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Kholodar SA, Lang G, Cortopassi WA, Iizuka Y, Brah HS, Jacobson MP, England PM. Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1. ACS Chem Biol 2021; 16:1159-1163. [PMID: 34165961 DOI: 10.1021/acschembio.1c00326] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nuclear receptor-related 1 protein, Nurr1, is a transcription factor critical for the development and maintenance of dopamine-producing neurons in the substantia nigra pars compacta, a cell population that progressively loses the ability to make dopamine and degenerates in Parkinson's disease. Recently, we demonstrated that Nurr1 binds directly to and is regulated by the endogenous dopamine metabolite 5,6-dihydroxyindole (DHI). Unfortunately, DHI is an unstable compound, and thus a poor tool for studying Nurr1 function. Here, we report that 5-chloroindole, an unreactive analog of DHI, binds directly to the Nurr1 ligand binding domain with micromolar affinity and stimulates the activity of Nurr1, including the transcription of genes governing the synthesis and packaging of dopamine.
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Kholodar SA, Finer-Moore JS, Świderek K, Arafet K, Moliner V, Stroud RM, Kohen A. Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog. Biochemistry 2021; 60:1243-1247. [PMID: 33829766 PMCID: PMC10627423 DOI: 10.1021/acs.biochem.1c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylation of 2-deoxyuridine-5'-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5'-monophosphate (dTMP) proceeds by forming a covalent ternary complex with dUMP and cosubstrate 5,10-methylenetetrahydrofolate. The crystal structure of an analog of this intermediate gives important mechanistic insights but does not explain the half-of-the-sites activity of the enzyme. Recent experiments showed that the C5 proton and the catalytic Cys are eliminated in a concerted manner from the covalent ternary complex to produce a noncovalent bisubstrate intermediate. Here, we report the crystal structure of TSase with a close synthetic analog of this intermediate in which it has partially reacted with the enzyme but in only one protomer, consistent with the half-of-the-sites activity of this enzyme. Quantum mechanics/molecular mechanics simulations confirmed that the analog could undergo catalysis. The crystal structure shows a new water 2.9 Å from the critical C5 of the dUMP moiety, which in conjunction with other residues in the network, may be the elusive general base that abstracts the C5 proton of dUMP during the reaction.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Janet S Finer-Moore
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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Bruning JM, Wang Y, Oltrabella F, Tian B, Kholodar SA, Liu H, Bhattacharya P, Guo S, Holton JM, Fletterick RJ, Jacobson MP, England PM. Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite. Cell Chem Biol 2019; 26:674-685.e6. [PMID: 30853418 PMCID: PMC7185887 DOI: 10.1016/j.chembiol.2019.02.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/06/2018] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson's disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and X-ray crystallography, we show that DHI binds to the ligand-binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson's disease.
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Affiliation(s)
- John M Bruning
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yan Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Francesca Oltrabella
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Boxue Tian
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Svetlana A Kholodar
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Harrison Liu
- Bioengineering Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Paulomi Bhattacharya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - James M Holton
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Robert J Fletterick
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Pamela M England
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.
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Abstract
Thymidylate synthase is an attractive target for antibiotic and anticancer drugs due to its essential role in the de novo biosynthesis of the DNA nucleotide thymine. The enzymatic reaction is initiated by a nucleophilic activation of the substrate via formation of a covalent bond to an active site cysteine. The traditionally accepted mechanism is then followed by a series of covalently bound intermediates, where that bond is only cleaved upon product release. Recent computational and experimental studies suggest that the covalent bond between the protein and substrate is actually quite labile. Importantly, these findings predict the existence of a noncovalently bound bisubstrate intermediate, not previously anticipated, which could be the target of a novel class of drugs inhibiting DNA biosynthesis. Here we report the synthesis of the proposed intermediate and findings supporting its chemical and kinetic competence. These findings substantiate the predicted nontraditional mechanism and the potential of this intermediate as a new drug lead.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
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Kholodar SA, Tombline G, Liu J, Tan Z, Allen CL, Gulick AM, Murkin AS. Alteration of the flexible loop in 1-deoxy-D-xylulose-5-phosphate reductoisomerase boosts enthalpy-driven inhibition by fosmidomycin. Biochemistry 2014; 53:3423-31. [PMID: 24825256 PMCID: PMC4045324 DOI: 10.1021/bi5004074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR),
which catalyzes the first committed step in the 2-C-methyl-d-erythritol 4-phosphate pathway of isoprenoid biosynthesis
used by Mycobacterium tuberculosis and other infectious
microorganisms, is absent in humans and therefore an attractive drug
target. Fosmidomycin is a nanomolar inhibitor of DXR, but despite
great efforts, few analogues with comparable potency have been developed.
DXR contains a strictly conserved residue, Trp203, within a flexible
loop that closes over and interacts with the bound inhibitor. We report
that while mutation to Ala or Gly abolishes activity, mutation to
Phe and Tyr only modestly impacts kcat and Km. Moreover, pre-steady-state kinetics
and primary deuterium kinetic isotope effects indicate that while
turnover is largely limited by product release for the wild-type enzyme,
chemistry is significantly more rate-limiting for W203F and W203Y.
Surprisingly, these mutants are more sensitive to inhibition by fosmidomycin,
resulting in Km/Ki ratios up to 19-fold higher than that of wild-type DXR. In
agreement, isothermal titration calorimetry revealed that fosmidomycin
binds up to 11-fold more tightly to these mutants. Most strikingly,
mutation strongly tips the entropy–enthalpy balance of total
binding energy from 50% to 75% and 91% enthalpy in W203F and W203Y,
respectively. X-ray crystal structures suggest that these enthalpy
differences may be linked to differences in hydrogen bond interactions
involving a water network connecting fosmidomycin’s phosphonate
group to the protein. These results confirm the importance of the
flexible loop, in particular Trp203, in ligand binding and suggest
that improved inhibitor affinity may be obtained against the wild-type
protein by introducing interactions with this loop and/or the surrounding
structured water network.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
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Kholodar SA, Novopashina DS, Meschaninova MI, Venyaminova AG. Multipyrene tandem probes for point mutations detection in DNA. J Nucleic Acids 2013; 2013:860457. [PMID: 24455205 PMCID: PMC3886547 DOI: 10.1155/2013/860457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 11/11/2013] [Indexed: 01/26/2023] Open
Abstract
Here we report design, synthesis and characterization of highly sensitive, specific and stable in biological systems fluorescent probes for point mutation detection in DNA. The tandems of 3'- and 5'-mono- and bis-pyrene conjugated oligo(2'-O-methylribonucleotides), protected by 3'-"inverted" thymidine, were constructed and their potential as new instruments for genetic diagnostics was studied. Novel probes have been shown to exhibit an ability to form stable duplexes with DNA target due to the stabilizing effect of multiple pyrene units at the junction. The relationship between fluorescent properties of developed probes, the number of pyrene residues at the tandem junction, and the location of point mutation has been studied. On the basis of the data obtained, we have chosen the probes possessing the highest fluorescence intensity along with the best mismatch discrimination and deletion and insertion detection ability. Application of developed probes for detection of polymorphism C677T in MTHFR gene has been demonstrated on model systems.
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Affiliation(s)
- Svetlana A. Kholodar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Novosibirsk 630090, Russia
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Kholodar SA, Murkin AS. DXP reductoisomerase: reaction of the substrate in pieces reveals a catalytic role for the nonreacting phosphodianion group. Biochemistry 2013; 52:2302-8. [PMID: 23473304 DOI: 10.1021/bi400092n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of the nonreacting phosphodianion group of 1-deoxy-d-xylulose-5-phosphate (DXP) in catalysis by DXP reductoisomerase (DXR) was investigated for the reaction of the "substrate in pieces". The truncated substrate 1-deoxy-l-erythrulose is converted by DXR to 2-C-methylglycerol with a kcat/Km that is 10(6)-fold lower than that for DXP. Phosphite dianion was found to be a nonessential activator, providing 3.2 kcal/mol of transition state stabilization for the truncated substrate. These results implicate a phosphate-driven conformational change involving loop closure over the DXR active site to generate an environment poised for catalysis.
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Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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Abstract
We report here the design and synthesis of new mono- and bis-pyrene-labeled oligo(2'-O-methylribonucleotide) tandems as perspective probes for SNP detection. The detection strategy is based on the eximer formation when two or more pyrene groups are brought into close proximity upon hybridization of the tandem components with DNA. The potential of SNP detection with tandems of pyrene-labeled oligo(2'-O-methylribonucleotides) by duplex melting curve analysis based on excimer fluorescence registration was demonstrated.
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Affiliation(s)
- Daria S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev ave., Novosibirsk 630090, Russia.
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Kholodar SA, Novopashina DS, Meschaninova MI, Lomzov AA, Venyaminova AG. Multipyrene tandem probes for detection of C677T polymorphism in MTHFR gene. ACTA ACUST UNITED AC 2010:143-4. [PMID: 19749301 DOI: 10.1093/nass/nrp072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We designed tandems of oligo(2'-O-methylribonucleotides) conjugates containing two bispyrene (5'-bisPyr and 3'-bisPyr) groups on their junction for detection of C677T polymorphism in the methylenetetrahydrofolate reductase gene (MHTFR). The potential of SNP detection with multipyrene tandems of oligo(2'-O-methylribonucleotides) was demonstrated.
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Affiliation(s)
- Svetlana A Kholodar
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia.
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