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Prokopowicz M, Jarmuła A, Casamayou-Boucau Y, Gordon F, Ryder A, Sobich J, Maj P, Cieśla J, Zieliński Z, Fita P, Rode W. Advanced Spectroscopy and APBS Modeling for Determination of the Role of His190 and Trp103 in Mouse Thymidylate Synthase Interaction with Selected dUMP Analogues. Int J Mol Sci 2021; 22:2661. [PMID: 33800923 PMCID: PMC7962005 DOI: 10.3390/ijms22052661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
A homo-dimeric enzyme, thymidylate synthase (TS), has been a long-standing molecular target in chemotherapy. To further elucidate properties and interactions with ligands of wild-type mouse thymidylate synthase (mTS) and its two single mutants, H190A and W103G, spectroscopic and theoretical investigations have been employed. In these mutants, histidine at position 190 and tryptophan at position 103 are substituted with alanine and glycine, respectively. Several emission-based spectroscopy methods used in the paper demonstrate an especially important role for Trp 103 in TS ligands binding. In addition, the Advanced Poisson-Boltzmann Solver (APBS) results show considerable differences in the distribution of electrostatic potential around Trp 103, as compared to distributions observed for all remaining Trp residues in the mTS family of structures. Together, spectroscopic and APBS results reveal a possible interplay between Trp 103 and His190, which contributes to a reduction in enzymatic activity in the case of H190A mutation. Comparison of electrostatic potential for mTS complexes, and their mutants, with the substrate, dUMP, and inhibitors, FdUMP and N4-OH-dCMP, suggests its weaker influence on the enzyme-ligand interactions in N4OH-dCMP-mTS compared to dUMP-mTS and FdUMP-mTS complexes. This difference may be crucial for the explanation of the "abortive reaction" inhibitory mechanism of N4OH-dCMP towards TS. In addition, based on structural analyses and the H190A mutant capacity to form a denaturation-resistant complex with N4-OH-dCMP in the mTHF-dependent reaction, His190 is apparently responsible for a strong preference of the enzyme active center for the anti rotamer of the imino inhibitor form.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, MISMaP College, University of Warsaw, ul. Banacha 2C, 02-097 Warsaw, Poland
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Adam Jarmuła
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Yannick Casamayou-Boucau
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Fiona Gordon
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Alan Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, University Road, H91 TK33 Galway, Ireland; (Y.C.-B.); (F.G.); (A.R.)
| | - Justyna Sobich
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Maj
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Joanna Cieśla
- Faculty of Chemistry, Warsaw University of Technology, ul Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Zbigniew Zieliński
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
| | - Piotr Fita
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, ul. Pasteura 5, 02-093 Warsaw, Poland;
| | - Wojciech Rode
- Nencki Institute of Experimental Biology, ul. Pasteura 3, 02-093 Warsaw, Poland; (A.J.); (J.S.); (P.M.); (Z.Z.)
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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Abstract
The antifolates were the first class of antimetabolites to enter the clinics more than 50 years ago. Over the following decades, a full understanding of their mechanisms of action and chemotherapeutic potential evolved along with the mechanisms by which cells develop resistance to these drugs. These principals served as a basis for the subsequent exploration and understanding of the mechanisms of resistance to a variety of diverse antineoplastics with different cellular targets. This section describes the bases for intrinsic and acquired antifolate resistance within the context of the current understanding of the mechanisms of actions and cytotoxic determinants of these agents. This encompasses impaired drug transport into cells, augmented drug export, impaired activation of antifolates through polyglutamylation, augmented hydrolysis of antifolate polyglutamates, increased expression and mutation of target enzymes, and the augmentation of cellular tetrahydrofolate-cofactor pools in cells. This chapter also describes how these insights are being utilized to develop gene therapy approaches to protect normal bone marrow progenitor cells as a strategy to improve the efficacy of bone marrow transplantation. Finally, clinical studies are reviewed that correlate the cellular pharmacology of methotrexate with the clinical outcome in children with neoplastic diseases treated with this antifolate.
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Affiliation(s)
- Rongbao Zhao
- Departments of Medicine and Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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Felder T, Dunlap RB, Dix D, Spencer T. Differences in natural ligand and fluoropyrimidine binding to human thymidylate synthase identified by transient-state spectroscopic and continuous variation methods. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:149-56. [PMID: 12009414 DOI: 10.1016/s0167-4838(02)00289-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Thymidylate synthase (TS) is a central target for the design of chemotherapeutic agents due to its vital role in DNA synthesis. Structural studies of binary complexes between Escherichia coli TS and various nucleotides suggest the chemotherapeutic agent FdUMP and the natural ligand dUMP bind similarly. We show, however, that FdUMP binding to human TS yields a substantially greater decrease in fluorescence than does dUMP. Because the difference in quenching due to ligand binding was approximately two-fold and this difference was not seen when using ecTS, the intriguing result indicated a significant difference in the mode of FdUMP binding to the human enzyme. We compared the binding affinities of dUMP, FdUMP, and TMP to TS from both species and found no significant differences for the individual ligands. Because binding affinities were not different among the ligands, the method of continuous variation was employed to determine binding stoichiometry. Similar to that found for dUMP binding to human and ecTS, FdUMP displayed single site occupancy with both enzymes. These results show that nucleotide binding differences exist for FdUMP and dUMP binding to the human enzyme. The observed differences are not due to differences in stoichiometry or ligand affinity. Therefore, although the crystal structure of human TS with various nucleotide ligands has not been solved, these results show that the differences observed using fluorescence methods result from as yet unidentified differential interactions between the human enzyme and nucleotide ligands.
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Affiliation(s)
- Takita Felder
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
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