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Svarovsky SA, Barchi JJ. Highly efficient preparation of tumor antigen-containing glycopeptide building blocks from novel pentenyl glycosides. Carbohydr Res 2004; 338:1925-35. [PMID: 14499569 DOI: 10.1016/s0008-6215(03)00323-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O-Glycosylated amino acids containing the tumor-associated T(Tf)-antigen (beta-D-Gal-(1-->3)-alpha-D-GalNAc) disaccharide unit were conveniently synthesized in seven steps starting from D-galactose via an n-pentenyl glycoside (NPG) building block. Azidonitration of 3,4,6-tri-O-acetyl-D-galactal, followed by nitrate displacement with simultaneous acetate hydrolysis with sodium 4-penten-1-oxide, afforded n-pentenyl 2-deoxy-2-azidogalactoside (3) in near quantitative yield. Subsequent high-yielding transformations resulted in the synthesis of the key glycosyl donor n-pentenyl beta-disaccharide 5 that was employed for the stereospecific preparation of glycosyl amino acids via NIS-promoted glycosylations with serine or threonine acceptors. The surprising utility of the reaction of sodium 4-penten-1-oxide with anomeric nitrates encouraged the detailed exploration of the action of a variety of nucleophiles on anomeric nitrates for the synthesis of useful 2-azido glycosyl donors directly from the 'classic' Lemieux azidonitration product of protected galactals. This expedient synthesis (28% overall yield from 1 to 7a) that makes use of heretofore rarely exploited pentenyl 2'-azidoglycosides, should be a valuable entry in the armamentarium of routes to biologically relevant glycopeptides in both mono- and multivalent forms.
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Marquez VE, Ben-Kasus T, Barchi JJ, Green KM, Nicklaus MC, Agbaria R. Experimental and structural evidence that herpes 1 kinase and cellular DNA polymerase(s) discriminate on the basis of sugar pucker. J Am Chem Soc 2004; 126:543-9. [PMID: 14719951 DOI: 10.1021/ja037929e] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two isomers of methanocarba (MC) thymidine (T), one an effective antiherpes agent with the pseudosugar moiety locked in the North (N) hemisphere of the pseudorotational cycle (1a, N-MCT) and the other an inactive isomer locked in the antipodean South (S) conformation (1b, S-MCT) were used to determine whether kinases and polymerases discriminate between their substrates on the basis of sugar conformation. A combined solid-state and solution conformational analysis of both compounds, coupled with the direct measurement of mono-, di-, and triphosphate levels in control cells, cells infected with the Herpes simplex virus, or cells transfected with the corresponding viral kinase gene (HSV-tk), suggests that kinases prefer substrates that adopt the S sugar conformation. On the other hand, the cellular DNA polymerase(s) of a murine tumor cell line transfected with HSV-tk incorporated almost exclusively the triphosphate of the locked N conformer (N-MCTTP), notwithstanding the presence of higher triphosphate levels of the S-conformer (S-MCTTP).
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Keay S, Szekely Z, Conrads TP, Veenstra TD, Barchi JJ, Zhang CO, Koch K, Michejda CJ. 359: Complete Characterization of an Antiproliferative Factor from Bladder Epithelial Cells of Interstitial Cystitis Patients. J Urol 2004. [DOI: 10.1016/s0022-5347(18)37621-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Svarovsky SA, Taraban MB, Barchi JJ. Facile photochemical synthesis of mixed siloxyacetal glycosides as potential pH-sensitized prodrugs for selective treatment of solid tumors. Org Biomol Chem 2004; 2:3155-61. [PMID: 15505722 DOI: 10.1039/b405786d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical reactions of a variety of acylsilanes with peracetylated free glycosides in anhydrous benzene at ambient temperature yielded novel, highly acid-sensitive siloxyacetal glycosides in 75-90% yields with complete retention of configuration at the anomeric center. Subsequent deacetylation of triisopropylsiloxy- and tert-butyldimethylsiloxy derivatives with sodium methoxide in methanol afforded deprotected siloxyacetal glycosides in nearly quantitative yields. Acid hydrolysis of trimethylsilyl siloxyacetals proceeded with a half-life of 17.5 minutes at pH 6.2 which is vastly superior to the decomposition rate of conventional acetals under similar conditions. The structure of one of the novel siloxyacetals was confirmed by X-ray crystallography. In vitro biological studies showed that glucose-derived siloxyacetals may serve as potential pH-activated prodrugs for selective treatment of solid tumors.
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Choi Y, George C, Comin MJ, Barchi JJ, Kim HS, Jacobson KA, Balzarini J, Mitsuya H, Boyer PL, Hughes SH, Marquez VE. A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude. J Med Chem 2003; 46:3292-9. [PMID: 12852759 DOI: 10.1021/jm030116g] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and biological evaluation of a bicyclo[3.1.0]hexene nucleoside designed as a conformational mimic of the anti-HIV agent stavudine (1, D4T) is described. The unsaturated methanocarbocyclic pseudosugar of N-MCD4T (2) was constructed from an iodo-substituted precursor by a DBU-catalyzed olefination reaction. Mitsunobu coupling with N(3)-benzoylthymine afforded the desired target after deprotection. Both D4T and N-MCD4T are in the North (N) hemisphere of the pseudorotational cycle but 70 degrees away from a perfect N (P = 0 degrees ) conformation toward the East and West hemispheres, respectively. Despite this large difference, the double bond reduces the puckering amplitude (nu(max)) of N-MCD4T to 6.81 degrees, and the superposition of both structures showed a RMS deviation of only 0.039 A. The combined structural analysis of P and nu(max) shows that while the value of P may differ substantially, the low nu(max) resolves the differences and becomes the dominant pseudorotational parameter. N-MCD4T is active against HIV-1 and HIV-2 in CEM, MT-2, and MT-4 cells, and while it is somewhat less potent than D4T, it also appears to be less toxic. The triphosphate (N-MCD4TTP) inhibits HIV reverse transcriptase with a 10-fold higher IC(50) than D4TTP. By virtue of its carbocyclic nature, N-MCD4T (2) is a more robust molecule stable to conditions that would cleave D4T.
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Nacro K, Lee J, Barchi JJ, Lewin NE, Blumberg PM, Marquez VE. Conformationally constrained analogues of diacylglycerol (DAG). Part 19: Asymmetric syntheses of (3R)- and (3S)-3-hydroxy-4,4-disubstituted heptono-1,4-lactones as protein kinase C (PK-C) ligands with increased hydrophilicity. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00477-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Teng K, Marquez VE, Milne GWA, Barchi JJ, Kazanietz MG, Lewin NE, Blumberg PM, Abushanab E. Conformationally constrained analogs of diacylglycerol. Interaction of .gamma.-lactones with the phorbol ester receptor of protein kinase C. J Am Chem Soc 2002. [DOI: 10.1021/ja00029a039] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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58
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Barchi JJ, Musser S, Marquez VE. The decomposition of 1-(.beta.-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one (zebularine) in alkali: mechanism and products. J Org Chem 2002. [DOI: 10.1021/jo00028a026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Siddiqui MA, Driscoll JS, Marquez VE, Roth JS, Shirasaka T, Mitsuya H, Barchi JJ, Kelley JA. Chemistry and anti-HIV properties of 2'-fluoro-2',3'-dideoxyarabinofuranosylpyrimidines. J Med Chem 2002; 35:2195-201. [PMID: 1351945 DOI: 10.1021/jm00090a008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis, chemistry, biochemistry, and anti-HIV activity of a series of 1-(2,3-dideoxy-2-fluoro-beta-D-threopentofuranosyl)pyrimidines have been studied in an attempt to find useful anti-AIDS drugs. Synthesis is carried out via a 2,3-dideoxyribose intermediate which facilitates the preparation of analogues by removing the sugar 3'-hydroxyl group prior to, rather than after, condensation with a uracil or cytosine aglycon. The 2'-F-dd-uridine analogues 7a-d (with H, F, Cl, and CH3 substitution in the 5-position) as well as the 4-deoxy compound (12b) are nonprotective to ATH8 or CEM cells infected with HIV-1. In the corresponding cytidine series, the 5-chloro analogue (11) is inactive. However, 2'-fluoro-2',3'-dideoxyarabinosylcytosine, 10a, and its 5-fluoro analogue, 10b, are both active. While neither compounds is a potent as ddC or 5-F-ddC (2b), 10b gives complete protection against the cytopathic effects of HIV in both host cell lines. 2'-Fluoro substitution confers increased chemical and enzymatic stability on dideoxynucleosides. Even though dideoxy pyrimidine nucleosides are inherently more stable than the corresponding purine analogues toward acid-catalyzed cleavage of the glycosidic bond, 2'-fluoro substitution (10a) still increases stabilization relative to ddC (2b). No detectable deamination by partially purified cytidine deaminase is observed with the 2'-fluoro compounds 10a, 10b, or 11 under conditions which rapidly deaminate cytidine. A small amount of 2'-F-dd-ara-U (7a) is formed from 10a in monkey plasma after greater than 24 h of exposure. The octanol-water partition coefficients for the dideoxynucleosides in this study indicate their hydrophilic character, with log P values varying from -0.28 to -1.18.
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Moore RE, Barchi JJ, Bartolin G. Use of borate complexation in assigning relative stereochemistry of acyclic polyhydroxylated compounds. J Org Chem 2002. [DOI: 10.1021/jo00203a017] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Bodenteich M, Marquez VE, Barchi JJ, Hallows WH, Goldstein BM, Driscoll JS. Synthesis of carbocyclic analogs of 1-.beta.-D-psicofuranosyl nucleosides. psico-Cyclopentenyladenosine (psicoplanocin A) and psico-cyclopentenylcytosine. J Org Chem 2002. [DOI: 10.1021/jo00074a030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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63
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Knapp S, Trope AF, Theodore MS, Hirata N, Barchi JJ. Ring expansion of ketones to 1,2-keto thioketals. Control of bond migration. J Org Chem 2002. [DOI: 10.1021/jo00178a006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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64
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Barchi JJ, Moore RE, Patterson GML. Acutiphycin and 20,21-didehydroacutiphycin, new antineoplastic agents from the cyanophyte Oscillatoria acutissima. J Am Chem Soc 2002. [DOI: 10.1021/ja00338a031] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
The new millennium has ushered in an era of science that will revolutionize a great majority of our daily activities. That revolution is being experienced by a growing number of the population who are pushing the average life expectancy closer to the 80-year mark. The primary reason for this increase is the changes we have made in the last 2-3 decades both in how we live our lives as well as how we treat our maladies when they arise. The advent of new techniques in diagnostics and surgery have allowed many to survive debilitating illnesses when their chances would have been slim only a few years ago. In addition, several new therapeutic agents have been developed in the latter part of the 20th century that have improved our quality of life and increased our overall survival time. New medicines to treat cardiovascular, degenerative, infectious, and neoplastic diseases are rapidly being discovered in an effort to further lengthen our lifetimes. The processes used by academic and industrial scientist to discover new drugs has recently experienced a true renaissance with many new and exciting techniques being developed in only the past 5-10 years. In this review, we will attempt to outline these latest protocols that chemists and biomedical scientist are currently employing to rapidly bring new drugs to the clinic.
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Luy B, Barchi JJ, Marino JP. S(3)E-E.COSY methods for the measurement of (19)F associated scalar and dipolar coupling constants. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 152:179-184. [PMID: 11531377 DOI: 10.1006/jmre.2001.2386] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A (1)H-(19)F spin state selective excitation (S(3)E) pulse sequence element has been applied in combination with (1)H homonuclear mixing to create E.COSY-type experiments designed to measure scalar J(HF2') and J(HH2') and residual dipolar D(HF2') and D(HH2') couplings in 2'-deoxy-2'-fluoro-sugars. The (1)H-(19)F S(3)E pulse sequence element, which resembles a simple INEPT sequence, achieves spin-state-selective correlation between geminal (1)H-(19)F spin pairs by linear combination of in-phase (19)F magnetization and anti-phase magnetization evolved from (1)H. Since the S(3)E sequence converts both (19)F and (1)H steady-state polarization into observable coherences, an approximately twofold signal increase is observed for fully relaxed (1)H-(19)F spin pairs with respect to a standard (1)H coupled (19)F 1D experiment. The improved sensitivity and resolution afforded by the use of (1)H-(19)F S(3)E E.COSY-type experiments for measuring couplings is demonstrated on the nucleoside 9-(2',3'-dideoxy-2'-fluoro-beta-D-threo-pentofuranosyl)adenine (beta-FddA) and on a selectively 2'-fluorine labeled 21mer RNA oligonucleotide.
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Chen IJ, Neamati N, Nicklaus MC, Orr A, Anderson L, Barchi JJ, Kelley JA, Pommier Y, MacKerell AD. Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets. Bioorg Med Chem 2000; 8:2385-98. [PMID: 11058033 DOI: 10.1016/s0968-0896(00)00180-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Integration of viral DNA into the host cell genome is a critical step in the life cycle of HIV. This essential reaction is catalyzed by integrase (IN) through two steps, 3'-processing and DNA strand transfer. Integrase is an attractive target for drug design because there is no known cellular analogue and integration is essential for successful replication of HIV. A computational three-dimensional (3-D) database search was used to identify novel HIV-1 integrase inhibitors. Starting from the previously identified Y3 (4-acetylamino-5-hydroxynaphthalene-2,7-disulfonic acid) binding site on the avian sarcoma virus integrase (ASV IN), a preliminary search of all compounds in the nonproprietary, open part of the National Cancer Institute 3-D database yielded a collection of 3100 compounds. A more rigorous scoring method was used to rescreen the 3100 compounds against both ASV IN and HIV-1 IN. Twenty-two of those compounds were selected for inhibition assays against HIV-1 IN. Thirteen of the 22 showed inhibitory activity against HIV-1 IN at concentrations less than 200 microM and three of them showed antiviral activities in HIV-1 infected CEM cells with effective concentrations (EC50) ranging from 0.8 to 200 microM. Analysis of the computer-generated binding modes of the active compounds to HIV-1 IN showed that simultaneous interaction with the Y3 site and the catalytic site is possible. In addition, interactions between the active compounds and the flexible loop involved in the binding of DNA by IN are indicated to occur. The structural details and the unique binding motif between the HIV-1 IN and its inhibitors identified in the present work may contribute to the future development of IN inhibitors.
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Mu L, Sarafianos SG, Nicklaus MC, Russ P, Siddiqui MA, Ford H, Mitsuya H, Le R, Kodama E, Meier C, Knispel T, Anderson L, Barchi JJ, Marquez VE. Interactions of conformationally biased north and south 2'-fluoro-2', 3'-dideoxynucleoside 5'-triphosphates with the active site of HIV-1 reverse transcriptase. Biochemistry 2000; 39:11205-15. [PMID: 10985766 DOI: 10.1021/bi001090n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations of a ternary complex of HIV-1 reverse transcriptase (RT), double-stranded DNA, and bound dideoxynucleoside-5'-triphosphate (RT-DNA-ddNTP), utilizing the ddNTPs ddATP, betaFddATP, and alphaFddATP, explain the experimentally observed order of potency of these 5'-triphosphates as inhibitors of RT: ddATP > betaFddATP > alphaFddATP. On the basis of RT's known preference to bind the incoming dNTP (or ddNTP) with a north conformation at the polymerase site, alphaFddATP, which in solution prefers almost exclusively a north conformation, was predicted to be the most potent inhibitor. However, Tyr115, which appears to function as a steric gate to preclude the binding of ribonucleoside 5'-triphosphates, prevents the effective binding of alphaFddATP in its preferred north conformation. The south-biased betaFddATP, while able to bind to RT without hindrance by Tyr115, has to pay a high energy penalty to be flipped to the active north conformation at the polymerase site. Finally, the more flexible and less conformationally biased ddATP is able to switch to a north conformation at the RT site with a smaller energy penalty than betaFddATP. These results highlight the opposite conformational preferences of HIV-1 RT for alphaFddATP and betaFddATP and help establish conformational guidelines for optimal binding at the polymerase site of this enzyme.
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Ford H, Dai F, Mu L, Siddiqui MA, Nicklaus MC, Anderson L, Marquez VE, Barchi JJ. Adenosine deaminase prefers a distinct sugar ring conformation for binding and catalysis: kinetic and structural studies. Biochemistry 2000; 39:2581-92. [PMID: 10704207 DOI: 10.1021/bi992112c] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several recent X-ray crystal structures of adenosine deaminase (ADA) in complex with various adenosine surrogates have illustrated the preferred mode of substrate binding for this enzyme. To define more specific structural details of substrate preferences for binding and catalysis, we have studied the ADA binding efficiencies and deamination kinetics of several synthetic adenosine analogues in which the furanosyl ring is biased toward a particular conformation. NMR solution studies and pseudorotational analyses were used to ascertain the preferred furanose ring puckers (P, nu(MAX)) and rotamer distributions (chi and gamma) of the nucleoside analogues. It was shown that derivatives which are biased toward a "Northern" (3'-endo, N) sugar ring pucker were deaminated up to 65-fold faster and bound more tightly to the enzyme than those that preferred a "Southern" (2'-endo, S) conformation. This behavior, however, could be modulated by other structural factors. Similarly, purine riboside inhibitors of ADA that prefer the N hemisphere were more potent inhibitors than S analogues. These binding propensities were corroborated by detailed molecular modeling studies. Docking of both N- and S-type analogues into the ADA crystal structure coordinates showed that N-type substrates formed a stable complex with ADA, whereas for S-type substrates, it was necessary for the sugar pucker to adjust to a 3'-endo (N-type) conformation to remain in the ADA substrate binding site. These data outline the intricate structural details for optimum binding in the catalytic cleft of ADA.
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Abstract
Tumorigenesis is accompanied by marked changes in the expression and presentation of various macromolecules at the cell surface. These tumor-associated adjustments result from the differential expression of genes coding for the production or post-translational modifications of these macromolecules during transformation to a particular tumor phenotype. In turn, tumor cells acquire distinct biophysical properties which set them apart from their normal counterparts. Alterations of carbohydrate structures and their organization on the surface of neoplastic cells is a hallmark of the tumorigenic and, most notably, the metastatic phenotype. Carbohydrate-protein and carbohydrate-carbohydrate interactions are critical events in the progression, dissemination and invasion of cancer cells. Many cell-cell contacts and subsequent remodeling of the tumor microenvironment are mediated by cell-surface glycans. The discovery of agents that modulate these interactions or interfere with the processing of tumor associated oligosaccharides is a fervent area of research today. This review will highlight the current status of the use of carbohydrate-based compounds that are being evaluated as potential anticancer therapeutics. In addition, the use of structures based on glycopeptides and carbohydrate mimetics will also be discussed.
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71
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Siddiqui MA, Driscoll JS, Abushanab E, Kelley JA, Barchi JJ, Marquez VE. The "beta-fluorine effect" in the non-metal hydride radical deoxygenation of fluorine-containing nucleoside xanthates. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1-12. [PMID: 10772699 DOI: 10.1080/15257770008032993] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
An alternative method to conduct a Barton-McCombie deoxygenation in nucleosides is described. The utility of the procedure is limited to structures with an electronegative substituent, particularly fluorine, in the beta-position relative to the radical center. The process is radical in nature and triggered by peroxides. The abstraction of hydrogen from the solvent is favorably influenced by the presence of a beta-fluorine.
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Chu RA, Takei J, Barchi JJ, Bai Y. Relationship between the native-state hydrogen exchange and the folding pathways of barnase. Biochemistry 1999; 38:14119-24. [PMID: 10571984 DOI: 10.1021/bi991799y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The previous native-state hydrogen exchange experiment with barnase failed to detect any partially unfolded intermediate state which was contrary to the experimental results from kinetic deuterium hydrogen exchange pulse labeling and protein engineering studies. This has been taken to suggest that the native-state hydrogen exchange method cannot be used alone as an analytical tool to study the folding pathways of proteins. Here, we revisited the pulse labeling experiment with barnase and detected no stable folding intermediate. This finding allows a reconciliation of the native-state HX data and the folding pathway of barnase. Along with alternative theoretical interpretations for a curved chevron plot of protein folding, these data suggest that further investigation of the nature of the intermediate of barnase is needed.
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73
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Sharma P, Steinbach PJ, Sharma M, Amin ND, Barchi JJ, Pant HC. Identification of substrate binding site of cyclin-dependent kinase 5. J Biol Chem 1999; 274:9600-6. [PMID: 10092646 DOI: 10.1074/jbc.274.14.9600] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclin-dependent kinase 5 (CDK5), unlike other CDKs, is active only in neuronal cells where its neuron-specific activator p35 is present. However, it phosphorylates serines/threonines in S/TPXK/R-type motifs like other CDKs. The tail portion of neurofilament-H contains more than 50 KSP repeats, and CDK5 has been shown to phosphorylate S/T specifically only in KS/TPXK motifs, indicating highly specific interactions in substrate recognition. CDKs have been shown to have a high preference for a basic residue (lysine or arginine) as the n+3 residue, n being the location in the primary sequence of a phosphoacceptor serine or threonine. Because of the lack of a crystal structure of a CDK-substrate complex, the structural basis for this specific interaction is unknown. We have used site-directed mutagenesis ("charged to alanine") and molecular modeling techniques to probe the recognition interactions for substrate peptide (PKTPKKAKKL) derived from histone H1 docked in the active site of CDK5. The experimental data and computer simulations suggest that Asp86 and Asp91 are key residues that interact with the lysines at positions n+2 and/or n+3 of the substrates.
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Ikeda H, Fernandez R, Wilk A, Barchi JJ, Huang X, Marquez VE. The effect of two antipodal fluorine-induced sugar puckers on the conformation and stability of the Dickerson-Drew dodecamer duplex [d(CGCGAATTCGCG)]2. Nucleic Acids Res 1998; 26:2237-44. [PMID: 9547286 PMCID: PMC147537 DOI: 10.1093/nar/26.9.2237] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UV thermal melting studies, CD and NMR spectroscopies were employed to assess the contribution of antipodal sugar conformations on the stability of the canonical B-DNA conformation of the Dickerson-Drew dodecamer duplex [[d(CGCGAATTCGCG)]2, (ODN 1)]. Different oligodeoxynucleotide versions of ODN 1 were synthesized with modified thymidine units favoring distinct sugar conformations by using a 3'- endo (north) 2'-fluoro-2'-deoxyribofuranosyl thymine (1) or a 2'- endo (south) 2'-fluoro-2'-deoxyarabinofuranosyl thymine (2). The results showed that two south thymidines greatly stabilized the double helix, whereas two north thymidines destabilized it by inducing a more A-like conformation in the middle of the duplex. Use of combinations of north and south thymidine conformers in the same oligo destabilized the double helix even further, but without inducing a conformational change. The critical length for establishing a detectable A-like conformation in the middle of a B-DNA ODN appears to be 4 bp. Our results suggest that manipulation of the conformation of DNA in a sequence-independent manner is possible.
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75
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Sharma P, Barchi JJ, Huang X, Amin ND, Jaffe H, Pant HC. Site-specific phosphorylation of Lys-Ser-Pro repeat peptides from neurofilament H by cyclin-dependent kinase 5: structural basis for substrate recognition. Biochemistry 1998; 37:4759-66. [PMID: 9537991 DOI: 10.1021/bi972746o] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent work has shown that high molecular weight neurofilament (NF) proteins are phosphorylated in their carboxy-terminal tail portion by the enzyme cyclin-dependent kinase 5 (CDK-5). The tail domain of neurofilaments contains 52 tripeptide repeats, viz. Lys-Ser-Pro, which mainly exist as KSPXK and KSPXXX motifs (X = amino acid). CDK-5 specifically phosphorylates the serine residues within the KSPXK sites. We probed the structural basis for this type of substrate selectivity by studying the conformation of synthetic peptides containing either KSPXK or KSPXXX repeats designed from native neurofilament sequences. Synthetic peptides with KSPXK repeats were phosphorylated on serine with a recombinant CDK-5/p25 complex whereas those with KSPXXX repeats were unreactive in this system. Circular dichroism (CD) studies in 50% TFE/H2O revealed a predominantly helical conformation for the KSPXXX-containing peptides, whereas the CD spectra for KSPXK-containing peptides indicated the presence of a high population of extended structures in water and 50% TFE solutions. However, detailed NMR analysis of one such peptide which included two such KSPXK repeats suggested a turn-like conformation encompassing the first KSPXK repeat. Restrained molecular dynamics calculations yielded an unusually stable, folded structure with a double "S"-like bend incorporating the central residues of the peptide. The data suggest that a transient reverse turn or loop-type structure may be a requirement for CDK-5-promoted phosphate transfer to neurofilament-specific peptide segments.
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