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Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol 2022; 7:1605-1620. [PMID: 36138165 PMCID: PMC9530025 DOI: 10.1038/s41564-022-01226-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Pharmaceuticals have extensive reciprocal interactions with the microbiome, but whether bacterial drug sensitivity and metabolism is driven by pathways conserved in host cells remains unclear. Here we show that anti-cancer fluoropyrimidine drugs inhibit the growth of gut bacterial strains from 6 phyla. In both Escherichia coli and mammalian cells, fluoropyrimidines disrupt pyrimidine metabolism. Proteobacteria and Firmicutes metabolized 5-fluorouracil to its inactive metabolite dihydrofluorouracil, mimicking the major host mechanism for drug clearance. The preTA operon was necessary and sufficient for 5-fluorouracil inactivation by E. coli, exhibited high catalytic efficiency for the reductive reaction, decreased the bioavailability and efficacy of oral fluoropyrimidine treatment in mice and was prevalent in the gut microbiomes of colorectal cancer patients. The conservation of both the targets and enzymes for metabolism of therapeutics across domains highlights the need to distinguish the relative contributions of human and microbial cells to drug efficacy and side-effect profiles.
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Affiliation(s)
- Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Than S Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Ben G H Guthrie
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Patrick H Bradley
- Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Joyce V Lee
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Melamed
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Ysabella Noelle Amora Malig
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Kathy N Lam
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Daryll Gempis
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Moriah Sandy
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wesley Kidder
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Erin L Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Chloe E Atreya
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Alan Venook
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Roy R Gerona
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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In Vitro Assessment of Fluoropyrimidine-Metabolizing Enzymes: Dihydropyrimidine Dehydrogenase, Dihydropyrimidinase, and β-Ureidopropionase. J Clin Med 2020; 9:jcm9082342. [PMID: 32707991 PMCID: PMC7464968 DOI: 10.3390/jcm9082342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/22/2023] Open
Abstract
Fluoropyrimidine drugs (FPs), including 5-fluorouracil, tegafur, capecitabine, and doxifluridine, are among the most widely used anticancer agents in the treatment of solid tumors. However, severe toxicity occurs in approximately 30% of patients following FP administration, emphasizing the importance of predicting the risk of acute toxicity before treatment. Three metabolic enzymes, dihydropyrimidine dehydrogenase (DPD), dihydropyrimidinase (DHP), and β-ureidopropionase (β-UP), degrade FPs; hence, deficiencies in these enzymes, arising from genetic polymorphisms, are involved in severe FP-related toxicity, although the effect of these polymorphisms on in vivo enzymatic activity has not been clarified. Furthermore, the clinical usefulness of current methods for predicting in vivo activity, such as pyrimidine concentrations in blood or urine, is unknown. In vitro tests have been established as advantageous for predicting the in vivo activity of enzyme variants. This is due to several studies that evaluated FP activities after enzyme metabolism using transient expression systems in Escherichia coli or mammalian cells; however, there are no comparative reports of these results. Thus, in this review, we summarized the results of in vitro analyses involving DPD, DHP, and β-UP in an attempt to encourage further comparative studies using these drug types and to aid in the elucidation of their underlying mechanisms.
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Huang YH, Ning ZJ, Huang CY. Crystal structure of dihydropyrimidinase in complex with anticancer drug 5-fluorouracil. Biochem Biophys Res Commun 2019; 519:160-165. [PMID: 31481233 DOI: 10.1016/j.bbrc.2019.08.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/29/2022]
Abstract
Dihydropyrimidinase (DHPase) catalyzes the reversible cyclization of dihydrouracil to N-carbamoyl-β-alanine in the second step of the pyrimidine degradation pathway. Whether 5-fluorouracil (5-FU), the best-known fluoropyrimidine that is used to target the enzyme thymidylate synthase for anticancer therapy, can bind to DHPase remains unknown. In this study, we found that 5-FU can form a stable complex with Pseudomonas aeruginosa DHPase (PaDHPase). The crystal structure of PaDHPase complexed with 5-FU was determined at 1.76 Å resolution (PDB entry 6KLK). Various interactions between 5-FU and PaDHPase were examined. Six residues, namely, His61, Tyr155, Asp316, Cys318, Ser289 and Asn337, of PaDHPase were involved in 5-FU binding. Except for Cys318, these residues are also known as the substrate-binding sites of DHPase. 5-FU interacts with the main chains of residues Ser289 (3.0 Å) and Asn337 (3.2 Å) and the side chains of residues Tyr155 (2.8 Å) and Cys318 (2.9 Å). Mutation at either Tyr155 or Cys318 of PaDHPase caused a low 5-FU binding activity of PaDHPase. This structure and the binding mode provided molecular insights into how the dimetal center in DHPase undergoes a conformational change during 5-FU binding. Further research can directly focus on revisiting the role of DHPase in anticancer therapy.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Zhi-Jun Ning
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan.
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Unexpected cyclization of N-aryl-N-carboxy-ethyl-β-alanines to 5,6-dihydrouracils. Chem Heterocycl Compd (N Y) 2012. [DOI: 10.1007/s10593-012-1105-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
5,6-dihydro-5-fluorouracil (5-DHFU) is a metabolite of the chemotherapy drug 5-fluorouracil (5-FU) of importance for biological studies. 5-DHFU has been prepared by enzymatic reduction of 5-FU and in very low yield by hydrogenation of 5-FU; however, a practical chemical synthesis is not available. Facile racemic syntheses of 5-DHFU from 5-FU or uracil, using p-methoxybenzyl protecting groups followed by L-Selectride reduction, are reported.
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Affiliation(s)
- Andrew L LaFrate
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Liem LK, Choong LHL, Woo KT. Porous graphitic carbon shows promise for the rapid screening partial DPD deficiency in lymphocyte dihydropyrimidine dehydrogenase in Chinese, Indian and Malay in Singapore by using semi-automated HPLC-radioassay. Clin Biochem 2002; 35:181-7. [PMID: 12074825 DOI: 10.1016/s0009-9120(02)00303-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVE Dihydropyrimidine dehydrogenase (DPD) catalyzes the degradation of thymine, uracil, and the chemotherapeutic drug 5-Fluorouracil. In general reverse-phase high pressure liquid chromatography is the standard method for separating 5-[2-(14)C]Fluorouracil and 5-[2-(14)C]Fluoro-5,6-dihydrouracil. However, the use of 100% aqueous solution (as HPLC mobile phase) may collapse the C-18 bonded phase and result in a retention time shift. The aim of this study is to develop a rapid, reproducible, sensitive method for screening partial DPD deficiency in healthy volunteers. DESIGN AND METHODS The activity of DPD was measured using 5-[2- (14)C]Fluorouracil (5-[2-(14)C]FUra) followed by separation of substrate and product 5-[2-(14)C]FUraH(2) with a 15 x 4.6 mm I.D., 5 microm particle size (d(p)) porous graphitic carbon (PGC) column (Hypercarb(R)) and HPLC with online detection of the radioactivity. This was standardized using the protein concentration of the cytosol (NanoOrange(R) Protein Quantitation). RESULTS Complete baseline separation of 5-[2-(14)C]Fluorouracil (5-[2-(14)C]FUra) and 5-[2-(14)C]Fluoro-5,6-dihydrouracil (5-[2-(14)C]FUraH(2)) was achieved using a porous graphitic carbon (PGC) column. The detection limit for 5-[2-(14)C]FUraH(2) was 0.4 pmol. CONCLUSIONS By using linear gradient separation (0.1% Trifluoroacetic acid [TFA] in water to 100% Methanol) protocols in concert with PGC columns (Hypercarb(R)), we have demonstrated that a PGC column has a distinct advantage over C-18 reverse phase columns in terms of column stability (pH 1-14). This method provides an improvement on the specific assay for DPD enzyme activity. It is rapid, reproducible and sensitive and can be used for routine screening for healthy and cancer patients for partial and profound DPD deficiency before treatment with 5- FUra.
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Affiliation(s)
- Lie Kuo Liem
- Donner Laboratory, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Paff MT, Baccanari DP, Davis ST, Cao S, Tansik RL, Rustum YM, Spector T. Preclinical development of eniluracil: enhancing the therapeutic index and dosing convenience of 5-fluorouracil. Invest New Drugs 2000; 18:365-71. [PMID: 11081572 DOI: 10.1023/a:1006401432488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Eniluracil (5-ethynyluracil, GW 776, 776C85) is being developed as a novel modulator of 5-fluorouracil (5-FU) for the treatment of cancer. Eniluracil is an effective mechanism-based inactivator of dihydropyrimidine dehydrogenase (DPD), the first enzyme in the catabolic pathway of 5-FU. By temporarily eliminating this prevalent enzyme, eniluracil provides predictable dosing of 5-FU and enables oral administration of 5-FU to replace intravenous bolus and continuously infused dosing. New DPD is synthesized with a half-life of 2.6 days. It also eliminates the formation of problematic 5-FU catabolites. Most importantly, in laboratory animals, eniluracil increases the therapeutic index and absolute efficacy of 5-FU. Accompanying reports in this journal indicate that eniluracil has promising clinical potential.
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Affiliation(s)
- M T Paff
- Glaxo Wellcome, Inc, Research Triangle Park, NC 27709, USA
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Cao S, Baccanari DP, Rustum YM, Davis ST, Tansik RL, Porter DJ, Spector T. alpha-fluoro-beta-alanine: effects on the antitumor activity and toxicity of 5-fluorouracil. Biochem Pharmacol 2000; 59:953-60. [PMID: 10692560 DOI: 10.1016/s0006-2952(99)00408-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have shown previously that (R)-5-fluoro-5,6-dihydrouracil (FUraH(2)) attenuates the antitumor activity of 5-fluorouracil (FUra) in rats bearing advanced colorectal carcinoma. Presently, we found that alpha-fluoro-beta-alanine (FBAL), the predominant catabolite of FUra that is formed rapidly via FUraH(2), also decreased the antitumor activity and potentiated the toxicity of FUra. In rats treated with Eniluracil (5-ethynyluracil, GW776), excess FBAL, in a 9:1 ratio to FUra, produced similar effects when administered 1 hr before, simultaneously with, or 2 hr after FUra. FBAL also decreased the antitumor activity of FUra in Eniluracil-treated mice bearing MOPC-315 myeloma at a 9:1 ratio with FUra, but not at a 2:1 ratio. FBAL did not affect the antitumor activity of FUra in mice bearing Colon 38 tumors. We also evaluated the effect of thymidylate synthase (TS) and thymidine kinase (TK) from tumor extracts after FUra +/- Eniluracil +/- FBAL treatment. The activity of TK was similar among the three groups at both 18 and 120 hr. There was also no difference in TS inhibition ( approximately 35%) at 18 hr. However, significantly more TS inhibition was observed in the Eniluracil/FUra group than in the FUra-alone group at 120 hr. FBAL did not alter the effect of Eniluracil/FUra in TS inhibition. Neither FUraH(2) nor FBAL affected the IC(50) of FUra in culture. Thus, the effect of FBAL did not result from direct competition with FUra uptake or immediate anabolism. Either another downstream catabolite that is not formed in cell culture is the active agent, or the effect requires the complexity of a living organism or an established tumor.
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Affiliation(s)
- S Cao
- Department of Pharmacology, Grace Cancer Drug Center, Roswell Park Cancer Institute, Buffalo, NY, USA.
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Van Kuilenburg AB, Van Lenthe H, Van Gennip AH. Radiochemical assay for determination of dihydropyrimidinase activity using reversed-phase high-performance liquid chromatography. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 729:307-14. [PMID: 10410956 DOI: 10.1016/s0378-4347(99)00173-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A radiochemical assay was developed to measure the activity of dihydropyrimidinase (DHP) in human liver homogenates. The method is based on the separation of radiolabeled dihydrouracil from N-carbamyl-beta-alanine by HPLC with on-line detection of radioactivity combined with detection of 14CO2 by liquid scintillation counting. The assay was linear with time and protein concentration. The minimum amount of radiolabeled products which could be determined proved to be 12 pmol using a purified stock solution of [2-(14)C]-5,6-dihydrouracil. This highly sensitive assay is especially suitable to identify patients with a dihydropyrimidinase deficiency.
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Affiliation(s)
- A B Van Kuilenburg
- Academic Medical Center, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
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10
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Porter DJ, Harrington JA, Almond MR, Chestnut WG, Tanoury G, Spector T. Enzymatic elimination of fluoride from alpha-fluoro-beta-alanine. Biochem Pharmacol 1995; 50:1475-84. [PMID: 7503799 DOI: 10.1016/0006-2952(95)02053-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Rat liver homogenates catalyzed the elimination of fluoride from (R,S)-alpha-fluoro-beta-alanine. The substrate specificity and physical properties of the defluorinating enzyme were similar to those of mitochondrial L-alanine-glyoxylate aminotransferase II (EC 2.6.1.44, AlaAT-II). Furthermore, AlaAT-II activity, measured with L-alanine and glyoxylate as substrates, copurified with the alpha-fluoro-beta-alanine-defluorinating enzyme. The NH2-terminal sequence (18 residues) of the enzyme did not show significant sequence similarity with any of the proteins currently listed in GenBank. The purified enzyme catalyzed the transamination of L-alanine (Ala) and glyoxylate (glyx) at pH 8.5 by a ping-pong mechanism with kinetic parameters of kcat = 17 sec-1, KL-Ala = 3.2 mM, and Kglyx = 0.3 mM, respectively. The kinetic parameters for the defluorination of (R)-alpha-fluoro-beta-alanine and (S)-alpha-fluoro-beta-alanine were kcat = 6.2 and 2.6 min-1, respectively, and Km = 2.7 and 0.88 mM, respectively. L-Alanine potently inhibited the defluorination reaction with an apparent Ki of 0.024 mM. (R,S)-alpha-Fluoro-beta-alanine converted the optical spectrum of the enzyme-bound cofactor from the pyridoxal form to the pyridoxamino form, which indicated that this cofactor may participate in the defluorination reaction. The product of the enzymatic reaction, malonic semialdehyde, reacted nonenzymatically with (R,S)-alpha-fluoro-beta-alanine to form an adduct that was detected spectrally. AlaAT-II was not inactivated during dehalogenation of (R,S)-alpha-fluoro-beta-alanine but was inactivated completely during dehalogenation of beta-chloro-L-alanine.
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Affiliation(s)
- D J Porter
- Division of Experimental Therapy, Wellcome Research Laboratories, Research Triangle Park, NC 27709, USA
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