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PubMed2002

Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove.

A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.

DNA↗
PubMed2004

DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives.

A number of studies indicate that DNA sequences such as AATT and TTAA have significantly different physical and interaction properties. To probe these interaction differences in detail and determine the influence of charge, we have synthesized three bisbenzimidazole derivatives, a diamidine, DB185, and monoamidines, DB183 and DB210, that are related to the well-known minor groove agent, Hoechst 33258. Footprinting studies with several natural and designed DNA fragments indicate that the synthetic compounds bind at AT sequences in the minor groove and interact more weakly at sites with TpA steps relative to sites without such steps. Circular dichroism spectroscopy also indicates that the compounds bind in the DNA minor groove. Surprisingly, Tm studies as a function of ratio indicate that the monoamidines bind to TTAA sequences as dimers, whereas the diamidine binds as a monomer. Biosensor-surface plasmon resonance (SPR) studies allowed us to quantitate the interaction differences in more detail. SPR results clearly show that the monoamidine compounds bind to the TTAA sequence in a cooperative 2:1 complex but bind as monomers to AATT. The dication binds to both sequences in monomer complexes but the binding to AATT is significantly stronger than binding to TTAA. Molecular dynamics simulations indicate that the AATT sequence has a narrow time-average minor groove width that is a very good receptor site for the bisbenzimidazole compounds. The groove in TTAA sequences is wider and the width must be reduced to form a favorable monomer complex. The monocations thus form cooperative dimers that stack in an antiparallel orientation and closely fit the structure of the TTAA minor groove. The amidine groups in the dimer are oriented in the 5' direction of the strand to which they are closest. Charge repulsion in the dication apparently keeps it from forming the dimer. It instead reduces the TTAA groove width, in an induced fit process, sufficiently to form a minor groove complex. The dimer-binding mode of DB183 and DB210 is a new DNA recognition motif and offers novel design concepts for selective targeting of DNA sequences with a wider minor groove, including those with TpA steps.

Benzimidazoles↗
PubMed2005

Copper(I) 1,2,4-triazolates and related complexes: studies of the solvothermal ligand reactions, network topologies, and photoluminescence properties.

One-pot solvothermal treatments of organonitriles, ammonia, and Cu(II) salts yielded Cu(I) and 3,5-disubstituted 1,2,4-triazolates. The organic triazolate components were derived from copper-mediated oxidative cycloaddition of nitriles and ammonia, in which a key intermediate 1,3,5-triazapentadienate was isolated as [Cu(II)(4-pytap)(2)] (4-Hpytap = 2,4-di(4-pyridyl)-1,3,5-triazapentadiene) via controlled solvothermal conditions. This intermediate could also be synthesized by Ni(II)-mediated reactions; however, the final triazoles were obtained only when Cu(II) was employed. Therefore, the reaction mechanism of these reactions was elucidated as follows: nitrile was first attacked by ammonia to form the amidine, which further reacted with another nitrile or self-condensed to yield 1,3,5-triazapentadiene, which was coordinated to two Cu(II) ions in its deprotonated form. A two-electron oxidation of the 1,3,5-triazapentadienate mediated by two Cu(II) ions gave one triazolate and Cu(I) cations. Other in situ ligand reactions, such as C-C bond cleavage and hydrolysis, were also found for the nitriles under these solvothermal conditions. Another remarkable feature of these crystalline Cu(I) triazolates is their simple, typical 3- or 4-connected network topologies. The self-assembly of these nets is presumably controlled by steric hindrance, which is subsequently applied to the rational design of the close-packed 2D networks [Cu(I)(tz)](infinity) and [Ag(I)(tz)](infinity) (Htz = 1,2,4-triazole), as well as the porous 3D network [Cu(I)(etz)](infinity) (Hetz = 3,5-diethyl-1,2,4-triazole). The interesting photoluminescence properties of these coinage d(10) metal complexes were also investigated.

Journal Article↗
PubMed2004

Singlet vinylcarbenes: spectroscopy and photochemistry.

The first direct spectroscopic characterization of singlet vinylcarbenes is reported. Several vinyl amidines were converted to the corresponding vinylchlorodiazirines through straightforward Graham oxidation. Irradiation of the diazirines at 8 K in N2 matrices gave the corresponding singlet vinylchlorocarbenes, which could be characterized by IR, UV/vis, and calculational modeling. Hence, vinylchlorocarbene, 1-methylvinylchlorocarbene, and 1-cyclopentenylchlorocarbene were all generated and investigated. The spectra are consistent with localized carbene structures compared to the very delocalized triplet vinylcarbenes. In all cases, the carbenes readily cyclize to the corresponding cyclopropenes on visible irradiation, together with H-shift in the parent vinylchlorocarbene. In the cyclopentenyl system, cyclization leads to a highly strained bicyclo[3.1.0]hexene.

Journal Article↗
PubMed2005

How bulky is a bulky ligand: energetic consequences of steric constraint in ligand-directed cluster assembly and disassembly.

Steric tuning of N-aryl groups of homologous amidinate ligands affords discrete dimeric and tetrameric copper(I) clusters in solid state, but they undergo dynamic dimer-dimer and tetramer-dimer interconversion in solution. A delicate interplay between steric constraint and mechanical stability shapes the reaction coordinate of this process. Thermodynamic and kinetic parameters dictating such cluster assembly and disassembly immediately suggest a means to experimentally quantify energies that are associated with ligand steric bulk.

Journal Article↗
PubMed2006

Construction of double-stranded metallosupramolecular polymers with a controlled helicity by combination of salt bridges and metal coordination.

We describe the construction of the first double-stranded metallosupramolecular helical polymers. We designed and synthesized a supramolecular duplex comprised of complementary m-terphenyl-based strands bearing a chiral amidine or achiral carboxylic acid together with two pyridine groups at the four ends. Supramolecular polymerization of the duplex with cis-PtPh2(DMSO)2 in 1,1,2,2-tetrachloroethane produced the double-stranded metallosupramolecular polymer with a controlled helicity of which the two complementary metallostrands are intertwined through the amidinium-carboxylate salt bridges. The structures and hydrodynamic dimensions of the metallosupramolecular polymers were characterized by 1H NMR, diffusion-ordered NMR, dynamic light scattering, absorption, and CD measurements. The polymeric structure was also visualized by atomic force microscopy.

Chemistry, Organic↗
PubMed2006

A conformational study of phospha(III)- and phospha(V)-guanidine compounds.

Spectroscopic, crystallographic, and computational studies of the substituent distribution about the "NCN" unit in a series of phospha(III)- and phospha(V)-guanidines, R(2)PC{NR'}{NHR'} and R(2)P(E)C{NR'}{NHR'} (R = Ph, Cy; R' = (i)Pr, Cy; E = S, Se), are reported. In the phosphorus(III) systems, the P-diphenyl substituted compounds are observed as only one isomer, shown by NMR spectroscopy to be the E(syn)-(alpha) configuration. In contrast, the corresponding P-dicyclohexyl derivatives exist as a mixture of E(syn)-(alpha) and Z(anti) in solution. Spectroscopic techniques are unable to determine whether the latter isomer exists as the alpha- or beta-conformer relative to rotation about the P-C(amidine)() bond; however, DFT calculations indicate a low-energy structure for the N,N'-dimethyl model complex in the beta-conformation. In their oxidized sulfo and seleno forms, the P-diphenyl compounds are present as an interconverting equilibrium mixture of the E(syn)-(beta) and Z(syn)-(beta) isomers in solution ( approximately 3:2 ratio), whereas for the P-dicyclohexyl analogues, the latter configuration (in which the nitrogen substituents are in a more sterically unfavorably cisoid arrangement about the imine double bond) is the dominant form. Intramolecular E...HN (E = S, Se) interactions are observed in solution for the Z(syn)-(beta) configuration of both P-substituted species, characterized by J(SeH) coupling in the NMR spectrum for the P(V)-seleno compounds and a bathochromic shift of the NH absorption in the infrared spectrum. An X-ray crystallographic analysis of representative Ph(2)P(E)- and Cy(2)P(E)-substituted species shows exclusively the E(syn)-(beta) configuration for the P-diphenyl substituted compounds and the Z(syn)-(beta) form for the P-dicyclohexyl derivatives, independent of the chalcogen and the nitrogen substituents. Results from a DFT analysis of model compounds fail to identify a compelling electronic argument for the observed preferences in substituent orientation, suggesting that steric factors play an important role in determining the subtle energetic differences at work in these systems.

Journal Article↗
PubMed1995

Dicationic diarylfurans as anti-Pneumocystis carinii agents.

Seven dicationic 2,5-diarylfurans have been synthesized, and their interactions with poly(dA-dT) and the duplex oligomer d(CGCCAATTCGCG)2 were evaluated by Tm measurements. The inhibition of topoisomerase II isolated from Giardia lamblia, the inhibition of growth of G. lamblia in cell culture by these furans, and the effectiveness of these compounds against Pneumocystis carinii in the immunosuppressed rat model have been assessed. Strong binding affinities to poly(dA-dT) and to the oligomer were observed for the dicationic furans, and the interaction strength is directly correlated to the biological activity of the compounds. An X-ray structure for the complex of the dicationic amidine derivative, 2,5-bis(4-guanylphenyl)furan (1), with the oligomer demonstrates the snug fit of these compounds with the AATT minor-groove binding site and hydrogen bonds to AT base pairs at the floor of the minor groove. The stronger DNA binding molecules are the most effective inhibitors of topoisomerase II and G. lamblia in cell culture, and there is a correlation for both DNA interaction and topoisomerase II inhibition with the biological activity of these compounds against G. lamblia. Compound 1 is the most effective against P. carinii, it is more active and less toxic than pentamidine on intravenous administration and it is also effective by oral dosage. The results presented here suggest a model for the biological action of these compounds in which the dication first binds in the minor groove of DNA and forms a complex that results in the inhibition of the microbial topoisomerase II enzyme.

Animals↗
PubMed1995

Synthesis of two distamycin analogues and their binding mode to d(CGCAAATTTGCG)2 in the 2:1 solution complexes as determined by two-dimensional 1H-NMR.

In the course of a study aimed at the synthesis of pyrrole amidine carboxamide DNA-binding agents as novel pharmacological agents, a series of carbamoyl analogues of distamycin, containing an increasing number of pyrrole units, have been obtained by total synthesis. The interaction of the tetrapyrrole carbamoyl 4 with the dodecamer d(CGCAAATTTGCG)2 in comparison with that of the corresponding formylamino analogue 3 has been examined by high-resolution 1H-NMR and molecular modeling. Either ligand binds to DNA in one-drug and symmetric two-drug modes at low drug:DNA ratios, while at high ratios only the two-drug complex was observed. In this article, the structure of 2:1 drugs DNA complexes has been studied by NMR and molecular modeling, which indicate that the two analogues bind the DNA in a similar fashion, in the minor groove of the 5'-AATTT region. In both complexes the two drugs are symmetrically placed along the complementary strands of DNA with the pyrrole ring of one molecule in close contact with those of the other one. Although another region of five consecutive A-T base pairs is available, no evidence of sliding of drug molecules between different binding sites, as in the case of the 2:1 complex of distamycin with the same dodecamer, is observed, thus indicating that increasing the number of N-methylpyrrolecarboxamide units from three to four cases a lengthening of the recognition sequence.

Base Sequence↗
PubMed1995

Synthesis and histamine H1 receptor agonist activity of a series of 2-phenylhistamines, 2-heteroarylhistamines, and analogues.

New histamine derivatives characterized by a (substituted) aryl, heteroaryl, benzyl, or heteroarylmethyl substituent in the C2 position of the imidazole ring have been prepared from appropriate imidates or amidines, respectively, and 2-oxo-4-phthalimido-1-butyl acetate (1). The compounds were screened as potential H1 receptor agonists on the isolated guinea pig ileum. The 3-halogenated 2-phenylhistamines (halogen = Br (35) and I (36)) were equipotent with histamine, while 2-(3-(trifluoromethyl)phenyl)histamine (2-[2-(3-(trifluoromethyl)phenyl)-1H-imidazol-4-yl]ethanamine (39)) was significantly more potent than histamine (39: pD2 = 6.81, relative activity = 128%). The 2-substituted histamine analogues were partial H1 receptor agonists on the endothelium-denuded isolated guinea pig aorta with pEC50 values generally smaller than observed on the guinea pig ileum, but the rank order of potency was found to be similar. The contractile effects on guinea pig ileum and aorta, respectively, could be blocked concentration-dependently by the H1 receptor antagonist mepyramine, yielding KB values for mepyramine in the nanomolar range. In vitro compounds 35 and 39 bound to [3H]mepyramine-labeled guinea pig cerebellar membranes with a pKi of 6.1 and 5.9, respectively. However, upon iv administration, 35 (3-100 mg/kg) and 39 (3-300 mg/kg) failed to inhibit the binding of [3H]mepyramine to mouse cerebral cortex in vivo, thereby indicating that these histamine derivatives are not able to penetrate the blood-brain barrier. In functional in vitro studies on histamine H2, H3, and other neurotransmitter receptors the selectivity of 39 was found to be 2138 (H1:H2), > 64 (H1:H3), 1000 (H1:M3), 105 (H1:alpha 1), 708 (H1:beta 1), and 71 (H1:5HT2A). Thus compound 39 is the most potent and selective H1 receptor agonist reported so far. These results make meta-substituted 2-phenylhistamines, especially 2-(3-(trifluoromethyl)phenyl)- and 2-(3-bromophenyl)histamine (39 and 35, respectively) valuable experimental tools for the selective stimulation of histamine H1 receptors and the study of H1 receptor-mediated functions.

Animals↗
PubMed2000

4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor kinase and their bioisosteric relationship to the 4-anilino-6,7-dialkoxyquinazoline inhibitors.

The synthesis and SAR of a series of 4-anilino-6, 7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor (EGF-R) kinase are described. Condensation of 3, 4-dialkoxyanilines with ethyl (ethoxymethylene)cyanoacetate followed by thermal cyclization gave, regiospecifically, 6,7-dialkoxy-4-oxo-1, 4-dihydroquinoline-3-carbonitriles. Chlorination (POCl(3)) followed by the reaction with substituted anilines furnished the 4-anilino-6, 7-dialkoxyquinoline-3-carbonitrile inhibitors of EGF-R kinase. An alternate synthesis of these compounds starts with a methyl 3, 4-dialkoxybenzoate. Nitration followed by reduction (Fe, NH(4)Cl, MeOH-H(2)O) gave a methyl 2-amino-4,5-dialkoxybenzoate. Amidine formation using DMF-acetal followed by cyclization using LiCH(2)CN furnished a 6,7-dialkoxy-4-oxo-1,4-dihydroquinoline-3-carbonitrile, which was transformed as before. Compounds containing acid, ester, amide, carbinol, and aldehyde groups at the 3-position of the quinoline ring were also prepared for comparison, as were several 1-anilino-6,7-dimethoxyisoquinoline-4-carbonitriles. The compounds were evaluated for their ability to inhibit the autophosphorylation of the catalytic domain of EGF-R. The SAR of these inhibitors with respect to the nature of the 6,7-alkoxy groups, the aniline substituents, and the substituent at the 3-position was studied. The compounds were further evaluated for their ability to inhibit the growth of cell lines that overexpress EGF-R or HER-2. It was found that 4-anilinoquinoline-3-carbonitriles are effective inhibitors of EGF-R kinase with activity comparable to the 4-anilinoquinazoline-based inhibitors. A new homology model of EGF-R kinase was constructed based on the X-ray structures of Hck and FGF receptor-1 kinase. The model suggests that with the quinazoline-based inhibitors, the N3 atom is hydrogen-bonded to a water molecule which, in turn, interacts with Thr 830. It is proposed that the quinoline-3-carbonitriles bind in a similar manner where the water molecule is displaced by the cyano group which interacts with the same Thr residue.

Aniline Compounds↗
PubMed2000

Identification of novel inhibitors of urokinase via NMR-based screening.

Using an NMR-based screen, a novel class of urokinase inhibitors were identified that contain a 2-aminobenzimidazole moiety. The inhibitory potency of this family of inhibitors is similar to that of inhibitors containing a guanidine or amidine group. However, unlike previously described guanidino- or amidino-based inhibitors which have pK(a) values greater than 9.0, urokinase inhibitors containing a 2-aminobenzimidazole have pK(a) values of 7.5. Thus, 2-aminobenzimidazoles may have improved pharmacokinetic properties which could increase the bioavailability of inhibitors which contain this moiety. A crystal structure of one of the lead inhibitors, 2-amino-5-hydroxybenzimidazole, complexed with urokinase reveals the electrostatic and hydrophobic interactions that stabilize complex formation and suggests nearby subsites that may be accessed to increase the potency of this new series of urokinase inhibitors.

Benzimidazoles↗
PubMed1994

Pentamidine congeners. 2. 2-butene-bridged aromatic diamidines and diimidazolines as potential anti-Pneumocystis carinii pneumonia agents.

We have synthesized cis and trans geometric isomers 1-8 as semirigid congeners of pentamidine. Compounds 1-4 were more potent than pentamidine in treating Pneumocystis carinii pneumonia in immunosuppressed rats. These compounds also demonstrated no clinical toxicity or histopathologic abnormalities. Introduction of methoxy substituents meta to the amidine or imidazoline groups of the phenyl rings as in compounds 5-8 generally resulted in compounds with decreased anti-P. carinii activity and increased toxicity to the host. Compounds 1-4 were evaluated as DNA binders. These compounds showed greater affinity for poly(dA).poly(dT) than for calf thymus DNA. The cis isomers, 1 and 2, demonstrated greater affinity for DNA than their trans counterparts 3 and 4. This difference in DNA binding affinity, however, did not reflect in a corresponding difference in the anti-P. carinii activity of these compounds.

Animals↗
PubMed1993

S-adenosylmethionine decarboxylase inhibitors: new aryl and heteroaryl analogues of methylglyoxal bis(guanylhydrazone).

A series of 3-acylbenzamidine (amidino)hydrazones 7a-h, the corresponding (hetero)aromatic congeners 7i-p, and 3,3'-bis-amidino-biaryls 25a-e were synthesized. The hydrazones 7a-p were prepared by conversion of the corresponding acyl nitriles 1a,c-d,i,n-p to the imido esters 3a,c-d,i and the amidines 5a,c-d,h-i, followed by a reaction with aminoguanidine, or vice versa. Similarly, the biaryl 3,3'-dinitriles 23a-e were converted, via the imino esters 24a-c or the imino thioesters 27d-e, to the diamidines 25a-e. These new products are conformationally constrained analogues of methylglyoxal bis(guanylhydrazone) (MGBG). They are up to 100 times more potent as inhibitors of rat liver S-adenosylmethionine decarboxylase (SMDC) and generally less potent inhibitors of rat small intestine diamine oxidase (DAO) than MGBG. Some of these SAMDC inhibitors, e.g., compounds 7a, 7e, 7i, 25a, and 25d, have shown antiproliferative effects against T24 human bladder carcinoma cells. These products, whose structure-activity relationships are discussed, are of interest as potential anticancer agents and drugs for the treatment of protozoal and Pneumocystis carinii infections.

Adenosylmethionine Decarboxylase↗
PubMed1992

Synthesis, specificity, and antifungal activity of inhibitors of the Candida albicans delta 24-sterol methyltransferase.

A series of side chain modified analogues of cholesterol and lanosterol (1-10) have been synthesized and evaluated as inhibitors of the Candida albicans delta 24-sterol methyltransferase. Two sterol substrate analogues 1 and 2 which contained a 24-thia substituent were relatively modest inhibitors of the enzyme (Ki = 1.5-72 microM). Compounds which mimic the carbocation intermediates proposed for the methyltransferase reaction, including sulfonium salts 4-6, amidines 7 and 8, and imidazoles 9 and 10 were substantially more potent inhibitors (Ki = 5-500 nM). All of the sterol analogues examined displayed less than 10-fold selectivity for inhibition of the methyltransferase versus the rat liver delta 24-sterol reductase. The sterol analogues were tested for in vitro antifungal activity against C. albicans, Candida tropicalis, and Torulopsis glabrata. The minimum inhibitory concentrations versus C. albicans correlated well with the Ki values for methyltransferase inhibition, and the potency of several compounds approached that of amphotericin B, although only modest fungicidal activity was observed.

Antifungal Agents↗
PubMed1992

Condensation of muscimol or thiomuscimol with aminopyridazines yields GABA-A antagonists.

Ten analogs of muscimol and thiomuscimol in which the amino function was delocalized in an amidinic system were prepared by N2 alkylation of 6-aryl-3-aminopyridazines with (chloromethyl)isoxazole or (chloromethyl)isothiazole derivatives. These muscimol and thiomuscimol derivatives show potent binding properties for GABA-A receptors (they displace [3H]GABA and [3H]gabazine) and provoke convulsions after iv injections. They fit well with the model pharmacophore proposed by our group for the GABA-A antagonists and show similar structure-activity profiles to that of the pyridazinyl-GABAs.

Animals↗
PubMed1989

Peripherally acting enkephalin analogues. 2. Polar tri- and tetrapeptides.

The design, synthesis, and biological activity of a series of D-Arg2-enkephalin-derived tetrapeptide amides and tripeptide aralkylamides are reported. These polar analogues were designed to be excluded from the central nervous system with their action thus limited to peripheral opioid receptors. The effects of the nature of the aromatic ring, aryl ring substitution, and aralkylamine chain length on activity were investigated; in a number of cases the N-terminal amino group of Tyr1 was converted to a guanidino group to further increase hydrophilicity. The peptides were all synthesized by classical solution methodology. The opioid activity of the peptides was assessed in vitro on the guinea pig ileum and their antinociceptive activity was determined in vivo in chemically induced writhing models (peripheral activity) and in the hot-plate test (central activity), in rodents. That the analgesic effects were predominantly mediated in the periphery was demonstrated by antagonism of antinociception by the peripheral opioid antagonist N-methylnalorphine and by comparison of the activities in the writhing and hot-plate tests. As a class, the tetrapeptides were more potent than the tripeptides; N alpha-amidination generally increased activity. A number of compounds exhibited very potent opioid activity and had the desired pharmacological profile, indicating a high degree of peripheral selectivity.

Analgesia↗
PubMed1985

The histamine H2 receptor agonist impromidine: synthesis and structure-activity considerations.

Impromidine (1) is a potent and selective histamine H2 receptor agonist and its structure comprises a strongly basic guanidine group containing two different imidazole-containing side chains. In this paper we report the synthesis of analogues in which both of the side chains and the guanidine group are modified and tested as agonists or antagonists at histamine H2 receptors on guinea pig atrium. A protonated amidine group linked by a chain of three carbon atoms to a tautomeric imidazole ring appears to be an essential feature for agonist activity and it is suggested that the second imidazole-containing side chain in impromidine mainly contributes toward affinity for histamine H2 receptors.

Animals↗