5-Fluoro-2'-deoxycytidine 5'-monophosphate is a mechanism-based inhibitor of thymidylate synthase

Chemistry of Fluorinated Pyrimidines in the Era of Personalized Medicine

We review developments in fluorine chemistry contributing to the more precise use of fluorinated pyrimidines (FPs) to treat cancer. 5-Fluorouracil (5-FU) is the most widely used FP and is used to treat > 2 million cancer patients each year. We review methods for 5-FU synthesis, including the incorporation of radioactive and stable isotopes to study 5-FU metabolism and biodistribution. We also review methods for preparing RNA and DNA substituted with FPs for biophysical and mechanistic studies. New insights into how FPs perturb nucleic acid structure and dynamics has resulted from both computational and experimental studies, and we summarize recent results. Beyond the well-established role for inhibiting thymidylate synthase (TS) by the 5-FU metabolite 5-fluoro-2′-deoxyuridine-5′-O-monophosphate (FdUMP), recent studies have implicated new roles for RNA modifying enzymes that are inhibited by 5-FU substitution including tRNA methyltransferase 2 homolog A (TRMT2A) and pseudouridylate synthase in 5-FU cytotoxicity. Furthermore, enzymes not previously implicated in FP activity, including DNA topoisomerase 1 (Top1), were established as mediating FP anti-tumor activity. We review recent literature summarizing the mechanisms by which 5-FU inhibits RNA- and DNA-modifying enzymes and describe the use of polymeric FPs that may enable the more precise use of FPs for cancer treatment in the era of personalized medicine.

Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology

The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A₁ ) and 5-chlorodeoxyuridine (T₁ ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A₁ , T₁ , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A₁ , T₁ , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.

Life on the salvage path: the deoxynucleoside kinase of Lactobacillus acidophilus R-26

In Lactobacillus acidophilus R-26, the synthesis of DNA precursor deoxynucleotides occurs exclusively by salvage of deoxynucleosides, beginning with phosphorylation by four deoxynucleoside kinases. Subunits bearing three of these activities are uniquely organized into two heterodimers, deoxyadenosine/deoxycytidine kinase (dAK/dCK) and deoxyadenosine/deoxyguanosine kinase (dAK/dGK), which, along with a distinct deoxythymidine kinase (TK), catalyze the parallel first committed steps of dNTP biosynthesis. Whereas TK is common to most prokaryotes (and eukaryotes), the other three activities that are the emphasis of this review are quite unusual in bacteria. Each activity is regulated in cis by its homologous end-product (dNTP) which is understood to act as a multisubstrate inhibitor capable of binding to both nucleoside and phosphate subsites. Conversely, the inactive dAK subunit is progressively activated by 1) association with a dGK or dCK subunit and 2) the conformationally driven heterotropic affect of dGuo or dCyd bound to the opposing subunit. Limited proteolysis has proven to be a powerful probe of conformational states. Further indication of conformational or structural differences between dAK and dGK (or dCK) is that the former follows an ordered kinetic path, while dGK or dCK exhibits rapid-equilibrium random kinetics. The multi-substrate behavior of end-product binding provides a convenient new diagnostic tool for distinguishing kinetic mechanisms. Tandem dak-dgk genes have been cloned from Lactobacillus DNA and expressed in Escherichia coli as dAK/dGK, utilizing the associated promoter. Sequence alignments reveal 65% identity in their DNA and 61% in their derived amino acid sequences. Encoded N-terminal sequences are identical for the first 18 residues, and both subunits share conserved sequences in common with adenylate kinase and viral TK. A more unusual conserved element, which appears to play a role in the activation of dAK, resembles the G2 loop of p21 ras. Remarkably, no homologous gene(s) for the dAK/dCK pair could be found. Comparisons of amino acid sequences, isoelectric pHs and subunit masses strongly indicated that native dCK and dGK are identical in sequence, except at their extreme N-termini (M-IVL for dCK and -TVIVL for dGK), suggesting that processing of a common precursor occurs in Lactobacillus. Accordingly, deletion of codons 2 and 3 from dgk resulted in the expression of dAK/dCK in the E. coli host; its kinetic properties are indistinguishable from those of native dAK/dCK. Subcloning the dgk or engineered dck gene resulted in expression of active dGK or dCK homodimers, each with a virtually unchanged Km toward its primary deoxynucleoside. However, in common with human dCK, dCK (or dGK) homodimer exhibits secondary activities with much larger Kms towards dAdo and dGuo (or dCyd). dCTP (or dGTP) is the best inhibitor of all three activities of the respective homodimer. Fully active heterodimers can be reconstituted simply by mixing a homodimer with independently expressed (inactive) dAK.

Thymidylate synthase inhibition: a structure-based rationale for drug design

Thymidylate synthase (TS) is a very interesting target in antiproliferative diseases. Its inhibition causes thimineless death of the cells and compounds inhibiting TS are widely used in anticancer therapy. The classical antifolate TS inhibitors are structural analogs of the folate cofactor; they often share the same metabolic pathways and this causes the development of resistance inside the cells. A detailed analysis of the available x-ray crystal structures of the complexes of the enzyme with different substrates and inhibitors support the finding of a structural basis of their biological activity. TS inhibitors nonstructural analog of folate, non-analog antifolate inhibitors (NAAI), are welcome as a new interesting research topic. Among the most recent and interesting ones, compounds from Agouron related to the indole structure, are independent on the folate metabolism, highly active and specific for human TS. Other compounds, phthalein derivatives, can inhibit TS enzymes from various sources and show an interesting biological activity profile: they inhibit better bacterial and fungal TS than human TS. The x-ray crystal structures of some of these inhibitors with TS show that they bind in a different binding site from that of the classical folate TS inhibitors. This indicates a potential allosteric binding site useful for future drug discovery studies.

Antibody immunoglobulin G (IgG) against human prostatic specific antigen (PSA) as a carrier protein for chemotherapeutic drugs to human prostate tumors: Part 1. A double immunofluorescence analysis

BACKGROUND

Adenocarcinoma of the prostate (CaP) is the the second highest cause of cancer deaths in U.S. males. Current chemotherapeutic and/or endocrine treatments do not specifically and selectively target tumor cells of prostate cancer and benign prostatic hyperplasia (BPH). We hypothesized that because of the specific binding characteristics of antibody immunoglobulin G (IgG) to human prostatic-specific antigen (PSA), PSA-IgG could function as a carrier protein for conjugated chemotherapeutic drugs and that the immunoconjugate would selectively bind to prostatic epithelial cells and their tumors, but not to epithelial cells of unrelated organs. Our objective was to test the hypothesis using human prostatectomy specimens.

METHODS

WE used several derivatives of 5'-fluorouracil, namely, 5'-fluoro- 2'-deoxyuridine (5'-Fu-2'-d), 5'-fluoro-2'-deoxyuridine-5' monophosphate (5'-Fu-2'-d-5'-mp), 5'-fluoro-2'-deoxyuridine-5'-(p-aminophenyl) monophosphate (5'-Fu-2'-d'-5'-amp), to conjugate with rabbit anti-PSA-IgG together with fluorescent markers (such as rhodamine and fluorescein or fluorescein isothiocyanate: FITC). Prostate specimens were obtained from prostatectomy patients who had not been treated with cytotoxic drugs before surgery. We evaluated formalin-fixed and paraffin-embedded sections as well as cryostat sections of frozen specimens for localization of PSA-IgG alone and PSA-IgG-drug immunoconjugate using immunoperoxidase (IP) and single and/or double immunofluorescence (IF) localization techniques.

RESULTS

Our study showed that the immunoconjugate (PSA-IgG-5'-Fu-2'-d) bound to PSA (molecular size of approximately 34 KDa) on nitrocellulose sheets in Western immunoblots of extracts of BPH and CaP tissues. This binding of immunoconjugate to PSA on immunoblots was similar to that of the unconjugated PSA-IgG. Immunostaining patterns for rabbit anti-PSA-IgG and PSA-IgG-5'-Fu-2'-d immunoconjugate were similar and specific for prostate epithelial cells and their tumors, as revealed by IP techniques. To demonstrate that both the antibody and drug localized in the same group of prostatic epithelial cells, we used an immunoconjugate in which the PSA-IgG was labeled with rhodamine and 5'-Fu-2'-d-5'-amp with FITC. Our study showed that fluorescence for rhodamine and FITC was present in the same group of prostatic epithelial cells. Phase contrast microscopy demonstrated details of prostatic glandular epithelium and connective tissues. Our study showed that fluorescence for rhodamine and FITC and immunostaining by IP techniques were not observed in prostate sections incubated with normal rabbit serum.

CONCLUSIONS

We have shown that conjugation of 5'-Fu derivatives to PSA-IgG did not affect either the selectivity or specificity of the antibody for prostatic epithelial cells. Differential immunofluorescence study has shown that PSA-IgG may function as a carrier protein for chemotherapeutic drugs to prostate epithelial cells and their tumors. Furthermore, FITC-labeled 5'-Fu-2'-d did not specifically localize in prostatic glands, kidney, lungs, bladder, or colon. Because of the specificity and selectivity of the immunoconjugate for prostatic epithelial cells and their tumors, the immunoconjugate could be used in small dosages to treat prostatic tumors and such treatment would greatly reduce many unpleasant side effects in patients. This is the first report to show that PSA-IgG can function as an organ specific carrier protein for chemotherapeutic drugs to human prostate epithelium and its tumors.