1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Zhu W, Doubleday PF, Catlin DS, Weerawarna PM, Butrin A, Shen S, Wawrzak Z, Kelleher NL, Liu D, Silverman RB. A Remarkable Difference That One Fluorine Atom Confers on the Mechanisms of Inactivation of Human Ornithine Aminotransferase by Two Cyclohexene Analogues of γ-Aminobutyric Acid. J Am Chem Soc 2020; 142:4892-4903. [PMID: 32114761 DOI: 10.1021/jacs.0c00193] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human ornithine aminotransferase (hOAT), a pyridoxal 5'-phosphate-dependent enzyme, plays a critical role in the progression of hepatocellular carcinoma (HCC). Pharmacological selective inhibition of hOAT has been shown to be a potential therapeutic approach for HCC. Inspired by the discovery of the nonselective aminotransferase inactivator (1R,3S,4S)-3-amino-4-fluoro cyclopentane-1-carboxylic acid (1), in this work, we rationally designed, synthesized, and evaluated a novel series of fluorine-substituted cyclohexene analogues, thereby identifying 8 and 9 as novel selective hOAT time-dependent inhibitors. Intact protein mass spectrometry and protein crystallography demonstrated 8 and 9 as covalent inhibitors of hOAT, which exhibit two distinct inactivation mechanisms resulting from the difference of a single fluorine atom. Interestingly, they share a similar turnover mechanism, according to the mass spectrometry-based analysis of metabolites and fluoride ion release experiments. Molecular dynamics (MD) simulations and electrostatic potential (ESP) charge calculations were conducted, which elucidated the significant influence of the one-fluorine difference on the corresponding intermediates, leading to two totally different inactivation pathways. The novel addition-aromatization inactivation mechanism for 9 contributes to its significantly enhanced potency, along with excellent selectivity over other aminotransferases.
Collapse
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
| | - Daniel S Catlin
- 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
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Sida Shen
- 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
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, LS-CAT, Sector 21, Northwestern University, Lemont, Illinois 60439, United States
| | - 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
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - 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
| |
Collapse
|
4
|
Prognostic value of liver stiffness measurement for the liver-related surgical outcomes of patients under hepatic resection: A meta-analysis. PLoS One 2018; 13:e0190512. [PMID: 29324802 PMCID: PMC5764309 DOI: 10.1371/journal.pone.0190512] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/15/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Previous studies have discussed the liver stiffness measurement (LSM) performance on predicting liver-related surgical outcomes for patients of hepatocellular carcinoma (HCC) under hepatic resection, yet there is much variation in reporting and consistency of findings. Therefore, we report a meta-analysis on this issue. METHODS We comprehensively searched PubMed, Embase, and Web of science to find the eligible cohort studies. The pooled Odds Ratios (OR) and 95% confidence intervals (CIs) were calculated to evaluate effect. The weighted mean LSM value was calculated as the optimal LSM cut-off value among studies. RESULTS 12 prospective cohort studies and one retrospective cohort study, including a total of 1942 cases were identified. The pooled results showed that preoperative LSM is significantly associated with the occurrence of overall postoperative complications (OR 1.76, 95% CI 1.46-2.11). In addition, a weighted mean LSM value of 14.2 kPa and 11.3KPa were suggested as the optimal LSM cut-off value reference using transient elastoqraphy (TE) for predicting overall postoperative complications in Asia countries and European countries, respectively. CONCLUSIONS Preoperative LSM should be taken into account cautiously in the management of patients undergoing hepatectomy of HCC. Future studies could focus on setting a prognostic model integrated with LSM in predicting post-hepatectomy outcomes.
Collapse
|
5
|
Yan H, Li Z, Shen Q, Wang Q, Tian J, Jiang Q, Gao L. Aberrant expression of cell cycle and material metabolism related genes contributes to hepatocellular carcinoma occurrence. Pathol Res Pract 2017; 213:316-321. [PMID: 28238542 DOI: 10.1016/j.prp.2017.01.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/20/2017] [Accepted: 01/22/2017] [Indexed: 12/11/2022]
Abstract
This study aims to deepen our understanding of the molecular mechanism underlying the occurrence of hepatocellular carcinoma (HCC). We first downloaded a gene expression profile dataset GSE29721 (10 HCC and 10 control samples) from Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/). Differentially expressed genes (DEGs) were identified by the paired t-test using limma package. Pathway and functional enrichment analyses were performed with DAVID tools. Transcription factors were annotated with TRANSFAC database and tumor associated genes (TAGs) were annotated with TAG and TSGene databases. Protein-protein interaction (PPI) network was conducted using STRING online tool and function module was further identified with BioNet package. Totally, 527 up-regulated DEGs and 587 down-regulated DEGs were identified. GO functional and KEGG pathway enrichment analyses showed that the up-regulated DEGs were mainly related to cell division and cell cycle, while the down-regulated DEGs were largely related to material metabolism, especially secondary metabolism. Proteins encoded by DEGs CDK1, BUB1, CDC20, NCAPG, NDC80, CDCA8, MAD2L1, CCNB1, CCNA2 and BIRC5 were hub genes with high degrees in the PPI network; further module analysis detected a subnetwork consisting of 55 proteins, such as CYP2B6, ACAA1, BHMT and ALDH2. Taken together, aberrant expression of cell cycle related genes (e.g., CDK1, CCNA2, CCNB1, BUB1, MAD2L1 and CDC20) and material metabolism related genes (e.g., CYP2B6, ACAA1, BHMT and ALDH2) may contribute to HCC occurrence.
Collapse
Affiliation(s)
- Hongxian Yan
- Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China.
| | - Zhaohui Li
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471003, PR China
| | - Quan Shen
- Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China
| | - Qian Wang
- Department of Hepatobiliary Surgery, Henan Cancer Hospital, Zhengzhou, Henan 650000, PR China
| | - Jianguo Tian
- Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China
| | - Qingfeng Jiang
- Department of Hepatobiliary Surgery, Henan Provincial People's Hospital, Zhengzhou, Henan 650000, PR China
| | - Linbo Gao
- Laboratory of Molecular and Translational Medicine, West China Institute of Women and Children's Health, Key Laboratory of Obstetric & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| |
Collapse
|