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de Dios SMR, Hass JL, Graham DL, Kumar N, Antony AE, Morton MD, Berkowitz DB. Information-Rich, Dual-Function 13C/ 2H-Isotopic Crosstalk NMR Assay for Human Serine Racemase (hSR) Provides a PLP-Enzyme "Partitioning Fingerprint" and Reveals Disparate Chemotypes for hSR Inhibition. J Am Chem Soc 2023; 145:3158-3174. [PMID: 36696670 PMCID: PMC11103274 DOI: 10.1021/jacs.2c12774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The first dual-function assay for human serine racemase (hSR), the only bona fide racemase in human biology, is reported. The hSR racemization function is essential for neuronal signaling, as the product, d-serine (d-Ser), is a potent N-methyl d-aspartate (NMDA) coagonist, important for learning and memory, with dysfunctional d-Ser-signaling being observed in some neuronal disorders. The second hSR function is β-elimination and gives pyruvate; this activity is elevated in colorectal cancer. This new NMR-based assay allows one to monitor both α-proton-exchange chemistry and β-elimination using only the native l-Ser substrate and hSR and is the most sensitive such assay. The assay judiciously employs segregated dual 13C-labeling and 13C/2H crosstalk, exploiting both the splitting and shielding effects of deuterium. The assay is deployed to screen a 1020-compound library and identifies an indolo-chroman-2,4-dione inhibitor family that displays allosteric site binding behavior (noncompetitive inhibition vs l-Ser substrate; competitive inhibition vs adenosine 5'-triphosphate (ATP)). This assay also reveals important mechanistic information for hSR; namely, that H/D exchange is ∼13-fold faster than racemization, implying that K56 protonates the carbanionic intermediate on the si-face much faster than does S84 on the re-face. Moreover, the 13C NMR peak pattern seen is suggestive of internal return, pointing to K56 as the likely enamine-protonating residue for β-elimination. The 13C/2H-isotopic crosstalk assay has also been applied to the enzyme tryptophan synthase and reveals a dramatically different partition ratio in this active site (β-replacement: si-face protonation ∼6:1 vs β-elimination: si-face protonation ∼1:3.6 for hSR), highlighting the value of this approach for fingerprinting the pyridoxal phosphate (PLP) enzyme mechanism.
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Affiliation(s)
| | | | | | - Nivesh Kumar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Aina E. Antony
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Martha D. Morton
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
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Jiang Z, Wei C, Luo Y, Xiao Y, Wang L, Guo W, Yuan X. Ornithine aminotransferase and carbamoyl phosphate synthetase 1 involved in ammonia metabolism serve as novel targets for early stages of gastric cancer. J Clin Lab Anal 2022; 36:e24692. [PMID: 36098904 PMCID: PMC9551119 DOI: 10.1002/jcla.24692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/24/2022] Open
Abstract
Objective The sensitivity and specificity of current biomarkers for gastric cancer were insufficient. The aim of the present study was to screen novel biomarkers and determine the diagnostic values of ornithine aminotransferase (OAT) and carbamoyl phosphate synthetase 1 (CPS1) for detecting gastric cancer. Methods With stable isotope tags, we labelled an initial discovery group of four paired gastric cancer tissue samples and identified with LC‐ESI‐MS/MS. A validation group of 159 gastric cancer samples and 30 healthy controls were used to validate the candidate targets. GSEA was used to explore the pathways activated in gastric cancer. Results Four hundred and thirty one proteins were found differentially expressed in gastric cancer tissues. Of these proteins, OAT and CPS1 were found over‐expressed in gastric cancer patients, with sensitivity of 70.4% (95% CI: 63.3%–77.6%) and specificity of 80.5% (95% CI: 74.3%–86.7%) for ornithine aminotransferase, and with sensitivity of 68.6% (95% CI: 61.3%–75.8%) and specificity of 73% (95% CI: 66%–79.9%) for carbamoyl phosphate synthetase 1. The co‐expression of OAT and CPS1 in gastric cancer tissues has a sensitivity of 81% (95% CI: 73.2%–88.8%) and specificity of 89% (95% CI: 83%–95%). Furthermore, both OAT and CPS1 were overexpressed in patients with local invasion T3 and T4 stages than those in patients with T1 and T2 stages. The co‐expression of OAT and CPS1 was strongly correlated with histological grade I 68% (95% CI: 58.7%–77.3%) and TNM stage I/II 52% (95% CI: 42%–62%). The areas under ROC curves were up to 0.758 for the co‐expression of OAT and CPS1 in gastric cancer. GSEA results showed that two gene sets and 30 gene sets were activated in OAT high‐ and CPS1 high‐expression patients with gastric cancer, respectively. Conclusions The present findings indicated a tight correlation between the co‐expression of OAT and CPS1 and the histological grade, local invasion, and TNM stages of gastric cancer. Therefore, OAT and CPS1 might be predictors for gastric cancer invasion and potential targets for anticancer drug design for gastric cancer.
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Affiliation(s)
- Zhen Jiang
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Chen Wei
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Yaomin Luo
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Yang Xiao
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
| | - Li Wang
- Research Center for Integrative Medicine, Affiliated Traditional Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Wubin Guo
- Department of General Surgery, the TCM Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiaoxia Yuan
- Department of Biochemistry and Molecular Biology, School of Preclinical Medicine and Forensic Medicine, North Sichuan Medical College, Nanchong, Sichuan Province, China
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Butrin A, Butrin A, Wawrzak Z, Moran GR, Liu D. Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase. J Biol Chem 2022; 298:101969. [PMID: 35460691 PMCID: PMC9136103 DOI: 10.1016/j.jbc.2022.101969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver and occurs predominantly in patients with underlying chronic liver diseases. Over the past decade, human ornithine aminotransferase (hOAT), which is an enzyme that catalyzes the metabolic conversion of ornithine into an intermediate for proline or glutamate synthesis, has been found to be overexpressed in HCC cells. hOAT has since emerged as a promising target for novel anticancer therapies, especially for the ongoing rational design effort to discover mechanism-based inactivators (MBIs). Despite the significance of hOAT in human metabolism and its clinical potential as a drug target against HCC, there are significant knowledge deficits with regard to its catalytic mechanism and structural characteristics. Ongoing MBI design efforts require in-depth knowledge of the enzyme active site, in particular, pKa values of potential nucleophiles and residues necessary for the molecular recognition of ligands. Here, we conducted a study detailing the fundamental active-site properties of hOAT using stopped-flow spectrophotometry and X-ray crystallography. Our results quantitatively revealed the pH dependence of the multistep reaction mechanism and illuminated the roles of ornithine α-amino and δ-amino groups in substrate recognition and in facilitating catalytic turnover. These findings provided insights of the catalytic mechanism that could benefit the rational design of MBIs against hOAT. In addition, substrate recognition and turnover of several fragment-sized alternative substrates of hOATs, which could serve as structural templates for MBI design, were also elucidated.
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Affiliation(s)
- Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Anastassiya Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
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Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB. Turnover and Inactivation Mechanisms for ( S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8689-8703. [PMID: 34097381 PMCID: PMC8367020 DOI: 10.1021/jacs.1c02456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inhibition of human ornithine δ-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
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Affiliation(s)
- Sida Shen
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Mauricio T. Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Glaucio M. Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Neil L. Kelleher
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois, 60611, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
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Zhu W, Doubleday PF, Butrin A, Weerawarna PM, Melani R, Catlin DS, Dwight TA, Liu D, Kelleher NL, Silverman RB. Remarkable and Unexpected Mechanism for ( S)-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8193-8207. [PMID: 34014654 PMCID: PMC8369387 DOI: 10.1021/jacs.1c03572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that was recently found to play an important role in the metabolic reprogramming of hepatocellular carcinoma (HCC) via the proline and glutamine metabolic pathways. The selective inhibition of hOAT by compound 10 exhibited potent in vivo antitumor activity. Inspired by the discovery of the aminotransferase inactivator (1S,3S)-3-amino-4-(difluoromethylene)cyclopentane-1-carboxylic acid (5), we rationally designed, synthesized, and evaluated a series of six-membered-ring analogs. Among them, 14 was identified as a new selective hOAT inactivator, which demonstrated a potency 22× greater than that of 10. Three different types of protein mass spectrometry approaches and two crystallographic approaches were employed to identify the structure of hOAT-14 and the formation of a remarkable final adduct (32') in the active site. These spectral studies reveal an enzyme complex heretofore not observed in a PLP-dependent enzyme, which has covalent bonds to two nearby residues. Crystal soaking experiments and molecular dynamics simulations were carried out to identify the structure of the active-site intermediate 27' and elucidate the order of the two covalent bonds that formed, leading to 32'. The initial covalent reaction of the activated warhead occurs with *Thr322 from the second subunit, followed by a subsequent nucleophilic attack by the catalytic residue Lys292. The turnover mechanism of 14 by hOAT was supported by a mass spectrometric analysis of metabolites and fluoride ion release experiments. This novel mechanism for hOAT with 14 will contribute to the further rational design of selective inactivators and an understanding of potential inactivation mechanisms by aminotransferases.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Pathum M. Weerawarna
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Daniel S. Catlin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Timothy A. Dwight
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Neil L. Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois 60611, United States,Corresponding authors (R.B.S.) . Phone: +1-847-491-5653, (N.L.K.) . Phone: +1-847-467-4362. (D.L.) . Phone: +1-773-508-3093
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