, Zhang B, Krüger A, Du X, Visser L, Dömling ASS, Wrenger C, Groves MR. Discovery of Small-Molecule Allosteric Inhibitors of PfATC as Antimalarials. J Am Chem Soc 2022; 144:19070-19077. [PMID: 36195578 PMCID: PMC9585585 DOI: 10.1021/jacs.2c08128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The discovery and
development of new drugs against malaria
remain
urgent. Aspartate transcarbamoylase (ATC) has been suggested to be
a promising target for antimalarial drug development. Here, we describe
a series of small-molecule inhibitors of P. falciparum ATC with low nanomolar binding affinities that selectively bind
to a previously unreported allosteric pocket, thereby inhibiting ATC
activation. We demonstrate that the buried allosteric pocket is located
close to the traditional ATC active site and that reported compounds
maintain the active site of PfATC in its low substrate
affinity/low activity conformation. These compounds inhibit parasite
growth in blood stage cultures at single digit micromolar concentrations,
whereas limited effects were seen against human normal lymphocytes.
To our knowledge, this series represent the first PfATC-specific allosteric inhibitors.
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Affiliation(s)
- Chao Wang
- XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Bidong Zhang
- XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo, Brazil
| | - Xiaochen Du
- XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Lidia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Alexander S S Dömling
- XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo, Brazil
| | - Matthew R Groves
- XB20 Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AD Groningen, The Netherlands
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9
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Claiborne MD, Sengupta S, Zhao L, Arwood ML, Sun IM, Wen J, Thompson EA, Mitchell-Flack M, Laiho M, Powell JD. Persistent CAD activity in memory CD8 + T cells supports rRNA synthesis and ribosomal biogenesis required at rechallenge. Sci Immunol 2022; 7:eabh4271. [PMID: 35622902 DOI: 10.1126/sciimmunol.abh4271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Memory CD8+ T cells are characterized by their ability to persist long after the initial antigen encounter and their capacity to generate a rapid recall response. Recent studies have identified a role for metabolic reprogramming and mitochondrial function in promoting the longevity of memory T cells. However, detailed mechanisms involved in promoting their rapid recall response are incompletely understood. Here, we identify a role for the initial and continued activation of the trifunctional rate-limiting enzyme of the de novo pyrimidine synthesis pathway CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) as critical in promoting the rapid recall response of previously activated CD8+ T cells. We found that CAD was rapidly phosphorylated upon naïve T cell activation in an mTORC1-dependent manner, yet remained phosphorylated long after initial activation. Previously activated CD8+ T cells displayed continued de novo pyrimidine synthesis in the absence of mitogenic signals, and interfering with this pathway diminished the speed and magnitude of cytokine production upon rechallenge. Inhibition of CAD did not affect cytokine transcript levels but diminished available pre-rRNA (ribosomal RNA), the polycistronic rRNA precursor whose synthesis is the rate-limiting step in ribosomal biogenesis. CAD inhibition additionally decreased levels of detectable ribosomal proteins in previously activated CD8+ T cells. Conversely, overexpression of CAD improved both the cytokine response and proliferation of memory T cells. Overall, our studies reveal a critical role for CAD-induced pyrimidine synthesis and ribosomal biogenesis in promoting the rapid recall response characteristic of memory T cells.
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Affiliation(s)
- Michael D Claiborne
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Liang Zhao
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Matthew L Arwood
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Im-Meng Sun
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiayu Wen
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elizabeth A Thompson
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marisa Mitchell-Flack
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan D Powell
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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10
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Walter M, Herr P. Re-Discovery of Pyrimidine Salvage as Target in Cancer Therapy. Cells 2022; 11:cells11040739. [PMID: 35203388 PMCID: PMC8870348 DOI: 10.3390/cells11040739] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Nucleotides are synthesized through two distinct pathways: de novo synthesis and nucleoside salvage. Whereas the de novo pathway synthesizes nucleotides from amino acids and glucose, the salvage pathway recovers nucleosides or bases formed during DNA or RNA degradation. In contrast to high proliferating non-malignant cells, which are highly dependent on the de novo synthesis, cancer cells can switch to the nucleoside salvage pathways to maintain efficient DNA replication. Pyrimidine de novo synthesis remains the target of interest in cancer therapy and several inhibitors showed promising results in cancer cells and in vivo models. In the 1980s and 1990s, poor responses were however observed in clinical trials with several of the currently existing pyrimidine synthesis inhibitors. To overcome the observed limitations in clinical trials, targeting pyrimidine salvage alone or in combination with pyrimidine de novo inhibitors was suggested. Even though this approach showed initially promising results, it received fresh attention only recently. Here we discuss the re-discovery of targeting pyrimidine salvage pathways for DNA replication alone or in combination with inhibitors of pyrimidine de novo synthesis to overcome limitations of commonly used antimetabolites in various preclinical cancer models and clinical trials. We also highlight newly emerged targets in pyrimidine synthesis as well as pyrimidine salvage as a promising target in immunotherapy.
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11
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Del Caño-Ochoa F, Ramón-Maiques S. Deciphering CAD: Structure and function of a mega-enzymatic pyrimidine factory in health and disease. Protein Sci 2021; 30:1995-2008. [PMID: 34288185 PMCID: PMC8442968 DOI: 10.1002/pro.4158] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD's architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
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12
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Wang W, Cui J, Ma H, Lu W, Huang J. Targeting Pyrimidine Metabolism in the Era of Precision Cancer Medicine. Front Oncol 2021; 11:684961. [PMID: 34123854 PMCID: PMC8194085 DOI: 10.3389/fonc.2021.684961] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 12/26/2022] Open
Abstract
Metabolic rewiring is considered as a primary feature of cancer. Malignant cells reprogram metabolism pathway in response to various intrinsic and extrinsic drawback to fuel cell survival and growth. Among the complex metabolic pathways, pyrimidine biosynthesis is conserved in all living organism and is necessary to maintain cellular fundamental function (i.e. DNA and RNA biosynthesis). A wealth of evidence has demonstrated that dysfunction of pyrimidine metabolism is closely related to cancer progression and numerous drugs targeting pyrimidine metabolism have been approved for multiple types of cancer. However, the non-negligible side effects and limited efficacy warrants a better strategy for negating pyrimidine metabolism in cancer. In recent years, increased studies have evidenced the interplay of oncogenic signaling and pyrimidine synthesis in tumorigenesis. Here, we review the recent conceptual advances on pyrimidine metabolism, especially dihydroorotate dehydrogenase (DHODH), in the framework of precision oncology medicine and prospect how this would guide the development of new drug precisely targeting the pyrimidine metabolism in cancer.
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Affiliation(s)
- Wanyan Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jiayan Cui
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Hui Ma
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jin Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
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13
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Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase. Nat Commun 2021; 12:947. [PMID: 33574254 PMCID: PMC7878868 DOI: 10.1038/s41467-021-21165-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/23/2020] [Indexed: 11/09/2022] Open
Abstract
Aspartate transcarbamoylase (ATC), an essential enzyme for de novo pyrimidine biosynthesis, is uniquely regulated in plants by feedback inhibition of uridine 5-monophosphate (UMP). Despite its importance in plant growth, the structure of this UMP-controlled ATC and the regulatory mechanism remain unknown. Here, we report the crystal structures of Arabidopsis ATC trimer free and bound to UMP, complexed to a transition-state analog or bearing a mutation that turns the enzyme insensitive to UMP. We found that UMP binds and blocks the ATC active site, directly competing with the binding of the substrates. We also prove that UMP recognition relies on a loop exclusively conserved in plants that is also responsible for the sequential firing of the active sites. In this work, we describe unique regulatory and catalytic properties of plant ATCs that could be exploited to modulate de novo pyrimidine synthesis and plant growth.
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14
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Del Caño-Ochoa F, Moreno-Morcillo M, Ramón-Maiques S. CAD, A Multienzymatic Protein at the Head of de Novo Pyrimidine Biosynthesis. Subcell Biochem 2020; 93:505-538. [PMID: 31939163 DOI: 10.1007/978-3-030-28151-9_17] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein that carries the enzymatic activities for the first three steps in the de novo biosynthesis of pyrimidine nucleotides: glutamine-dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase and Dihydroorotase. This metabolic pathway is essential for cell growth and proliferation and is conserved in all living organisms. However, the fusion of the first three enzymatic activities of the pathway into a single multienzymatic protein only occurs in animals. In prokaryotes, by contrast, these activities are encoded as distinct monofunctional enzymes that function independently or by forming more or less transient complexes. Whereas the structural information about these enzymes in bacteria is abundant, the large size and instability of CAD has only allowed a fragmented characterization of its structure. Here we retrace some of the most significant efforts to decipher the architecture of CAD and to understand its catalytic and regulatory mechanisms.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - María Moreno-Morcillo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - Santiago Ramón-Maiques
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain.
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15
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Pietsch M, Viht K, Schnitzler A, Ekambaram R, Steinkrüger M, Enkvist E, Nienberg C, Nickelsen A, Lauwers M, Jose J, Uri A, Niefind K. Unexpected CK2β-antagonistic functionality of bisubstrate inhibitors targeting protein kinase CK2. Bioorg Chem 2020; 96:103608. [PMID: 32058103 DOI: 10.1016/j.bioorg.2020.103608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/11/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023]
Abstract
Protein kinase CK2, a heterotetrameric holoenzyme composed of two catalytic chains (CK2α) attached to a homodimer of regulatory subunits (CK2β), is a target for drug development for cancer therapy. Here, we describe the tetraiodobenzimidazole derivative ARC-3140, a bisubstrate inhibitor addressing the ATP site and the substrate-binding site of CK2 with extraordinary affinity (Ki = 84 pM). In a crystal structure of ARC-3140 in complex with CK2α, three copies of the inhibitor are visible, one of them at the CK2β interface of CK2α. Subsequent interaction studies based on microscale thermophoresis and fluorescence anisotropy changes revealed a significant impact of ARC-3140 and of its tetrabromo equivalent ARC-1502 on the CK2α/CK2β interaction. A structural inspection revealed that ARC-3140, unlike CK2β antagonists described so far, interferes with both sub-interfaces of the bipartite CK2α/CK2β interaction. Thus, ARC-3140 is a lead for the further development of highly effective compounds perturbating the quaternary structure of the CK2α2β2 holoenzyme.
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Affiliation(s)
- Markus Pietsch
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Alexander Schnitzler
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany
| | - Ramesh Ekambaram
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Michaela Steinkrüger
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Christian Nienberg
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Anna Nickelsen
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Miriam Lauwers
- Institut II für Pharmakologie, Zentrum für Pharmakologie, Medizinische Fakultät, Universität zu Köln, Gleueler Str. 24, D-50931 Köln, Germany
| | - Joachim Jose
- Institut für Pharmazeutische und Medizinische Chemie, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstr. 48, D-48149 Münster, Germany
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.
| | - Karsten Niefind
- Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany.
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16
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Abt ER, Rosser EW, Durst MA, Lok V, Poddar S, Le TM, Cho A, Kim W, Wei L, Song J, Capri JR, Xu S, Wu N, Slavik R, Jung ME, Damoiseaux R, Czernin J, Donahue TR, Lavie A, Radu CG. Metabolic Modifier Screen Reveals Secondary Targets of Protein Kinase Inhibitors within Nucleotide Metabolism. Cell Chem Biol 2019; 27:197-205.e6. [PMID: 31734178 DOI: 10.1016/j.chembiol.2019.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 08/30/2019] [Accepted: 10/25/2019] [Indexed: 01/02/2023]
Abstract
Biosynthesis of the pyrimidine nucleotide uridine monophosphate (UMP) is essential for cell proliferation and is achieved by the activity of convergent de novo and salvage metabolic pathways. Here we report the development and application of a cell-based metabolic modifier screening platform that leverages the redundancy in pyrimidine metabolism for the discovery of selective UMP biosynthesis modulators. In evaluating a library of protein kinase inhibitors, we identified multiple compounds that possess nucleotide metabolism modifying activity. The JNK inhibitor JNK-IN-8 was found to potently inhibit nucleoside transport and engage ENT1. The PDK1 inhibitor OSU-03012 (also known as AR-12) and the RAF inhibitor TAK-632 were shown to inhibit the therapeutically relevant de novo pathway enzyme DHODH and their affinities were unambiguously confirmed through in vitro assays and co-crystallization with human DHODH.
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Affiliation(s)
- Evan R Abt
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Ethan W Rosser
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew A Durst
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; The Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Vincent Lok
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Soumya Poddar
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Thuc M Le
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Arthur Cho
- Department of Nuclear Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Woosuk Kim
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Liu Wei
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Janet Song
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Joseph R Capri
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Shili Xu
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Nanping Wu
- Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | - Roger Slavik
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Johannes Czernin
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA
| | - Timothy R Donahue
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA; Department of Surgery, University of California Los Angeles, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; The Jesse Brown VA Medical Center, Chicago, IL, USA
| | - Caius G Radu
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA; Ahmanson Translational Imaging Division, University of California Los Angeles, Los Angeles, CA, USA.
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17
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Ladds MJGW, Laín S. Small molecule activators of the p53 response. J Mol Cell Biol 2019; 11:245-254. [PMID: 30689917 PMCID: PMC6478124 DOI: 10.1093/jmcb/mjz006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/21/2018] [Accepted: 01/18/2019] [Indexed: 01/10/2023] Open
Abstract
Drugging the p53 pathway has been a goal for both academics and pharmaceutical companies since the designation of p53 as the 'guardian of the genome'. Through growing understanding of p53 biology, we can see multiple routes for activation of both wild-type p53 function and restoration of mutant p53. In this review, we focus on small molecules that activate wild-type p53 and that do so in a non-genotoxic manner. In particular, we will describe potential approaches to targeting proteins that alter p53 stability and function through posttranslational modification, affect p53's subcellular localization, or target RNA synthesis or the synthesis of ribonucleotides. The plethora of pathways for exploitation of p53, as well as the wide-ranging response to p53 activation, makes it an attractive target for anti-cancer therapy.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Solnavägen 9, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Tomtebodavägen 23A, Solna, Stockholm, Sweden
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Solnavägen 9, Karolinska Institutet, Stockholm, Sweden
- SciLifeLab, Tomtebodavägen 23A, Solna, Stockholm, Sweden
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18
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Madak JT, Bankhead A, Cuthbertson CR, Showalter HD, Neamati N. Revisiting the role of dihydroorotate dehydrogenase as a therapeutic target for cancer. Pharmacol Ther 2018; 195:111-131. [PMID: 30347213 DOI: 10.1016/j.pharmthera.2018.10.012] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Identified as a hallmark of cancer, metabolic reprogramming allows cancer cells to rapidly proliferate, resist chemotherapies, invade, metastasize, and survive a nutrient-deprived microenvironment. Rapidly growing cells depend on sufficient concentrations of nucleotides to sustain proliferation. One enzyme essential for the de novo biosynthesis of pyrimidine-based nucleotides is dihydroorotate dehydrogenase (DHODH), a known therapeutic target for multiple diseases. Brequinar, leflunomide, and teriflunomide, all of which are potent DHODH inhibitors, have been clinically evaluated but failed to receive FDA approval for the treatment of cancer. Inhibition of DHODH depletes intracellular pyrimidine nucleotide pools and results in cell cycle arrest in S-phase, sensitization to current chemotherapies, and differentiation in neural crest cells and acute myeloid leukemia (AML). Furthermore, DHODH is a synthetic lethal susceptibility in several oncogenic backgrounds. Therefore, DHODH-targeted therapy has potential value as part of a combination therapy for the treatment of cancer. In this review, we focus on the de novo pyrimidine biosynthesis pathway as a target for cancer therapy, and in particular, DHODH. In the first part, we provide a comprehensive overview of this pathway and its regulation in cancer. We further describe the relevance of DHODH as a target for cancer therapy using bioinformatic analyses. We then explore the preclinical and clinical results of pharmacological strategies to target the de novo pyrimidine biosynthesis pathway, with an emphasis on DHODH. Finally, we discuss potential strategies to harness DHODH as a target for the treatment of cancer.
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Affiliation(s)
- Joseph T Madak
- Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Armand Bankhead
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christine R Cuthbertson
- Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Hollis D Showalter
- Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Rogel Cancer Center, Ann Arbor, MI 48109, USA.
| | - Nouri Neamati
- Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Rogel Cancer Center, Ann Arbor, MI 48109, USA.
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19
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Peters GJ. Antipyrimidine effects of five different pyrimidine de novo synthesis inhibitors in three head and neck cancer cell lines. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:329-339. [PMID: 29723133 DOI: 10.1080/15257770.2018.1460479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The pyrimidine de novo nucleotide synthesis consists of 6 sequential steps. Various inhibitors against these enzymes have been developed and evaluated in the clinic for their potential anticancer activity: acivicin inhibits carbamoyl-phosphate-synthase-II, N-(phosphonacetyl)-L- aspartate (PALA) inhibits aspartate-transcarbamylase, Brequinar sodium and dichloroallyl-lawsone (DCL) inhibit dihydroorotate-dehydrogenase, and pyrazofurin (PF) inhibits orotate-phosphoribosyltransferase. We compared their growth inhibition against 3 cell lines from head-and-neck-cancer (HEP-2, UMSCC-14B and UMSCC-14C) and related the sensitivity to their effects on nucleotide pools. In all cell lines Brequinar and PF were the most active compounds with IC50 (50% growth inhibition) values between 0.06-0.37 µM, Acivicin was as potent (IC50s 0.26-1 µM), but DCL was 20-31-fold less active. PALA was most inactive (24-128 µM). At equitoxic concentrations, all pure antipyrimidine de novo inhibitors depleted UTP and CTP after 24 hr exposure, which was most pronounced for Brequinar (between 6-10% of UTP left, and 12-36% CTP), followed by DCL and PF, which were almost similar (6-16% UTP and 12-27% CTP), while PALA was the least active compound (10-70% UTP and 13-68% CTP). Acivicin is a multi-target inhibitor of more glutamine requiring enzymes (including GMP synthetase) and no decrease of UTP was found, but a pronounced decrease in GTP (31-72% left). In conclusion, these 5 inhibitors of the pyrimidine de novo nucleotide synthesis varied considerably in their efficacy and effect on pyrimidine nucleotide pools. Inhibitors of DHO-DH were most effective suggesting a primary role of this enzyme in controlling pyrimidine nucleotide pools.
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Affiliation(s)
- Godefridus J Peters
- a Department of Medical Oncology , VU University Medical Center , MB Amsterdam , The Netherlands
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20
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Deng Y, Wang ZV, Gordillo R, An Y, Zhang C, Liang Q, Yoshino J, Cautivo KM, De Brabander J, Elmquist JK, Horton JD, Hill JA, Klein S, Scherer PE. An adipo-biliary-uridine axis that regulates energy homeostasis. Science 2017; 355:355/6330/eaaf5375. [PMID: 28302796 DOI: 10.1126/science.aaf5375] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022]
Abstract
Uridine, a pyrimidine nucleoside present at high levels in the plasma of rodents and humans, is critical for RNA synthesis, glycogen deposition, and many other essential cellular processes. It also contributes to systemic metabolism, but the underlying mechanisms remain unclear. We found that plasma uridine levels are regulated by fasting and refeeding in mice, rats, and humans. Fasting increases plasma uridine levels, and this increase relies largely on adipocytes. In contrast, refeeding reduces plasma uridine levels through biliary clearance. Elevation of plasma uridine is required for the drop in body temperature that occurs during fasting. Further, feeding-induced clearance of plasma uridine improves glucose metabolism. We also present findings that implicate leptin signaling in uridine homeostasis and consequent metabolic control and thermoregulation. Our results indicate that plasma uridine governs energy homeostasis and thermoregulation in a mechanism involving adipocyte-dependent uridine biosynthesis and leptin signaling.
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Affiliation(s)
- Yingfeng Deng
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhao V Wang
- Division of Cardiology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ruth Gordillo
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yu An
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chen Zhang
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Qiren Liang
- Department of Biochemistry and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jun Yoshino
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Kelly M Cautivo
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jef De Brabander
- Department of Biochemistry and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joel K Elmquist
- Division of Hypothalamic Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jay D Horton
- Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joseph A Hill
- Division of Cardiology, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University School of Medicine, St. Louis, MO, USA
| | - Philipp E Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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21
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Brown KK, Spinelli JB, Asara JM, Toker A. Adaptive Reprogramming of De Novo Pyrimidine Synthesis Is a Metabolic Vulnerability in Triple-Negative Breast Cancer. Cancer Discov 2017; 7:391-399. [PMID: 28255083 DOI: 10.1158/2159-8290.cd-16-0611] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/22/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023]
Abstract
Chemotherapy resistance is a major barrier to the treatment of triple-negative breast cancer (TNBC), and strategies to circumvent resistance are required. Using in vitro and in vivo metabolic profiling of TNBC cells, we show that an increase in the abundance of pyrimidine nucleotides occurs in response to chemotherapy exposure. Mechanistically, elevation of pyrimidine nucleotides induced by chemotherapy is dependent on increased activity of the de novo pyrimidine synthesis pathway. Pharmacologic inhibition of de novo pyrimidine synthesis sensitizes TNBC cells to genotoxic chemotherapy agents by exacerbating DNA damage. Moreover, combined treatment with doxorubicin and leflunomide, a clinically approved inhibitor of the de novo pyrimidine synthesis pathway, induces regression of TNBC xenografts. Thus, the increase in pyrimidine nucleotide levels observed following chemotherapy exposure represents a metabolic vulnerability that can be exploited to enhance the efficacy of chemotherapy for the treatment of TNBC.Significance: The prognosis for patients with TNBC with residual disease after chemotherapy is poor. We find that chemotherapy agents induce adaptive reprogramming of de novo pyrimidine synthesis and show that this response can be exploited pharmacologically, using clinically approved inhibitors of de novo pyrimidine synthesis, to sensitize TNBC cells to chemotherapy. Cancer Discov; 7(4); 391-9. ©2017 AACR.See related article by Mathur et al., p. 380This article is highlighted in the In This Issue feature, p. 339.
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Affiliation(s)
- Kristin K Brown
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts. .,Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Jessica B Spinelli
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - John M Asara
- Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts. .,Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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Ruiz-Ramos A, Velázquez-Campoy A, Grande-García A, Moreno-Morcillo M, Ramón-Maiques S. Structure and Functional Characterization of Human Aspartate Transcarbamoylase, the Target of the Anti-tumoral Drug PALA. Structure 2016; 24:1081-94. [PMID: 27265852 DOI: 10.1016/j.str.2016.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 01/30/2023]
Abstract
CAD, the multienzymatic protein that initiates and controls de novo synthesis of pyrimidines in animals, associates through its aspartate transcarbamoylase (ATCase) domain into particles of 1.5 MDa. Despite numerous structures of prokaryotic ATCases, we lack structural information on the ATCase domain of CAD. Here, we report the structure and functional characterization of human ATCase, confirming the overall similarity with bacterial homologs. Unexpectedly, human ATCase exhibits cooperativity effects that reduce the affinity for the anti-tumoral drug PALA. Combining structural, mutagenic, and biochemical analysis, we identified key elements for the necessary regulation and transmission of conformational changes leading to cooperativity between subunits. Mutation of one of these elements, R2024, was recently found to cause the first non-lethal CAD deficit. We reproduced this mutation in human ATCase and measured its effect, demonstrating that this arginine is part of a molecular switch that regulates the equilibrium between low- and high-affinity states for the ligands.
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Affiliation(s)
- Alba Ruiz-Ramos
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50009 Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain; Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - María Moreno-Morcillo
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain
| | - Santiago Ramón-Maiques
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain.
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Murphy JR, Donini S, Kappock TJ. An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase. Acta Crystallogr F Struct Biol Commun 2015; 71:1292-9. [PMID: 26457521 PMCID: PMC4601594 DOI: 10.1107/s2053230x15015939] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/25/2015] [Indexed: 11/29/2022] Open
Abstract
Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. As a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.
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Affiliation(s)
- Jesse R. Murphy
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
| | - Stefano Donini
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
| | - T. Joseph Kappock
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
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25
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Abstract
CAD is a large multifunctional polypeptide that initiates and controls the de novo biosynthesis of pyrimidines in animals. In this issue of Structure, Grande-García and colleagues provide the first atomic information of this antitumoral target by reporting the crystal structure of the dihydroorotase domain of human CAD.
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Affiliation(s)
- Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto Química-Física "Rocasolano," CSIC, Serrano 119, 28006 Madrid, Spain.
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Evans HG, Fernando R, Vaishnav A, Kotichukkala M, Heyl D, Hachem F, Brunzelle JS, Edwards BFP, Evans DR. Intersubunit communication in the dihydroorotase-aspartate transcarbamoylase complex of Aquifex aeolicus. Protein Sci 2014; 23:100-9. [PMID: 24353170 DOI: 10.1002/pro.2396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 11/06/2022]
Abstract
Aspartate transcarbamoylase and dihydroorotase, enzymes that catalyze the second and third step in de novo pyrimidine biosynthesis, are associated in dodecameric complexes in Aquifex aeolicus and many other organisms. The architecture of the dodecamer is ideally suited to channel the intermediate, carbamoyl aspartate from its site of synthesis on the ATC subunit to the active site of DHO, which catalyzes the next step in the pathway, because both reactions occur within a large, internal solvent-filled cavity. Channeling usually requires that the reactions of the enzymes are coordinated so that the rate of synthesis of the intermediate matches its rate of utilization. The linkage between the ATC and DHO subunits was demonstrated by showing that the binding of the bisubstrate analog, N-phosphonacetyl-L-aspartate to the ATC subunit inhibits the activity of the distal DHO subunit. Structural studies identified a DHO loop, loop A, interdigitating between the ATC domains that would be expected to interfere with domain closure essential for ATC catalysis. Mutation of the DHO residues in loop A that penetrate deeply between the two ATC domains inhibits the ATC activity by interfering with the normal reciprocal linkage between the two enzymes. Moreover, a synthetic peptide that mimics that part of the DHO loop that binds between the two ATC domains was found to be an allosteric or noncompletive ATC inhibitor (K(i) = 22 μM). A model is proposed suggesting that loop A is an important component of the functional linkage between the enzymes.
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Affiliation(s)
- Hedeel Guy Evans
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, 48197; Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan, 48201
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Buller AR, Freeman MF, Schildbach JF, Townsend CA. Exploring the role of conformational heterogeneity in cis-autoproteolytic activation of ThnT. Biochemistry 2014; 53:4273-81. [PMID: 24933323 PMCID: PMC4095933 DOI: 10.1021/bi500385d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
In
the past decade, there have been major achievements in understanding
the relationship between enzyme catalysis and protein structural plasticity.
In autoprocessing systems, however, there is a sparsity of direct
evidence of the role of conformational dynamics, which are complicated
by their intrinsic chemical reactivity. ThnT is an autoproteolytically
activated enzyme involved in the biosynthesis of the β-lactam
antibiotic thienamycin. Conservative mutation of ThnT results in multiple
conformational states that can be observed via X-ray crystallography,
establishing ThnT as a representative and revealing system for studing
how conformational dynamics control autoactivation at a molecular
level. Removal of the nucleophile by mutation to Ala disrupts the
population of a reactive state and causes widespread structural changes
from a conformation that promotes autoproteolysis to one associated
with substrate catalysis. Finer probing of the active site polysterism
was achieved by EtHg derivatization of the nucleophile, which indicates
the active site and a neighboring loop have coupled dynamics. Disruption
of these interactions by mutagenesis precludes the ability to observe
a reactive state through X-ray crystallography, and application of
this insight to other autoproteolytically activated enzymes offers
an explanation for the widespread crystallization of inactive states.
We suggest that the N → O(S) acyl shift in cis-autoproteolysis might occur through a si-face attack,
thereby unifying the fundamental chemistry of these enzymes through
a common mechanism.
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Affiliation(s)
- Andrew R Buller
- Department of Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States
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Ruiz-Ramos A, Lallous N, Grande-García A, Ramón-Maiques S. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the aspartate transcarbamoylase domain of human CAD. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1425-30. [PMID: 24316846 PMCID: PMC3855736 DOI: 10.1107/s1744309113031114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/12/2013] [Indexed: 11/10/2022]
Abstract
Aspartate transcarbamoylase (ATCase) catalyzes the synthesis of N-carbamoyl-L-aspartate from carbamoyl phosphate and aspartate in the second step of the de novo biosynthesis of pyrimidines. In prokaryotes, the first three activities of the pathway, namely carbamoyl phosphate synthetase (CPSase), ATCase and dihydroorotase (DHOase), are encoded as distinct proteins that function independently or in noncovalent association. In animals, CPSase, ATCase and DHOase are part of a 243 kDa multifunctional polypeptide named CAD. Up-regulation of CAD is essential for normal and tumour cell proliferation. Although the structures of numerous prokaryotic ATCases have been determined, there is no structural information about any eukaryotic ATCase. In fact, the only detailed structural information about CAD is that it self-assembles into hexamers and trimers through interactions of the ATCase domains. Here, the expression, purification and crystallization of the ATCase domain of human CAD is reported. The recombinant protein, which was expressed in bacteria and purified with good yield, formed homotrimers in solution. Crystallization experiments both in the absence and in the presence of the inhibitor PALA yielded small crystals that diffracted X-rays to 2.1 Å resolution using synchrotron radiation. The crystals appeared to belong to the hexagonal space group P6(3)22, and Matthews coefficient calculation indicated the presence of one ATCase subunit per asymmetric unit, with a solvent content of 48%. However, analysis of the intensity statistics suggests a special case of the P21 lattice with pseudo-symmetry and possibly twinning.
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Affiliation(s)
- Alba Ruiz-Ramos
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Nada Lallous
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Araceli Grande-García
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Santiago Ramón-Maiques
- Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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Banerjee AK, Arora N, Murty USN. Aspartate carbamoyltransferase of Plasmodium falciparum as a potential drug target for designing anti-malarial chemotherapeutic agents. Med Chem Res 2012. [DOI: 10.1007/s00044-011-9757-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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POSTER COMMUNICATIONS. Br J Pharmacol 2012. [DOI: 10.1111/j.1476-5381.1982.tb17355.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Richmond AL, Kabi A, Homer CR, García NM, Nickerson KP, NesvizhskiI AI, Sreekumar A, Chinnaiyan AM, Nuñez G, McDonald C. The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells. Gastroenterology 2012; 142:1483-92.e6. [PMID: 22387394 PMCID: PMC3565430 DOI: 10.1053/j.gastro.2012.02.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Polymorphisms that reduce the function of nucleotide-binding oligomerization domain (NOD)2, a bacterial sensor, have been associated with Crohn's disease (CD). No proteins that regulate NOD2 activity have been identified as selective pharmacologic targets. We sought to discover regulators of NOD2 that might be pharmacologic targets for CD therapies. METHODS Carbamoyl phosphate synthetase/aspartate transcarbamylase/dihydroorotase (CAD) is an enzyme required for de novo pyrimidine nucleotide synthesis; it was identified as a NOD2-interacting protein by immunoprecipitation-coupled mass spectrometry. CAD expression was assessed in colon tissues from individuals with and without inflammatory bowel disease by immunohistochemistry. The interaction between CAD and NOD2 was assessed in human HCT116 intestinal epithelial cells by immunoprecipitation, immunoblot, reporter gene, and gentamicin protection assays. We also analyzed human cell lines that express variants of NOD2 and the effects of RNA interference, overexpression and CAD inhibitors. RESULTS CAD was identified as a NOD2-interacting protein expressed at increased levels in the intestinal epithelium of patients with CD compared with controls. Overexpression of CAD inhibited NOD2-dependent activation of nuclear factor κB and p38 mitogen-activated protein kinase, as well as intracellular killing of Salmonella. Reduction of CAD expression or administration of CAD inhibitors increased NOD2-dependent signaling and antibacterial functions of NOD2 variants that are and are not associated with CD. CONCLUSIONS The nucleotide synthesis enzyme CAD is a negative regulator of NOD2. The antibacterial function of NOD2 variants that have been associated with CD increased in response to pharmacologic inhibition of CAD. CAD is a potential therapeutic target for CD.
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Affiliation(s)
- Amy L. Richmond
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Amrita Kabi
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Craig R. Homer
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Kourtney P. Nickerson
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
| | | | - Arun Sreekumar
- Department of Molecular and Cell Biology, Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas
| | - Arul M. Chinnaiyan
- Department of Pathology, Comprehensive Cancer Center, Ann Arbor, Michigan,Michigan Center for Translational Pathology, Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan
| | - Gabriel Nuñez
- Department of Pathology, Comprehensive Cancer Center, Ann Arbor, Michigan
| | - Christine McDonald
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio
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Lipscomb WN, Kantrowitz ER. Structure and mechanisms of Escherichia coli aspartate transcarbamoylase. Acc Chem Res 2012; 45:444-53. [PMID: 22011033 DOI: 10.1021/ar200166p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes catalyze a particular reaction in cells, but only a few control the rate of this reaction and the metabolic pathway that follows. One specific mechanism for such enzymatic control of a metabolic pathway involves molecular feedback, whereby a metabolite further down the pathway acts at a unique site on the control enzyme to alter its activity allosterically. This regulation may be positive or negative (or both), depending upon the particular system. Another method of enzymatic control involves the cooperative binding of the substrate, which allows a large change in enzyme activity to emanate from only a small change in substrate concentration. Allosteric regulation and homotropic cooperativity are often known to involve significant conformational changes in the structure of the protein. Escherichia coli aspartate transcarbamoylase (ATCase) is the textbook example of an enzyme that regulates a metabolic pathway, namely, pyrimidine nucleotide biosynthesis, by feedback control and by the cooperative binding of the substrate, L-aspartate. The catalytic and regulatory mechanisms of this enzyme have been extensively studied. A series of X-ray crystal structures of the enzyme in the presence and absence of substrates, products, and analogues have provided details, at the molecular level, of the conformational changes that the enzyme undergoes as it shifts between its low-activity, low-affinity form (T state) to its high-activity, high-affinity form (R state). These structural data provide insights into not only how this enzyme catalyzes the reaction between l-aspartate and carbamoyl phosphate to form N-carbamoyl-L-aspartate and inorganic phosphate, but also how the allosteric effectors modulate this activity. In this Account, we summarize studies on the structure of the enzyme and describe how these structural data provide insights into the catalytic and regulatory mechanisms of the enzyme. The ATCase-catalyzed reaction is regulated by nucleotide binding some 60 Å from the active site, inducing structural alterations that modulate catalytic activity. The delineation of the structure and function in this particular model system will help in understanding the molecular basis of cooperativity and allosteric regulation in other systems as well.
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Affiliation(s)
- William N. Lipscomb
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467-3860, United States
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33
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Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase. Arch Biochem Biophys 2011; 519:81-90. [PMID: 22198283 DOI: 10.1016/j.abb.2011.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/20/2022]
Abstract
The allosteric enzyme aspartate transcarbamoylase (ATCase) from Escherichia coli has been the subject of investigations for approximately 50 years. This enzyme controls the rate of pyrimidine nucleotide biosynthesis by feedback inhibition, and helps to balance the pyrimidine and purine pools by competitive allosteric activation by ATP. The catalytic and regulatory components of the dodecameric enzyme can be separated and studied independently. Many of the properties of the enzyme follow the Monod, Wyman Changeux model of allosteric control thus E. coli ATCase has become the textbook example. This review will highlight kinetic, biophysical, and structural studies which have provided a molecular level understanding of how the allosteric nature of this enzyme regulates pyrimidine nucleotide biosynthesis.
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34
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Harris KM, Cockrell GM, Puleo DE, Kantrowitz ER. Crystallographic snapshots of the complete catalytic cycle of the unregulated aspartate transcarbamoylase from Bacillus subtilis. J Mol Biol 2011; 411:190-200. [PMID: 21663747 PMCID: PMC3211067 DOI: 10.1016/j.jmb.2011.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/19/2011] [Accepted: 05/24/2011] [Indexed: 01/07/2023]
Abstract
Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered release of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.
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Affiliation(s)
- Katharine M. Harris
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - Gregory M. Cockrell
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - David E. Puleo
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467 USA
- Corresponding author. E. R. Kantrowitz, Department of Chemistry, Boston College, Merkert Chemistry Center 239, Chestnut Hill, MA 02467 USA.,
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Shipov AE, Genkina GK, Petrovskii PV, Goryunov EI, Makarov MV. Novel Biologically Active 1,3,2-Oxazaphosphinane Derivatives. PHOSPHORUS SULFUR 2011. [DOI: 10.1080/10426507.2010.520281] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Anatolii E. Shipov
- a A. N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Russian Federation
| | - Galina K. Genkina
- a A. N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Russian Federation
| | - Pavel V. Petrovskii
- a A. N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Russian Federation
| | - Evgenii I. Goryunov
- a A. N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Russian Federation
| | - Michael V. Makarov
- a A. N. Nesmeyanov Institute of Organoelement Compounds , Russian Academy of Sciences , Russian Federation
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Henklein P, Gloede J. Ungewöhnliche Aminolyse eines Carbonsäure-Kohlensäure-Anhydrids. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/zfch.19890290108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Shipov AE, Genkina GK, Goryunov EI, Goryunova IB, Petrovskii PV. Phosphorus-containing derivatives of L-aspartic and L-glutamic acids. Russ Chem Bull 2010. [DOI: 10.1007/s11172-010-0054-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Le Calvez PB, Scott CJ, Migaud ME. Multisubstrate adduct inhibitors: drug design and biological tools. J Enzyme Inhib Med Chem 2010; 24:1291-318. [PMID: 19912064 DOI: 10.3109/14756360902843809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In drug discovery, different methods exist to create new inhibitors possessing satisfactory biological activity. The multisubstrate adduct inhibitor (MAI) approach is one of these methods, which consists of a covalent combination between analogs of the substrate and the cofactor or of the multiple substrates used by the target enzyme. Adopted as the first line of investigation for many enzymes, this method has brought insights into the enzymatic mechanism, structure, and inhibitory requirements. In this review, the MAI approach, applied to different classes of enzyme, is reported from the point of view of biological activity.
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Lavogina D, Enkvist E, Uri A. Bisubstrate inhibitors of protein kinases: from principle to practical applications. ChemMedChem 2010; 5:23-34. [PMID: 19774589 DOI: 10.1002/cmdc.200900252] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bisubstrate inhibitors consist of two conjugated fragments, each targeted to a different binding site of a bisubstrate enzyme. The design of bisubstrate inhibitors presupposes the formation of the ternary complex in the course of the catalyzed reaction. The principle advantage of bisubstrate inhibitors is their ability to generate more interactions with the target enzyme that could result in improved affinity and selectivity of the conjugates, when compared with single-site inhibitors. Among phosphotransferases, the approach was first successfully used for adenylate kinase in 1973. Since then, several types of bisubstrate inhibitors have been developed for protein kinases, including conjugates of peptides with nucleotides, adenosine derivatives and potent ATP-competitive inhibitors. Earlier bisubstrate inhibitors had pharmacokinetic qualities that were unsuitable for cellular experiments and hence were mostly used for in vitro studies. The recently constructed conjugates of adenosine derivatives and D-arginine-rich peptides (ARCs) possess high kinase affinity, high biological and chemical stability and good cell plasma membrane penetrative properties that enable their application in the regulation of cellular protein phosphorylation balances in cell and tissue experiments.
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Affiliation(s)
- Darja Lavogina
- Institute of Chemistry, Jakobi 2, 51014 Tartu (Estonia).
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42
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Coudray L, Pennebaker AF, Montchamp JL. Synthesis and in vitro evaluation of aspartate transcarbamoylase inhibitors. Bioorg Med Chem 2009; 17:7680-9. [PMID: 19828320 PMCID: PMC2783949 DOI: 10.1016/j.bmc.2009.09.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 09/18/2009] [Accepted: 09/22/2009] [Indexed: 11/22/2022]
Abstract
The design, synthesis, and evaluation of a series of novel inhibitors of aspartate transcarbamoylase (ATCase) are reported. Several submicromolar phosphorus-containing inhibitors are described, but all-carboxylate compounds are inactive. Compounds were synthesized to probe the postulated cyclic transition-state of the enzyme-catalyzed reaction. In addition, the associated role of the protonation state at the phosphorus acid moiety was evaluated using phosphinic and carboxylic acids. Although none of the synthesized inhibitors is more potent than N-phosphonacetyl-l-aspartate (PALA), the compounds provide useful mechanistic information, as well as the basis for the design of future inhibitors and/or prodrugs.
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Affiliation(s)
- Laëtitia Coudray
- Department of Chemistry, Box 298860, Texas Christian University, Fort Worth, Texas 76129, USA
| | - Anne F. Pennebaker
- Department of Chemistry, Box 298860, Texas Christian University, Fort Worth, Texas 76129, USA
| | - Jean-Luc Montchamp
- Department of Chemistry, Box 298860, Texas Christian University, Fort Worth, Texas 76129, USA
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Abstracts. Cancer Invest 2009. [DOI: 10.3109/07357909309045592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Coudray L, Kantrowitz ER, Montchamp JL. Submicromolar phosphinic inhibitors of Escherichia coli aspartate transcarbamoylase. Bioorg Med Chem Lett 2008; 19:900-2. [PMID: 19097895 DOI: 10.1016/j.bmcl.2008.11.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 11/28/2022]
Abstract
The design, syntheses, and enzymatic activity of two submicromolar competitive inhibitors of aspartate transcarbamoylase (ATCase) are described. The phosphinate inhibitors are analogs of N-phosphonacetyl-l-aspartate (PALA) but have a reduced charge at the phosphorus moiety. The mechanistic implications are discussed in terms of a possible cyclic transition-state during enzymatic catalysis.
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Affiliation(s)
- Laëtitia Coudray
- Department of Chemistry, Texas Christian University, Box 298860, Fort Worth, TX 76129, USA
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Heath TD, Brown CS. Liposome Dependent Delivery of N-(Phosphonacetyl)-L-Aspartic Acid to Cellsin Vitro. J Liposome Res 2008. [DOI: 10.3109/08982108909035999] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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46
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Wang J, Eldo J, Kantrowitz ER. Structural model of the R state of Escherichia coli aspartate transcarbamoylase with substrates bound. J Mol Biol 2007; 371:1261-73. [PMID: 17603076 PMCID: PMC2720131 DOI: 10.1016/j.jmb.2007.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 06/01/2007] [Accepted: 06/05/2007] [Indexed: 01/07/2023]
Abstract
The allosteric enzyme aspartate transcarbamoylase (ATCase) exists in two conformational states. The enzyme, in the absence of substrates is primarily in the low-activity T state, is converted to the high-activity R state upon substrate binding, and remains in the R state until substrates are exhausted. These conformational changes have made it difficult to obtain structural data on R-state active-site complexes. Here we report the R-state structure of ATCase with the substrate Asp and the substrate analog phosphonoactamide (PAM) bound. This R-state structure represents the stage in the catalytic mechanism immediately before the formation of the covalent bond between the nitrogen of the amino group of Asp and the carbonyl carbon of carbamoyl phosphate. The binding mode of the PAM is similar to the binding mode of the phosphonate moiety of N-(phosphonoacetyl)-l-aspartate (PALA), the carboxylates of Asp interact with the same residues that interact with the carboxylates of PALA, although the position and orientations are shifted. The amino group of Asp is 2.9 A away from the carbonyl oxygen of PAM, positioned correctly for the nucleophilic attack. Arg105 and Leu267 in the catalytic chain interact with PAM and Asp and help to position the substrates correctly for catalysis. This structure fills a key gap in the structural determination of each of the steps in the catalytic cycle. By combining these data with previously determined structures we can now visualize the allosteric transition through detailed atomic motions that underlie the molecular mechanism.
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Affiliation(s)
- Jie Wang
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
| | - Joby Eldo
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467
- E-mail address of corresponding author:
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Llácer JL, Polo LM, Tavárez S, Alarcón B, Hilario R, Rubio V. The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction. J Bacteriol 2007; 189:1254-65. [PMID: 17028272 PMCID: PMC1797358 DOI: 10.1128/jb.01216-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Angstroms-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K(i) = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.
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Affiliation(s)
- José L Llácer
- Instituto de Biomedicina de Valencia (IBV-CSIC), C/Jaime Roig 11, 46010 Valencia, Spain
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Fetler L, Kantrowitz ER, Vachette P. Direct observation in solution of a preexisting structural equilibrium for a mutant of the allosteric aspartate transcarbamoylase. Proc Natl Acad Sci U S A 2007; 104:495-500. [PMID: 17202260 PMCID: PMC1766413 DOI: 10.1073/pnas.0607641104] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many signaling and metabolic pathways rely on the ability of some of the proteins involved to undergo a substrate-induced transition between at least two structural states. Among the various models put forward to account for binding and activity curves of those allosteric proteins, the Monod, Wyman, and Changeux model for allostery theory has certainly been the most influential, although a central postulate, the preexisting equilibrium between the low-activity, low-affinity quaternary structure and the high-activity, high-affinity quaternary structure states in the absence of substrates, has long awaited direct experimental substantiation. Upon substrate binding, allosteric Escherichia coli aspartate transcarbamoylase adopts alternate quaternary structures, stabilized by a set of interdomain and intersubunit interactions, which are readily differentiated by their solution x-ray scattering curves. Disruption of a salt link, which is observed only in the low-activity, low-affinity quaternary structure, between Lys-143 of the regulatory chain and Asp-236 of the catalytic chain yields a mutant enzyme that is in a reversible equilibrium between at least two states in the absence of ligand, a major tenet of the Monod, Wyman, and Changeux model. By using this mutant as a magnifying glass of the structural effect of ligand binding, a comparative analysis of the binding of carbamoyl phosphate (CP) and analogs points out the crucial role of the amine group of CP in facilitating the transition toward the high-activity, high-affinity quaternary state. Thus, the cooperative binding of aspartate in aspartate transcarbamoylase appears to result from the combination of the preexisting quaternary structure equilibrium with local changes induced by CP binding.
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Affiliation(s)
- Luc Fetler
- *Centre de Recherche, Institut Curie, F-75248 Paris, France
- Laboratoire Physico-Chimie, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 168, F-75248 Paris, France
| | - Evan R. Kantrowitz
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467; and
| | - Patrice Vachette
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Unité Mixte de Recherche 8619, Centre National de la Recherche Scientifique, Université Paris-Sud, Bâtiment 430, F-91405 Orsay Cedex, France
- To whom correspondence should be addressed. E-mail:
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De Vos D, Xu Y, Hulpiau P, Vergauwen B, Van Beeumen JJ. Structural Investigation of Cold Activity and Regulation of Aspartate Carbamoyltransferase from the Extreme Psychrophilic Bacterium Moritella profunda. J Mol Biol 2007; 365:379-95. [PMID: 17070547 DOI: 10.1016/j.jmb.2006.09.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 09/21/2006] [Accepted: 09/25/2006] [Indexed: 11/28/2022]
Abstract
Aspartate carbamoyltransferase (EC 2.1.3.2) is extensively studied as a model for cooperativity and allosteric regulation. The structure of the Escherichia coli enzyme has been thoroughly analyzed by X-ray crystallography, and recently the crystal structures of two hyperthermophilic ATCases of the same structural class have been characterized. We here report the detailed functional and structural investigation of the ATCase from the psychrophilic deep sea bacterium Moritella profunda. Our analysis indicates that the enzyme conforms to the E. coli model in that two allosteric states exist that are influenced by similar homotropic interactions. The heterotropic properties differ in that CTP and UTP inhibit the holoenzyme, but ATP seems to exhibit a dual regulatory pattern, activating the enzyme at low concentrations and inhibiting it in the mM range. The crystal structure of the unliganded M. profunda ATCase shows resemblance to a more extreme T state reported previously for an E. coli ATCase mutant. A detailed molecular analysis reveals potential features of adaptation to cold activity and cold regulation. Moreover, M. profunda ATCase presents similarities with certain mutants of E. coli ATCase altered in their kinetic properties or temperature relationships. Finally, structural and functional comparison of ATCases across the full physiological temperature range agrees with an important, but fundamentally different role for electrostatics in protein adaptation at both extremes, i.e. an increased stability through the formation of ion pairs and ion pair networks at high physiological temperatures, and an increased flexibility through enhanced protein solvation at low temperatures.
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Affiliation(s)
- Dirk De Vos
- Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
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Eldo J, Heng S, Kantrowitz ER. Design, synthesis, and bioactivity of novel inhibitors of E. coli aspartate transcarbamoylase. Bioorg Med Chem Lett 2006; 17:2086-90. [PMID: 17336518 PMCID: PMC1930159 DOI: 10.1016/j.bmcl.2006.12.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
A series of inhibitors of the aspartate transcarbamoylase, an enzyme involved in pyrimidine nucleotide biosynthesis, has been synthesized. These inhibitors are analogues of a highly potent inhibitor of this enzyme, N-phosphonacetyl-L-aspartate (PALA). Analogues have been synthesized with modifications at the alpha- and beta-carboxylates as well as at the aspartate moiety. The ability of these compounds to inhibit the enzyme was evaluated. These studies, with functional group modified PALA derivatives, showed that amide groups can be a useful substitute of the carboxylate in order to reduce the charge on the molecule, and indicate that the relative position of the functional group in the beta-position is more critical than the nature of the functional group. Some of the molecules synthesized here are potent inhibitors of the enzyme.
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