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Wang C, Krüger A, Du X, Wrenger C, Groves MR. Novel Highlight in Malarial Drug Discovery: Aspartate Transcarbamoylase. Front Cell Infect Microbiol 2022; 12:841833. [PMID: 35310840 PMCID: PMC8931299 DOI: 10.3389/fcimb.2022.841833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 – a potent, yet unselective, antimalarial – is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.
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Affiliation(s)
- Chao Wang
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Xiaochen Du
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Matthew R. Groves, ; Carsten Wrenger,
| | - Matthew R. Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
- *Correspondence: Matthew R. Groves, ; Carsten Wrenger,
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Lei Z, Wang B, Lu Z, Wang N, Tan H, Zheng J, Jia Z. New regulatory mechanism-based inhibitors of aspartate transcarbamoylase for potential anticancer drug development. FEBS J 2020; 287:3579-3599. [PMID: 31967710 DOI: 10.1111/febs.15220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 11/27/2022]
Abstract
Aspartate transcarbamoylase (ATCase) is a key enzyme which regulates and catalyzes the second step of de novo pyrimidine synthesis in all organisms. Escherichia coli ATCase is a prototypic enzyme regulated by both product feedback and substrate cooperativity, whereas human ATCase is a potential anticancer target. Through structural and biochemical analyses, we revealed that R167/130's loop region in ATCase serves as a gatekeeper for the active site, playing a new and unappreciated regulatory role in the catalytic cycle of ATCase. Based on virtual compound screening simultaneously targeting the new regulatory region and active site of human ATCase, two compounds were identified to exhibit strong inhibition of ATCase activity, proliferation of multiple cancer cell lines, and growth of xenograft tumors. Our work has not only revealed a previously unknown regulatory region of ATCase that helps uncover the catalytic and regulatory mechanism of ATCase, but also successfully guided the identification of new ATCase inhibitors for anticancer drug development using a dual-targeting strategy. DATABASE: Structure data are available in Protein Data Bank under the accession numbers: 6KJ7 (G166P ecATCase), 6KJ8 (G166P ecATCase-holo), 6KJ9 (G128/130A ecATCase), and 6KJA (G128/130A ecATCase-holo).
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Affiliation(s)
- Zhen Lei
- College of Chemistry, Beijing Normal University, China
| | - Biying Wang
- College of Chemistry, Beijing Normal University, China
| | - Zhifang Lu
- College of Chemistry, Beijing Normal University, China
| | - Nan Wang
- College of Chemistry, Beijing Normal University, China.,Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
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Shi D, Allewell NM, Tuchman M. From Genome to Structure and Back Again: A Family Portrait of the Transcarbamylases. Int J Mol Sci 2015; 16:18836-64. [PMID: 26274952 PMCID: PMC4581275 DOI: 10.3390/ijms160818836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Enzymes in the transcarbamylase family catalyze the transfer of a carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate. The two best-characterized members, aspartate transcarbamylase (ATCase) and ornithine transcarbamylase (OTCase), are present in most organisms from bacteria to humans. Recently, structures of four new transcarbamylase members, N-acetyl-l-ornithine transcarbamylase (AOTCase), N-succinyl-l-ornithine transcarbamylase (SOTCase), ygeW encoded transcarbamylase (YTCase) and putrescine transcarbamylase (PTCase) have also been determined. Crystal structures of these enzymes have shown that they have a common overall fold with a trimer as their basic biological unit. The monomer structures share a common CP binding site in their N-terminal domain, but have different second substrate binding sites in their C-terminal domain. The discovery of three new transcarbamylases, l-2,3-diaminopropionate transcarbamylase (DPTCase), l-2,4-diaminobutyrate transcarbamylase (DBTCase) and ureidoglycine transcarbamylase (UGTCase), demonstrates that our knowledge and understanding of the spectrum of the transcarbamylase family is still incomplete. In this review, we summarize studies on the structures and function of transcarbamylases demonstrating how structural information helps to define biological function and how small structural differences govern enzyme specificity. Such information is important for correctly annotating transcarbamylase sequences in the genome databases and for identifying new members of the transcarbamylase family.
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Affiliation(s)
- Dashuang Shi
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
| | - Norma M Allewell
- Department of Cell Biology and Molecular Genetics, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
- Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA.
| | - Mendel Tuchman
- Center for Genetic Medicine Research, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
- Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA.
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Cornish-Bowden A. Understanding allosteric and cooperative interactions in enzymes. FEBS J 2013; 281:621-32. [DOI: 10.1111/febs.12469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/24/2013] [Accepted: 07/30/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Athel Cornish-Bowden
- Unité de Bioénergétique et Ingénierie des Protéines; Institut de Microbiologie de la Méditerranée; Centre National de la Recherche Scientifique and Aix-Marseille Université; France
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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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Ujam OT, Henderson W, Nicholson BK, Fitchett CM. The reactivity of [Pt2(μ-S)2(PPh3)4] towards difunctional chloroacetamide alkylating agents: Formation of cyclized or bridged products. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Houghton SR, Melton J, Fortunak J, Brown Ripin DH, Boddy CN. Rapid, mild method for phosphonate diester hydrolysis: development of a one-pot synthesis of tenofovir disoproxil fumarate from tenofovir diethyl ester. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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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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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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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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