Sequence selective recognition in the minor groove of dsDNA by pyrrole,imidazole-substituted bis-benzimidazole conjugates

A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.     

Equilibrium and Kinetics of Bromine Hydrolysis

Equilibrium constants for bromine hydrolysis, K(1) = [HOBr][H(+)][Br(-)]/[Br(2)(aq)], are determined as a function of ionic strength (&mgr;) at 25.0 degrees C and as a function of temperature at &mgr; approximately 0 M. At &mgr; approximately 0 M and 25.0 degrees C, K(1) = (3.5 +/- 0.1) x 10(-)(9) M(2) and DeltaH degrees = 62 +/- 1 kJ mol(-)(1). At &mgr; = 0.50 M and 25.0 degrees C, K(1) = (6.1 +/- 0.1) x 10(-)(9) M(2) and the rate constant (k(-)(1)) for the reverse reaction of HOBr + H(+) + Br(-) equals (1.6 +/- 0.2) x 10(10) M(-)(2) s(-)(1). This reaction is general-acid-assisted with a Br?nsted alpha value of 0.2. The corresponding Br(2)(aq) hydrolysis rate constant, k(1), equals 97 s(-)(1), and the reaction is general-base-assisted (beta = 0.8).     

Synthesis,characterization and biological activities of two novel orthopalladated complexes: Interactions with DNA and bovine serum albumin,antitumour activity and molecular docking studies

[Pd(L₁)(C,N)]CF₃SO₃ and [Pd(L₂)(C,N)]CF₃SO₃ (L₁ = 2,2′ ‐bipyridine, L₂ = 1,10‐phenanthroline and C,N = benzylamine) novel orthopalladated complexes have been synthesized and characterized using various techniques. The binding of the complexes with native calf thymus DNA (CT‐DNA) was monitored using UV–visible absorption spectrophotometry, fluorescence spectroscopy and thermal denaturation studies. Our results indicate that these complexes can strongly bind to CT‐DNA via partial intercalative mode. In addition, fluorescence spectrometry of bovine serum albumin (BSA) with the complexes shows that the fluorescence quenching mechanism of BSA is a static process. The results of site‐competitive replacement experiments with specific site markers clearly indicate that the complexes bind to site I of BSA. Notably, the complexes exhibit significant in vitro cytotoxicity against two human cancer cell lines (Jurkat and MCF‐7) with IC₅₀ values varying from 37 to 53 μM. Finally, a molecular docking experiment effectively proves the binding of the Pd(II) complexes to DNA and BSA.     

Phosphinate Inhibitors of the D-Glutamic Acid-Adding Enzyme of Peptidoglycan Biosynthesis

We report the synthesis and initial evaluation of the first effective inhibitors of the D-glutamic acid-adding enzyme (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase or MurD). This enzyme plays a key role in bacterial peptidoglycan biosynthesis and is therefore a target for antibiotic design. Phosphinic acid 3 is a dipeptide analog linked to uridine diphosphate by a hydrophobic spacer. It is a good inhibitor of the enzyme (IC(50) = 0.68 &mgr;M) as it closely resembles the tetrahedral intermediate that is presumed to form in the ligation reaction. Compound 4 lacks the terminal UMP group, and compound 5 lacks both the linker and UDP functionalities. These are less effective inhibitors of the enzyme with IC(50) values of 29 &mgr;M and >1 mM, respectively. Preincubation of the enzyme in the presence of inhibitor 3 and ATP does not result in irreversible inhibition or in the formation of a slowly decomplexing species, suggesting that the phosphinic acid is not phosphorylated in the active site.     

DFT-PCM studies of solvent effects on the cross-interaction constants in benzhydryl cation and anion formation

The Hammett rho+ and rho- values have been determined by varying substituent Y' for a given Y in the benzhydryl cation and anion formation (YH4C6-CH-C6H4Y' where C is a cationic or an anionic center) at the RHF/3-21G, RHF/6-31G, RHF/6-31+G, and B3LYP/6-31+G levels. The failure of RHF theory in accounting for the stabilization by delocalization leads to the smaller magnitudes of rho+ and rho- with electron-donating and -withdrawing substituents, Y, respectively, than the corresponding DFT values. The effects of solvent (benzene, dichloroethane, and acetonitrile) on the rho values were calculated by applying the conductor polarizable continuum model method to the DFT results. Finally, the cross-interaction constants (rho(YY)') and their variation with solvent were determined. As the polarity (dielectric constant, epsilon) of the solvent is increased, the magnitude of rho+ and rho- decreased, whereas that of rho(YY)' increased. Satisfactory correlations were obtained between rho values (rho+, rho- and rho(YY)') and the Kirkwood function f(k) (= epsilon - 1/2epsilon + 1). The rho(YY)' values are negative with a magnitude greater for the anionic (rho(YY)'-) than the cationic (rho(YY)'+) system.     

Independent generation and characterization of a C2'-oxidized abasic site in chemically synthesized oligonucleotides

Abasic lesions, which are formed endogenously and as a consequence of exogenous agents, are lethal and mutagenic. Hydrogen atom abstraction from C2' in DNA under aerobic conditions produces an oxidized abasic lesion (C2-AP), along with other forms of DNA damage. The effects of C2-AP on DNA structure and function are not well understood. A method for the solid-phase synthesis of oligonucleotides containing C2-AP lesions is reported. The lesion is released via periodate oxidation of a triol containing a vicinal diol. The triol is introduced via a phosphoramidite that is compatible with standard oligonucleotide synthesis and deprotection conditions. UV-melting studies indicate that the C2-AP lesion has a comparable effect on the thermal stability of duplex DNA as other abasic lesions. The C2-AP lesion is rapidly cleaved by piperidine at 90 degrees C. However, cleavage by NaOH (0.1 M, 37 degrees C) shows that C2-AP is considerably less labile (t(1/2) = 3.3 +/- 0.2 h) than other abasic lesions.     

Fe(III)Fe(III) and Fe(II)Fe(III) Complexes as Synthetic Analogues for the Oxidized and Reduced Forms of Purple Acid Phosphatases

Novel Fe(III)Fe(III) and Fe(II)Fe(III) complexes [Fe(2)(BBPMP)(&mgr;-OAc)(&mgr;-X)](n)() (1, X = OAc(-), n = 1+; 2, X = OH(-), n = 1+; 3, X = OAc(-), n = 0; 4, X = OH(-), n = 0), where BBPMP(3)(-) is the anion of 2,6-bis[(2-hydroxybenzyl)(2-pyridylmethyl)aminomethyl]-4-methylphenol, and OAc(-) is acetate, were prepared in order to provide models for the active site of purple acid phosphatases (PAPs). Complex 1 was obtained by the reaction of H(3)BBPMP with Fe(ClO(4))(2).6H(2)O in methanol and sodium acetate trihydrate under ambient conditions, while complex 3 was synthesized as described for 1, under an argon atmosphere with low levels of dioxygen. 2 was isolated from 1in acetonitrile by a substitution of the bridging acetate group by hydroxide, while 4 was generated in solution during a spectropotentiostatic experiment on 2, under argon. Complex 1, [Fe(III)(2)(BBPMP)(&mgr;-OAc)(2)]ClO(4).H(2)O, has been characterized by X-ray crystallography. Crystal data: monoclinic, space group P2(1)/n, a = 14.863(5) ?, b = 12.315(3) ?, c = 20.872(8) ?, beta = 90.83(3) degrees, Z = 4. IR, M?ssbauer, magnetic, electronic absorption, and electrochemical properties of 1-3 have been investigated, and some of these properties represent a contribution to the understanding of the dinuclear iron center of PAPs. Complexes 2, [Fe(III)(2)(BBPMP)(&mgr;-OAc)(&mgr;-OH)]ClO(4) (lambda(max) = 568 nm/epsilon = 4760 M(-)(1) cm(-)(1)), and 4 [Fe(II)Fe(III)(BBPMP)(&mgr;-OAc)(&mgr;-OH)] (lambda(max) = 516 nm/epsilon = 4560 M(-)(1) cm(-)(1)), constitute good synthetic analogues for the chromophoric site for the oxidized and reduced forms, respectively, of the enzyme.     

Synthesis and Characterization of Heterodinuclear IrCo, RuCo, IrNi, and RuNi Complexes Containing Pyrazolate and Pyrazolylborate Ligands

Treatment of the metallo ligands [ML(pz)(2)(Hpz)] (pz = pyrazolate; L = C(5)Me(5), M = Ir (1); L = mesitylene, M = Ru (3)) with [M'Cl{HB(3-i-Pr-4-Br-pz)(3)}] (M' = Co (4), Ni (5)) yields heterodinuclear complexes of formula [LM(&mgr;-pz)(2)(&mgr;-Cl)M'{HB(3-i-Pr-4-Br-pz)(3)}] (L = C(5)Me(5); M = Ir; M' = Co (6), Ni (7). L = mesitylene; M = Ru; M' = Co (8)). The related complex [Ru(eta(6)-p-cymene)(pz)(2)(Hpz)] (2) reacts with equimolar amounts of 4 or 5 to give mixtures of the corresponding bis(&mgr;-pyrazolato) &mgr;-chloro complexes [(eta(6)-p-cymene)Ru(&mgr;-pz)(2)(&mgr;-Cl)M'{HB(3-i-Pr-4-Br-pz)(3)}] (M' = Co (9), Ni (10)) and the triply pyrazolato-bridged complexes [(eta(6)-p-cymene)Ru(&mgr;-pz)(3)M'{HB(3-i-Pr-4-Br-pz)(3)}] (M' = Co (11), Ni (12)). Complex 1 reacts with 5 in the presence of KOH to give the IrNi complex [(eta(5)-C(5)Me(5))Ir(&mgr;-pz)(3)Ni{HB(3-i-Pr-4-Br-pz)(3)}] (13) whereas its reaction with 4 and KOH rendered the bis(&mgr;-pyrazolato) &mgr;-hydroxo complex [(eta(5)-C(5)Me(5))Ir(&mgr;-pz)(2)(&mgr;-OH)Co{HB(3-i-Pr-4-Br-pz)(3)}] (14). The molecular structure of the heterobridged IrCo complex (6) and those of the homobridged RuNi (12) and IrNi (13) complexes have been determined by X-ray analyses. Compound 6 crystallizes in the monoclinic space group P2(1)/n, with a = 10.146(5) ?, b = 18.435(4) ?, c = 22.187(13) ?, beta = 97.28(4) degrees, and Z = 4. Complex 12 is monoclinic, space group P2(1), with a = 10.1169(7) ?, b = 21.692(2) ?, c = 11.419(1) ?, beta = 112.179(7) degrees, and Z = 2. Compound 13 crystallizes in the monoclinic space group Cc, with a = 13.695(2) ?, b = 27.929(6) ?, c = 13.329(2) ?, beta = 94.11(4) degrees, and Z = 4. All the neutral complexes 6, 12, and 13 consist of linear M.M'.B backbones with two (6) or three (12, 13) pyrazolate ligands bridging the dimetallic M.M' units and three substituted 3-i-Pr-4-Br-pz groups joining M' to the boron atoms. The presence in the proximity of the first-row metal M' of the three space-demanding isopropyl substituents of the pyrazolate groups induces a significant trigonal distortion of the octahedral symmetry, yielding clearly different M'-N bond distances on both sides of the ideal octahedral coordination sphere of these metals.     

Evaluation of alternatives to warfarin as probes for Sudlow site I of human serum albumin: characterization by high-performance affinity chromatography

Warfarin is often used as a site-specific probe for examining the binding of drugs and other solutes to Sudlow site I of human serum albumin (HSA). However, warfarin has strong binding to HSA and the two chiral forms of warfarin have slightly different binding affinities for this protein. Warfarin also undergoes a slow change in structure when present in common buffers used for binding studies. This report examined the use of four related, achiral compounds (i.e., coumarin, 7-hydroxycoumarin, 7-hydroxy-4-methylcoumarin, and 4-hydroxycoumarin) as possible alternative probes for Sudlow site I in drug binding studies. High-performance affinity chromatography and immobilized HSA columns were used to compare and evaluate the binding properties of these probe candidates. Binding for each of the tested probe candidates to HSA was found to give a good fit to a two-site model. The first group of sites had moderate-to-high affinities for the probe candidates with association equilibrium constants that ranged from 6.4 x 10(3)M(-1) (coumarin) to 5.5 x 10(4)M(-1) (4-hydroxycoumarin) at pH 7.4 and 37 degrees C. The second group of weaker, and probably non-specific, binding regions, had association equilibrium constants that ranged from 3.8 x 10(1)M(-1) (7-hydroxy-4-methylcoumarin) to 7.3 x 10(2)M(-1) (coumarin). Competition experiments based on zonal elution indicated that all of these probe candidates competed with warfarin at their high affinity regions. Warfarin also showed competition with coumarin, 7-hydroxycoumarin and 7-hydroxy-4-methycoumarin for their weak affinity sites but appeared to not bind and/or compete for all of the weak sites of 4-hydroxycoumarin. It was found from this group that 4-hydroxycoumarin was the best alternative to warfarin for examining the interactions of drugs at Sudlow site I on HSA. These results also provided information on how the major structural components of warfarin contribute to the binding of this drug at Sudlow site I.     

A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes

A fluorescent pyrazine derivative, 3,5-diamino-6-chloro-2-pyrazine carbonitrile (DCPC), is presented as a promising light-up ligand for single-nucleotide polymorphisms (SNPs) typing. In solutions buffered to pH 7.0 (I = 0.11 M, at 5 degrees C), DCPC can bind to thymine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-GTGTG CGTTG ANA TGGAC GCAGA-3'/3'-CACAC GCAAC TXT ACCTG CGTCT-5', X = abasic site, N = target nucleotide) with a dissociation constant of 2.6 microM. The binding of DCPC is accompanied by a significant enhancement of its fluorescence (lambda(max), 412 nm), and the response is highly selective to thymine base. These binding and sensing properties allow a clear detection of thymine-related mutations present in polymerase chain reaction (PCR) amplification products.     

Antitumor activity of 4-amino and 8-methyl-4-(3diethylamino propylamino)pyrimido[4',5':4,5]thieno (2,3-b) quinolines

The interaction of 4-aminopyrimido [4',5':4,5] thieno (2,3-b) quinoline and 8-methyl-4-(3-diethylaminopropylamino) pyrimido [4',5':4,5] thieno (2,3-b) quinoline with DNA was studied by UV-Vis and fluorescence spectrophotometry as well as by hydrodynamic methods. On binding to DNA, the absorption spectra underwent bathochromic and hypochromic shifts and the fluorescence was quenched. These compounds are able to bind to DNA with an affinity of about 10(6) M(-1) for calf thymus DNA at ionic strength 0.01 M and their intercalating characteristic (lengthening of the DNA) depends upon the length of the chain. Binding to the GC-rich DNA of Micrococcus lysodeikticus was stronger than the binding to calf thymus DNA at ionic strength 0.01 M. The cytotoxicities of these compounds on leukemia HL-60, melanoma B16F10 and neuro 2a cells are quite similar and inhibition (IC50) is in the range of 0.992-3.968 microM. The anticancer efficacy against B16 melanoma, has provided evidence of major antitumor activity for 8-methyl-4-(3diethylaminopropylamino) pyrimido [4',5':4,5] thieno(2,3-b)quinoline. Single or multiple intraperitonial (i.p) doses of drug proved high level activity against the subcutaneous (s.c) grafted B16 melanoma, significantly increasing survival (p<0.001) and inhibiting tumor growth (T/C of 4%). This study offers a new intercalation functional group to DNA-targeted drug design.     

Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms

Alloxazine can bind to adenine selectively over other nucleobases opposite an abasic site in DNA duplexes (5'-TCC AGX GCA AC-3'/3'-AGG TCN CGT TG-5', X=AP site, N=A, T, C, G) with a dissociation constant of 0.82 microM (pH 7.0, I=0.11 M, at 5 degrees C), and it is applicable to SNPs typing of PCR amplification products based on the binding-induced fluorescence response.     

Deoxyribozymes with 2'-5' RNA ligase activity

In vitro selection was used to identify deoxyribozymes that ligate two RNA substrates. In the ligation reaction, a 2'-5' RNA phosphodiester linkage is created from a 2',3'-cyclic phosphate and a 5'-hydroxyl group. The new Mg(2+)-dependent deoxyribozymes provide 50-60% yield of ligated RNA in overnight incubations at pH 7.5 and 37 degrees C, and they afford 40-50% yield in 1 h at pH 9.0 and 37 degrees C. Various RNA substrate sequences may be joined by simple Watson-Crick covaration of the DNA binding arms that interact with the two RNA substrates. The current deoxyribozymes have some RNA substrate sequence requirements at the nucleotides immediately surrounding the ligation junction (either UAUA GGAA or UAUN GGAA, where the arrow denotes the ligation site and N equals any nucleotide). One of the new deoxyribozymes was used to prepare by ligation the Tetrahymena group I intron RNA P4-P6 domain, a representative structured RNA. Nondenaturing gel electrophoresis revealed that a 2'-5' linkage between nucleotides A233 and G234 of P4-P6 does not disrupt its Mg(2+)-dependent folding (DeltaDeltaG degrees ' < 0.2 kcal/mol). This demonstrates that a 2'-5' linkage does not necessarily interfere with structure in a folded RNA. Therefore, these non-native linkages may be acceptable in modified RNAs when structure/function relationships are investigated. Deoxyribozymes that ligate RNA should be particularly useful for preparing site-specifically modified RNAs for studies of RNA structure, folding, and catalysis.