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Molecular Mechanism of Thymidylate Synthase Inhibition by N 4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies. Int J Mol Sci 2021; 22:ijms22094758. [PMID: 33946210 PMCID: PMC8125507 DOI: 10.3390/ijms22094758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
Novel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N4-hydroxy-dCMP (N4-OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N4-OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N4-OH-dCMP and N5,10-methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C(5) methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS (cf. PDB ID: 4EZ8), and with conclusions based on the present structure of the parasitic nematode Trichinella spiralis, both co-crystallized with N4-OH-dCMP and N5,10-methylenetetrahdrofolate. The crystal structure of the mouse TS-N4-OH-dCMP complex soaked with N5,10-methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one-carbon group bound to the N(10) atom, thus too distant from the pyrimidine C(5) atom to enable the electrophilic attack and methylene group transfer.
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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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Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase. Sci Rep 2020; 10:10404. [PMID: 32591631 PMCID: PMC7320145 DOI: 10.1038/s41598-020-67079-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/21/2020] [Indexed: 01/06/2023] Open
Abstract
Substrate channeling studies have frequently failed to provide conclusive results due to poor understanding of this subtle phenomenon. We analyzed the mechanism of NADH-channeling from D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to L-lactate Dehydrogenase (LDH) using enzymes from different cells. Enzyme kinetics studies showed that LDH activity with free NADH and GAPDH-NADH complex always take place in parallel. The channeling is observed only in assays that mimic cytosolic conditions where free NADH concentration is negligible and the GAPDH-NADH complex is dominant. Molecular dynamics and protein-protein interaction studies showed that LDH and GAPDH can form a leaky channeling complex only at the limiting NADH concentrations. Surface calculations showed that positive electric field between the NAD(H) binding sites on LDH and GAPDH tetramers can merge in the LDH-GAPDH complex. NAD(H)-channeling within the LDH-GAPDH complex can be an extension of NAD(H)-channeling within each tetramer. In the case of a transient LDH-(GAPDH-NADH) complex, the relative contribution from the channeled and the diffusive paths depends on the overlap between the off-rates for the LDH-(GAPDH-NADH) complex and the GAPDH-NADH complex. Molecular evolution or metabolic engineering protocols can exploit substrate channeling for metabolic flux control by fine-tuning substrate-binding affinity for the key enzymes in the competing reaction paths.
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Chionh YT, Cui J, Koh J, Mendenhall IH, Ng JHJ, Low D, Itahana K, Irving AT, Wang LF. High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress. Cell Stress Chaperones 2019; 24:835-849. [PMID: 31230214 PMCID: PMC6629734 DOI: 10.1007/s12192-019-01013-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/29/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023] Open
Abstract
Bats, unique among mammals with powered flight, have many species with the longest size-proportionate lifespan of all mammals. Evolutionary adaptations would have been required to survive the elevated body temperatures during flight. Heat shock protein (HSP), highly conserved master regulators of cell stress, expression was examined across tissues and various cell lines in bats. Basal expression level of major HSPs (HSP70 and HSP90) is significantly higher in two different bat species compared to other mammals. This HSP expression could be a bat-unique, key factor to modulate cellular stress and death. Consequently, bat cells survive prolonged heat treatment, along with other stress stimuli, in a HSP-dependent manner, whereas other mammalian cells succumbed. This suggests HSP expression in bats could be an important adaption to intrinsic metabolic stresses like flight and therefore an important model to study stress resilience and longevity in general.
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Affiliation(s)
- Yok Teng Chionh
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jie Cui
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Javier Koh
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Justin H J Ng
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Dolyce Low
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Koji Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Aaron T Irving
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Lin-Fa Wang
- Programme in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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Lopez-Zavala AA, Guevara-Hernandez E, Vazquez-Lujan LH, Sanchez-Paz A, Garcia-Orozco KD, Contreras-Vergara CA, Lopez-Leal G, Arvizu-Flores AA, Ochoa-Leyva A, Sotelo-Mundo RR. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites. PeerJ 2018; 6:e5023. [PMID: 29922516 PMCID: PMC6005164 DOI: 10.7717/peerj.5023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.,Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Eduardo Guevara-Hernandez
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Luz H Vazquez-Lujan
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Arturo Sanchez-Paz
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biologicas del Noroeste, Hermosillo, Sonora, Mexico
| | - Karina D Garcia-Orozco
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Carmen A Contreras-Vergara
- Laboratorio de Genetica de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Gamaliel Lopez-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
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Panecka-Hofman J, Pöhner I, Spyrakis F, Zeppelin T, Di Pisa F, Dello Iacono L, Bonucci A, Quotadamo A, Venturelli A, Mangani S, Costi M, Wade RC. Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors. Biochim Biophys Acta Gen Subj 2017; 1861:3215-3230. [DOI: 10.1016/j.bbagen.2017.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 01/06/2023]
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Jarmuła A, Wilk P, Maj P, Ludwiczak J, Dowierciał A, Banaszak K, Rypniewski W, Cieśla J, Dąbrowska M, Frączyk T, Bronowska AK, Jakowiecki J, Filipek S, Rode W. Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics simulations in search for nematode-specific inhibitors of TS. J Mol Graph Model 2017; 77:33-50. [PMID: 28826032 DOI: 10.1016/j.jmgm.2017.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 01/01/2023]
Abstract
Three crystal structures are presented of nematode thymidylate synthases (TS), including Caenorhabditis elegans (Ce) enzyme without ligands and its ternary complex with dUMP and Raltitrexed, and binary complex of Trichinella spiralis (Ts) enzyme with dUMP. In search of differences potentially relevant for the development of species-specific inhibitors of the nematode enzyme, a comparison was made of the present Ce and Ts enzyme structures, as well as binary complex of Ce enzyme with dUMP, with the corresponding mammalian (human, mouse and rat) enzyme crystal structures. To complement the comparison, tCONCOORD computations were performed to evaluate dynamic behaviors of mammalian and nematode TS structures. Finally, comparative molecular docking combined with molecular dynamics and free energy of binding calculations were carried out to search for ligands showing selective affinity to T. spiralis TS. Despite an overall strong similarity in structure and dynamics of nematode vs mammalian TSs, a pool of ligands demonstrating predictively a strong and selective binding to TsTS has been delimited. These compounds, the E63 family, locate in the dimerization interface of TsTS where they exert species-specific interactions with certain non-conserved residues, including hydrogen bonds with Thr174 and hydrophobic contacts with Phe192, Cys191 and Tyr152. The E63 family of ligands opens the possibility of future development of selective inhibitors of TsTS and effective agents against trichinellosis.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland.
| | - Piotr Wilk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Macromolecular Crystallography (BESSY-MX), Berlin, Germany
| | - Piotr Maj
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Jan Ludwiczak
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland; Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Anna Dowierciał
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Cieśla
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Magdalena Dąbrowska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | - Tomasz Frączyk
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
| | | | | | | | - Wojciech Rode
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warszawa, Poland
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