A Fatal Combination: A Thymidylate Synthase Inhibitor with DNA Damaging Activity

2′-deoxy-5-ethynyluridine (EdU) has been previously shown to be a cell poison whose toxicity depends on the particular cell line. The reason is not known. Our data indicates that different efficiency of EdU incorporation plays an important role. The EdU-mediated toxicity was elevated by the inhibition of 2′-deoxythymidine 5′-monophosphate synthesis. EdU incorporation resulted in abnormalities of the cell cycle including the slowdown of the S phase and a decrease in DNA synthesis. The slowdown but not the cessation of the first cell division after EdU administration was observed in all of the tested cell lines. In HeLa cells, a 10 μM EdU concentration led to the cell death in the 100% of cells probably due to the activation of an intra S phase checkpoint in the subsequent S phase. Our data also indicates that this EdU concentration induces interstrand DNA crosslinks in HeLa cells. We suppose that these crosslinks are the primary DNA damage resulting in cell death. According to our results, the EdU-mediated toxicity is further increased by the inhibition of thymidylate synthase by EdU itself at its higher concentrations.     

Polymorphism of the Thymidylate Synthase Gene and Thymidylate Synthase Levels in Colon Cancer Cell Lines and Different Tissues of Colorectal Cancer Patients

In a panel of 18 colon cancer cell lines we found that the thymidylate synthase (TS) genotype was related to TS enzyme activity, but not to TS protein and mRNA levels. In addition, no relation with drug sensitivity was observed. TS genotyping of different tissues from 78 colorectal cancer patients revealed a high level of homology in polymorphic status between normal and malignant tissues and the heterozygous genotype to be the most frequent.     

Thymidylate Synthase Polymorphism and Microsatellite Instability: Association in Colorectal Cancer

5‐Fluorouracil (5FU) is the main drug used for the treatment of colorectal cancer (CRC) and Thymidilate Synthase (TS) is its target enzyme. TS gene has regulatory tandemly repeated sequences in its 5′ and 3′untraslated region (5′–3′ UTR). CRC often shows a kind of genomic instability called Microsatellite Instability (MSI) that is associated with TS levels and survival. Our data show that the genotype 2R/2R (homozygosity for 2 tandem repeat sequences in the 5′UTR) is more frequently associated with MSI + and lower TS levels. More over we did not find any significant association between the 2R/3R (heterozygosity for 2 and 3 tandem repeat sequences in the 5′UTR) and 3R/3R (homozygosity for 3 tandem repeat sequences in the 5′ UTR) genotypes with the MSI + and MSI ?, while these genotypes were associated with a higher TS expression. As a consequence we can hypothesise that patients bearing CRC with the MSI +, the 2R/2R genotype and with low TS levels could have a better prognosis and they could not be drug resistant.     

Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine

Varicella zoster virus (VZV) is a highly infectious human herpesvirus that is the causative agent for chicken pox and shingles. VZV encodes a functional thymidylate synthase (TS), which is the sole enzyme that produces dTMP from dUMP de novo. To study substrate binding, the complex structure of TS_VZV with dUMP was determined to a resolution of 2.9 Å. In the absence of a folate co-substrate, dUMP binds in the conserved TS active site and is coordinated similarly as in the human encoded TS (TS_HS) in an open conformation. The interactions between TS_VZV with dUMP and a cofactor analog, raltitrexed, were also studied using differential scanning fluorimetry (DSF), suggesting that TS_VZV binds dUMP and raltitrexed in a sequential binding mode like other TS. The DSF also revealed interactions between TS_VZV and in vitro phosphorylated brivudine (BVDU_P), a highly potent anti-herpesvirus drug against VZV infections. The binding of BVDU_P to TS_VZV was further confirmed by the complex structure of TS_VZV and BVDU_P solved at a resolution of 2.9 Å. BVDU_P binds similarly as dUMP in the TS_HS but it induces a closed conformation of the active site. The structure supports that the 5-bromovinyl substituent on BVDU_P is likely to inhibit TS_VZV by preventing the transfer of a methylene group from its cofactor and the subsequent formation of dTMP. The interactions between TS_VZV and BVDU_P are consistent with that TS_VZV is indeed a target of brivudine in vivo. The work also provided the structural basis for rational design of more specific TS_VZV inhibitors.     

An Innovative Strategy for Dual Inhibitor Design and Its Application in Dual Inhibition of Human Thymidylate Synthase and Dihydrofolate Reductase Enzymes

Due to the diligence of inherent redundancy and robustness in many biological networks and pathways, multitarget inhibitors present a new prospect in the pharmaceutical industry for treatment of complex diseases. Nevertheless, to design multitarget inhibitors is concurrently a great challenge for medicinal chemists. We have developed a novel computational approach by integrating the affinity predictions from structure-based virtual screening with dual ligand-based pharmacophore to discover potential dual inhibitors of human Thymidylate synthase (hTS) and human dihydrofolate reductase (hDHFR). These are the key enzymes in folate metabolic pathway that is necessary for the biosynthesis of RNA, DNA, and protein. Their inhibition has found clinical utility as antitumor, antimicrobial, and antiprotozoal agents. A druglike database was utilized to perform dual-target docking studies. Hits identified through docking experiments were mapped over a dual pharmacophore which was developed from experimentally known dual inhibitors of hTS and hDHFR. Pharmacophore mapping procedure helped us in eliminating the compounds which do not possess basic chemical features necessary for dual inhibition. Finally, three structurally diverse hit compounds that showed key interactions at both active sites, mapped well upon the dual pharmacophore, and exhibited lowest binding energies were regarded as possible dual inhibitors of hTS and hDHFR. Furthermore, optimization studies were performed for final dual hit compound and eight optimized dual hits demonstrating excellent binding features at target systems were also regarded as possible dual inhibitors of hTS and hDHFR. In general, the strategy used in the current study could be a promising computational approach and may be generally applicable to other dual target drug designs.     

A New Look at the Molecular Mechanism of Thymidylate Synthase and Its Interaction with Nucleotide Analogues

Abstract

The increasing availability of the crystal structures of a variety of complexes of thymidylate synthase¹ (TS) and its mutants with nucleotide and folate analogues, has greatly advanced our understanding of the mechanism of catalysis, and the detailed interaction of the enzyme with inhibitors.     

Synthesis and Cytotoxic Activity of Selenophenfurin,a New Inhibitor of IMP Dehydrogenase

Abstract

The synthesis of 5-β-D-ribofuranosylselenophene-3-carboxamide (selenophenfurin) is reported. Selenophenfurin was found active as cytotoxic agent and as inosine monophosphate dehydrogenase inhibitor.     

ATP合成酶的结合变化机制和旋转催化——1997年诺贝尔化学奖的部分工作介绍

保罗.博耶(P.D.Boyer)教授为阐明ATP酶作用机制所提出的结合变化机制有两个基本要点：一是ATP合成所需要的能量原则上是用于促进酶上紧密结合的ATP的释放和无机磷、ADP的结合;二是在净ATP形成过程中,酶上的各催化部位是高度协同地顺序起作用的.γ亚基在F₁-ATP酶中的旋转运动使三个催化部位构象不对称是实现结合变化的基础.高分辨率牛心线粒体F₁-ATP酶的晶体结构发表以后,出现了一些支持旋转催化机制的直接实验证据.     

Dynamic Modulation of Thymidylate Synthase Gene Expression and Fluorouracil Sensitivity in Human Colorectal Cancer Cells

Biomarkers have revolutionized cancer chemotherapy. However, many biomarker candidates are still in debate. In addition to clinical studies, a priori experimental approaches are needed. Thymidylate synthase (TS) expression is a long-standing candidate as a biomarker for 5-fluorouracil (5-FU) treatment of cancer patients. Using the Tet-OFF system and a human colorectal cancer cell line, DLD-1, we first constructed an in vitro system in which TS expression is dynamically controllable. Quantitative assays have elucidated that TS expression in the transformant was widely modulated, and that the dynamic range covered 15-fold of the basal level. 5-FU sensitivity of the transformant cells significantly increased in response to downregulated TS expression, although being not examined in the full dynamic range because of the doxycycline toxicity. Intriguingly, our in vitro data suggest that there is a linear relationship between TS expression and the 5-FU sensitivity in cells. Data obtained in a mouse model using transformant xenografts were highly parallel to those obtained in vitro. Thus, our in vitro and in vivo observations suggest that TS expression is a determinant of 5-FU sensitivity in cells, at least in this specific genetic background, and, therefore, support the possibility of TS expression as a biomarker for 5-FU-based cancer chemotherapy.     

Thymidylate synthetase. Catalysis of dehalogenation of 5-bromo- and 5-iodo-2'-deoxyuridylate.

Tymidylate synthetase catalyzes the facile dehalogenation of 5-bromo-2'-deoxyuridylate (BrdUMP) and 5-iodo-2'-deoxyuridylate )IdUMP) to give 2'-deoxyuridylate (dUMP), the natural substrate of the enzyme. The reaction does not require folate cofactors and stoichiometrically consumes 2 equiv of thiol. In addition to dUMP, a minor product is formed during the debromination of BrdUMP which has been identified as a 5-alkylthio derivative formed by displacement of bromide ion by thiolate. The reaction has been found to proceed with a substantial alpha-secondary inverse tritium isotope effect (kT/kH = 1.212--1.258) with [2-14C,6-3H]-BrdUMP as the substrate. Similarly, an inverse tritiumisotope effect of 1.18 was observed in the nonenzymatic chemical counterpart of this reaction, the cysteine-promoted dehalogenation of [2-14C,6-3H]-5-bromo-2'-deoxyuridine. Previous evidence for the mechanism of action of this enzyme has rested largely on chemical model studies and on information obtained from its stoichiometric interaction with the inhibitor 5-fluoro-2'-deoxyuridylate. The magnitude of the secondary isotope effect during the enzymatic dehalogenation described here provides direct proof for nucleophilic catalysis and formation of 5,6-dihydroprimidine intermediates in a reaction catalyzed by thymidylate synthetase.     

Flavonoids and Melanins: A Common Strategy across Two Kingdoms

Ultraviolet (UV) radiations alter a number of metabolic functions in vivant. They produce damages to lipids, nucleic acids and proteins, generating reactive oxygen species such as singlet oxygen (O₂), hydroxyl radical (HO) and superoxide anion (O₂^-). Plants and animals, after their water emersion, have developed biochemical mechanisms to protect themselves from that environmental threat through a common strategy. Melanins in animals and flavonoids in plants are antioxidant pigments acting as free radical scavenging mechanisms. Both are phenol compounds constitutively synthesized and enhanced after exposure to UV rays, often conferring a red-brown-dark tissue pigmentation.Noteworthy, beside anti-oxidant scavenging activity, melanins and flavonoids have acquired secondary functions that, both in plants and animals, concern reproductions and fitness. Plants highly pigmented are more resistant to biotic and abiotic stresses. Darker wild vertebrates are generally more aggressive, sexually active and resistant to stress than lighter individuals. Flavonoids have been associated with signal attraction between flowers and insects and with plant-plant interaction. Melanin pigmentation has been proposed as trait in bird communication, acting as honest signals of quality.This review shows how the molecular mechanisms leading to tissue pigmentation have many functional analogies between plants and animals and how their origin lies in simpler organisms such as Cyanobacteria. Comparative studies between plant and animal kingdoms can reveal new insight of the antioxidant strategies in vivant.     

ATP合成酶的结合变化机制和旋转催化──1997年诺贝尔化学奖的部分工作介绍

保罗博耶（Ｐ．Ｄ．Ｂｏｙｅｒ）教授为阐明ＡＴＰ酶作用机制所提出的结合变化机制有两个基本要点：一是ＡＴＰ合成所需要的能量原则上是用于促进酶上紧密结合的ＡＴＰ的释放和无机磷、ＡＤＰ的结合;二是在净ＡＴＰ形成过程中,酶上的各催化部位是高度协同地顺序起作用的．γ亚基在Ｆ１ＡＴＰ酶中的旋转运动使三个催化部位构象不对称是实现结合变化的基础．高分辨率牛心线粒体Ｆ１ＡＴＰ酶的晶体结构发表以后,出现了一些支持旋转催化机制的直接实验证据     

Length Polymorphism of Thymidylate Synthase Regulatory Region in Chinese Populations and Evolution of the Novel Alleles

The tandemly repeated 28-bp sequence in the 5-terminal regulatory region of human thymidylate synthase (TSER), which has been reported to be polymorphic in different populations, was surveyed in 668 Chinese from 9 Han groups, 8 ethnic populations, and 36 individuals representing a three-generation pedigree. Amplified fragments were separated by electrophoresis on 4% agarose gel. In addition to the reported double and triple repeats of the 28-bp sequence in TSER, we also detected a novel quintuple repeat in this region. The transient expression activity of TSER with the quintuple repeat is almost the same as that of the reported TSER with the triple repeat. All three alleles of the repeat type (2, 3, and 5) were further confirmed by sequencing. The frequencies of the TSER allele 2 and 3 were 18.82 and 81% in totally unrelated Chinese samples, respectively, while the frequency of allele 3 was variable in different Chinese populations with a range from 62 to 95%. On the basis of the sequences of the different alleles, the existence of the tandem repeats in each allele might be explained by slipped-strand mispairing during DNA replication.     

Nucleoside and Nucleotide Inhibitors of Inosine Monophosphate (IMP) Dehydrogenase as Potential Antitumor Inhibitors

Abstract

A review of various nucleoside and nucleotide inhibitors of IMP dehydrogenase suggests that such inhibitors may also exhibit significant antitumor effects. The details of the precise mode of action and structure activity relationships remain to be established. This new area of research should prove fruitful for uncovering useful and more specific antitumor agents.     

A Link between Hinge-Bending Domain Motions and the Temperature Dependence of Catalysis in 3-Isopropylmalate Dehydrogenase

Enzyme function depends on specific conformational motions. We show that the temperature dependence of enzyme kinetic parameters can provide insight into these functionally relevant motions. While investigating the catalytic properties of IPMDH from Escherichia coli, we found that its catalytic efficiency (k_cat/K_M,IPM) for the substrate IPM has an unusual temperature dependence, showing a local minimum at ∼35°C. In search of an explanation, we measured the individual constants k_cat and K_M,IPM as a function of temperature, and found that the van 't Hoff plot of K_M,IPM shows sigmoid-like transition in the 20-40°C temperature range. By means of various measurements including hydrogen-deuterium exchange and fluorescence resonance energy transfer, we showed that the conformational fluctuations, including hinge-bending domain motions increase more steeply with temperatures >30°C. The thermodynamic parameters of ligand binding determined by isothermal titration calorimetry as a function of temperature were found to be strongly correlated to the conformational fluctuations of the enzyme. Because the binding of IPM is associated with a hinge-bending domain closure, the more intense hinge-bending fluctuations at higher temperatures increasingly interfere with IPM binding, thereby abruptly increasing its dissociation constant and leading to the observed unusual temperature dependence of the catalytic efficiency.     

Function and Regulation of Isoforms of Carbon Monoxide Dehydrogenase/Acetyl Coenzyme A Synthase in Methanosarcina acetivorans

Conversion of acetate to methane (aceticlastic methanogenesis) is an ecologically important process carried out exclusively by methanogenic archaea. An important enzyme for this process as well as for methanogenic growth on carbon monoxide is the five-subunit archaeal CO dehydrogenase/acetyl coenzyme A (CoA) synthase multienzyme complex (CODH/ACS) catalyzing both CO oxidation/CO(2) reduction and cleavage/synthesis of acetyl-CoA. Methanosarcina acetivorans C2A contains two very similar copies of a six-gene operon (cdh genes) encoding two isoforms of CODH/ACS (Cdh1 and Cdh2) and a single CdhA subunit, CdhA3. To address the role of the CODH/ACS system in M. acetivorans, mutational as well as promoter/reporter gene fusion analyses were conducted. Phenotypic characterization of cdh disruption mutants (three single and double mutants, as well as the triple mutant) revealed a strict requirement of either Cdh1 or Cdh2 for acetotrophic or carboxidotrophic growth, as well as for autotrophy, which demonstrated that both isoforms are bona fide CODH/ACS. While expression of the Cdh2-encoding genes was generally higher than that of genes encoding Cdh1, both appeared to be regulated differentially in response to growth phase and to changing substrate conditions. While dispensable for growth, CdhA3 clearly affected expression of cdh1, suggesting that it functions in signal perception and transduction rather than in catabolism. The data obtained argue for a functional hierarchy and regulatory cross talk of the CODH/ACS isoforms.     

Structure of the TSC2 GAP Domain: Mechanistic Insight into Catalysis and Pathogenic Mutations

1. Download : Download high-res image (277KB)
2. Download : Download full-size image

     

Thymidylate Synthase in Plant Cells: Kinetic and Molecular Properties of the Enzyme from Daucus carota L. Cell Cultures

Thymidylate synthase activity was assayed in cell homogenatesfrom wild or domestic carrot (Daucus carota L.) suspension culturesusing the tritium-release method. The specific activity measuredwas lower than that previously reported for bacterial extracts,and its level did not change a great deal during a 14 day growthcycle. The enzyme was partially purified (about 9 fold) by ammoniumsulfate fractionation and ion-exchange chromatography. Kineticparameters such as pH optimum, K_m values for substrate and cofactor,and degree of inhibition by 5-fluoro-2'-deoxyuridine monophosphatewere characterized. The apparent mol wt, evaluated by gel-filtration chromatography,was 185 kDa, which was much higher than that reported for enzymesof bacterial and vertebrate origins and somewhat higher thanthat reported for the thymidylate synthase-dihydrofolate reductasebifunctional polypeptide of some protozoa. (Received April 20, 1987; Accepted February 15, 1988)