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Dasari M, Pelly SC, Geng J, Gold HB, Pribut N, Sharma SK, D’Erasmo MP, Bartsch PW, Sun C, Toti K, Arnold RS, Petros JA, Xu L, Jiang Y, Miller EJ, Liotta DC. Discovery of 5'-Substituted 5-Fluoro-2'-deoxyuridine Monophosphate Analogs: A Novel Class of Thymidylate Synthase Inhibitors. ACS Pharmacol Transl Sci 2023; 6:702-709. [PMID: 37200809 PMCID: PMC10186355 DOI: 10.1021/acsptsci.2c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Indexed: 02/25/2023]
Abstract
5-Fluorouracil and 5-fluorouracil-based prodrugs have been used clinically for decades to treat cancer. Their anticancer effects are most prominently ascribed to inhibition of thymidylate synthase (TS) by metabolite 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP). However, 5-fluorouracil and FdUMP are subject to numerous unfavorable metabolic events that can drive undesired systemic toxicity. Our previous research on antiviral nucleotides suggested that substitution at the nucleoside 5'-carbon imposes conformational restrictions on the corresponding nucleoside monophosphates, rendering them poor substrates for productive intracellular conversion to viral polymerase-inhibiting triphosphate metabolites. Accordingly, we hypothesized that 5'-substituted analogs of FdUMP, which is uniquely active at the monophosphate stage, would inhibit TS while preventing undesirable metabolism. Free energy perturbation-derived relative binding energy calculations suggested that 5'(R)-CH3 and 5'(S)-CF3 FdUMP analogs would maintain TS potency. Herein, we report our computational design strategy, synthesis of 5'-substituted FdUMP analogs, and pharmacological assessment of TS inhibitory activity.
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Affiliation(s)
- Madhuri Dasari
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Stephen C. Pelly
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Jiafeng Geng
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Hannah B. Gold
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Nicole Pribut
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Savita K. Sharma
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Michael P. D’Erasmo
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Perry W. Bartsch
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Carrie Sun
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Kiran Toti
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
| | - Rebecca S. Arnold
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - John A. Petros
- Department
of Urology, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Lingjie Xu
- Junrui
Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Yi Jiang
- Junrui
Biotechnology, Hangzhou, Zhejiang 310000, China
| | - Eric J. Miller
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Dennis C. Liotta
- Department
of Chemistry, Emory University College of
Arts and Sciences, Atlanta, Georgia 30322, United States
- Winship
Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
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Galmés MÀ, Nödling AR, He K, Luk LYP, Świderek K, Moliner V. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chem Sci 2022; 13:4779-4787. [PMID: 35655887 PMCID: PMC9067594 DOI: 10.1039/d2sc00778a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pK a of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach.
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Affiliation(s)
- Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
| | - Alexander R Nödling
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Kaining He
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Louis Y P Luk
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I 12071 Castellón Spain +34 964728070
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
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Zhao LN, Kaldis P. Pairing structural reconstruction with catalytic competence to evaluate the mechanisms of key enzymes in the folate-mediated one-carbon pathway. FEBS J 2022; 290:2279-2291. [PMID: 35303396 DOI: 10.1111/febs.16439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/05/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Mammalian metabolism comprises a series of interlinking pathways that include two major cycles: the folate and methionine cycles. The folate-mediated metabolic cycle uses several oxidation states of tetrahydrofolate to carry activated one-carbon units to be readily used and interconverted within the cell. They are required for nucleotide synthesis, methylation and metabolism, and particularly for proliferation of cancer cells. Based on the latest progress in genome-wide CRISPR loss-of-function viability screening of 789 cell lines, we focus on the most cancer-dependent enzymes in this pathway, especially those that are hyperactivated in cancer, to provide new insight into the chemical basis for cancer drug development. Since the complete 3D structure of several of these enzymes of the one-carbon pathway in their active form are not available, we used homology modelling integrated with the interpretation of the reaction mechanism. In addition, have reconstructed the most likely scenario for the reactions taking place paired with their catalytic competence that provides a testable framework for this pathway.
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Affiliation(s)
- Li Na Zhao
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Philipp Kaldis
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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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] [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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Jiménez‐Grávalos F, Gallegos M, Martín Pendás Á, Novikov AS. Challenging the electrostatic
σ
‐hole picture of halogen bonding using minimal models and the interacting quantum atoms approach. J Comput Chem 2021; 42:676-687. [DOI: 10.1002/jcc.26488] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/10/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Affiliation(s)
| | - Miguel Gallegos
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
| | - Ángel Martín Pendás
- Department of Analytical and Physical Chemistry University of Oviedo Oviedo Spain
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