NZ-105, a new 1,4-dihydropyridine derivative: correlation between dihydropyridine receptor binding and inhibition of calcium uptake in rabbit aorta.

The correlation between the binding of NZ-105, a newly synthesized 1,4-dihydropyridine (DHP) derivative, on DHP receptors and its inhibitory activity on transmembrane 45Ca2+ uptake was investigated. 3H-NZ-105 bound rabbit aortic microsomes more slowly than did 3H-nitrendipine (3H-NTD): the association and dissociation rate constants of 3H-NZ-105 were about 70 times and 10 times less than those of 3H-NTD, respectively. The dissociation constant (Kd) of 3H-NZ-105 (4.48 nM) was about 6 times larger than that of 3H-NTD (0.79 nM), and the maximum number of binding sites (Bmax) for 3H-NZ-105 (112.5 fmoles/mg protein) was about the same as that for 3H-NTD (106.2 fmoles/mg protein). Unlabelled NZ-105 and nicardipine fully, and in a concentration-dependent manner, displaced 3H-NZ-105 specific binding. Pre-incubation with NZ-105 also concentration-dependently (more than 0.1 microM) inhibited the transmembrane 45Ca2+ uptake increment induced by a high-K+ (50 mM) solution. The inhibitory efficacy of NZ-105 became larger as the incubation period with this compound increased (from 1 hr incubation to 3 hr incubation), and recovery was difficult even after washout for 3 hr. Based on these results, we conclude that NZ-105 causes blockade of voltage-dependent calcium channels (VDCs) by binding to DHP receptors. Moreover, the very slow onset and recovery from NZ-105-induced vasodilation may be attributable to the slow and long-lasting inhibition of transmembrane calcium uptake, which accompanies its very slow binding to and dissociation from DHP receptors.     

Function oriented synthesis: the design, synthesis, PKC binding and translocation activity of a new bryostatin analog

Bryostatin 1 represents a novel and potent therapeutic lead with a unique activity profile. Its natural and synthetic availability is severely limited. Function oriented synthesis provides a means to address this supply problem through the design of synthetically more accessible simplified structures that at the same time incorporate improved functional activity. Pharmacophore searching and a new computer aided visualization of a possible binding mode are combined with an understanding of function and knowledge of synthesis to design and prepare a new and simplified compound with bryostatin-like function in biological systems. This new compound is a potent ligand for protein kinase C in vitro (K(i) = 8.0 nM). More significantly, the described molecule retains the functional ability to translocate a PKCdelta-GFP fusion protein in RBL cells. The extent of protein translocation and the sub-cellular localization induced by this new compound is similar to that seen in response to bryostatin 1, indicating that the new molecule retains the functional activity of the natural product but is simpler and can be synthesized in a practical fashion.     

The alkoxyacetic acids as calcium and magnesium chelating agents in vitro

Alkoxyacetic acids (AAAs) are known urinary metabolites of the corresponding ethylene glycol monoalkyl ethers with a wide range of industrial and domestic applications. Hemolysis is the principal toxic effect of AAAs in humans and animals. The mechanism of red-cell damage is not known. It is suggested that some disturbances in ion balance, mainly related to calcium are one of the reasons of hemolysis. No comparative studies in the available literature on the chelating properties of numerous AAAs in respect to calcium were found. Therefore, a comparison was made between chelating effects of five AAAs on calcium and magnesium in vitro. It was demonstrated that calcium was bound at lower AAAs concentrations than magnesium. The chelating effect of AAAs expressed by EC50 values was positively correlated with both pKa values and Log P values of the examined acids. The obtained data indicate that the acidity and hydrophilic properties are responsible for the chelating effect of AAAs on calcium and magnesium in vitro. These data do not provide an explanation for differences in the hemolytic activity of the examined compounds.     

Enzyme inhibition as a source of new drugs

The significance of enzymes as targets of drug action is discussed. New approaches to the rational design of enzyme inhibitors are characterized by a pronounced shift of emphasis toward the targets of drug action, as the structure and function of an increasing number of enzymes are described in great detail. The most promising of the recently developed approaches is the design of mechanism-based enzyme inhibitors and, in particular, suicide inactivators. These require enzymic activation of “latent” functional groups to chemically reactive species. The various functionalities currently encountered are reviewed, grouped into chemical categories. The various aspects of the selectivity and the specificity of mechanism-based enzyme inhibitors, as well as the stability of drug-enzyme complexes, are discussed in detail. Reversible covalent bond formation is demonstrated by the recovery of thymidylate synthetase activity after inactivation by various 5-substituted pyrimidine analogs, using purified bacterial enzyme preparations or intact mammalian cells. The fragmentation and secondary reactions of the inhibitor within the complex are described using typical examples of the action of penicillin on its targets and clavulanate on /3-lactamase, respectively. The perspectives of enzyme inhibitory drug development are discussed, and some of the many areas currently undergoing rapid exploration are mentioned. It is concluded that the rational design of enzyme inhibitors will play an ever-increasing and significant role in new drug discovery and development.     

Oligopyrrole carboxamides linked with a nucleobase as potential DNA minor groove binding ligands: synthesis, DNA binding and biological evaluation

The synthesis of a series of new oligopyrrole carboxamides closely related to netropsin and distamycin A, linked with a nucleobase is reported. The new compounds possess similar structure elements as the known peptide nucleic acids which are interesting sequence reading DNA ligands. Cytotoxicity in vitro, the DNA binding characteristics and the inhibition of topoisomerase I were studied. Four of the compounds, 27, 31, 33 and 37 bind to DNA probably at AT sequences like netropsin or distamycin A in the minor groove. Surprisingly, no cytotoxicity and no inhibition of topoisomerase I was found.     

Design, synthesis, and binding studies of new potent ligands of cannabinoid receptors

Despite their different chemical structures, delta9-tetrahydrocannabinol (THC) and anandamide (AEA) have common pharmacological properties. This study was aimed at finding new cannabinoid receptor ligands that overcome the instability of AEA and its analogues. To this end we planned the synthesis of a series of compounds which retained both a rigid structure, like that of plant cannabinoids, and a flexible portion similar to that of anandamide. Binding studies on CB1 and CB2 receptors, anandamide membrane transporter (AMT), and fatty acid amide hydrolase (FAAH) showed that some of the newly developed compounds have high affinity and specificity for cannabinoid CB1 and CB2 receptors. Compound 25 is a potent CB1 and CB2 ligand, with affinity constants significantly lower than AEA and similar to WIN 55-212, compound 52 is a potent CB2 ligand, although not very selective over CB1 receptors, and compound 43 is CB2 ligand, with at least a 26-fold selectivity over CB1 receptors. Compound 25 behaved as a inverse agonist at CB1 receptors as assessed in the cyclic AMP functional assay.     

Repaglinide-gemfibrozil drug interaction: inhibition of repaglinide glucuronidation as a potential additional contributing mechanism

AIM

To further explore the mechanism underlying the interaction between repaglinide and gemfibrozil, alone or in combination with itraconazole.

METHODS

Repaglinide metabolism was assessed in vitro (human liver subcellular fractions, fresh human hepatocytes, and recombinant enzymes) and the resulting incubates were analyzed, by liquid chromatography-mass spectrometry (LC-MS) and radioactivity counting, to identify and quantify the different metabolites therein. Chemical inhibitors, in addition to a trapping agent, were also employed to elucidate the importance of each metabolic pathway. Finally, a panel of human liver microsomes (genotyped for UGT1A1*28 allele status) was used to determine the importance of UGT1A1 in the direct glucuronidation of repaglinide.

RESULTS

The results of the present study demonstrate that repaglinide can undergo direct glucuronidation, a pathway that can possibly contribute to the interaction with gemfibrozil. For example, [³H]-repaglinide formed glucuronide and oxidative metabolites (M2 and M4) when incubated with primary human hepatocytes. Gemfibrozil effectively inhibited (∼78%) both glucuronide and M4 formation, but had a minor effect on M2 formation. Concomitantly, the overall turnover of repaglinide was also inhibited (∼80%), and was completely abolished when gemfibrozil was co-incubated with itraconazole. These observations are in qualitative agreement with the in vivo findings. UGT1A1 plays a significant role in the glucuronidation of repaglinide. In addition, gemfibrozil and its glucuronide inhibit repaglinide glucuronidation and the inhibition by gemfibrozil glucuronide is time-dependent.

CONCLUSIONS

Inhibition of UGT enzymes, especially UGT1A1, by gemfibrozil and its glucuronide is an additional mechanism to consider when rationalizing the interaction between repaglinide and gemfibrozil.     

O'-(epoxyalkyl)tyrosines and (epoxyalkyl)phenylalanine as irreversible inactivators of serine proteases: synthesis and inhibition mechanism

A series of O'-(epoxyalkyl)tyrosines and a carboxy terminal (epoxyalkyl)tyrosine and -phenylalanine were synthesized as potential serine protease inhibitors. N-Acetyl derivatives showed irreversible inactivation vis-a-vis subtilisin, while the N-benzoyl ones were specific toward chymotrypsin. The most potent inactivation of chymotrypsin was achieved by a O'-(3,4-epoxybutyl)-L-tyrosine derivative. The inactivation was shown to be stereospecific since a D derivative led to no irreversible inactivation. Placement of the epoxyalkyl group at the carboxy terminus led to potent rapid inactivation. Under these conditions some of the activity was later recovered. The two classes of inactivators (O'-epoxyalkyl and carboxy-epoxyalkyl) appear to operate by different mechanisms. Most importantly, it was found that irreversible inactivation by O'-(epoxyalkyl)-L-tyrosine only resulted if the carboxy terminus was a substrate (i.e. a compound with free carboxy terminus did not lead to inactivation). The ultimate activity kinetic assay (Daniels, S. B.; et al. J. Biol. Chem. 1983, 258, 15046-15053.) indicated that the epoxyalkyl group on the phenolic oxygen had an optimal length of four carbons with respect to the turnover ratio (the ratio of molecules undergoing turnover compared to those that inactivate the enzyme) for chymotrypsin. A different kinetic assay (Ashani, Y.; Wins, P.; Wilson, I. B. Biochim. Biophys. Acta 1972, 284, 427-434.) demonstrated that substratelike turnover was proceeding at considerably slower rates than for the corresponding true substrates and with rate-limiting deacylation of the acyl-enzyme. Amino acid analysis subsequent to acid hydrolysis demonstrated that Met had been selectively alkylated by the O'-(epoxyalkyl)tyrosine derivative. By contrast, alpha-chymotrypsin inactivated with N-benzoyl-L-Phe-2,3-epoxypropyl ester then subjected to amino acid analysis showed no change in the content of any amino acid that would serve as a potential nucleophile to the inhibitor. Yet, the L-Phe content increased, indicating that a covalent bond had been formed between the inhibitor and the enzyme. Either the bond between the inhibitor and the enzyme did not withstand the hydrolytic conditions and/or there was less than 10% decrease in the amino acids with nucleophilic side chains upon inactivation. Finally, two tripeptides containing O'-(epoxyalkyl)-L-tryosines were synthesized [N-(tert-butoxycarbonyl)-L-alanyl-L-alanyl-O'-(2,3-epoxypropyl)-L-tyrosi ne ethyl ester and N-(trifluoroacetyl)-L-valyl-O'-(2,3-epoxypropyl)-L-tyrosyl-L-valine methyl ester] as potential elastase inhibitors and were found to reversibly and competitively inhibit porcine pancreatic elastase.     

N-modified analogues of cocaine: synthesis and inhibition of binding to the cocaine receptor.

Cocaine methiodide (2), N-norcocaine (1b), N-benzyl-N-norcocaine (1c), and N-nor-N-acetylcocaine (1d) were synthesized and evaluated for their ability to inhibit binding of [3H]-3 beta-(4-fluorophenyl)tropane-2 beta-carboxylic acid methyl ester (WIN 35,428) to the cocaine receptor. The study showed that removal of the N-methyl group to give 1b, or replacement with the larger N-benzyl group to give 1c, has a relatively small effect on binding potency. In contrast, replacement of the N-methyl group by the acetyl moiety to give 1d, or the addition of a methyl group to give 2, reduces affinity for the receptor by a large factor. In order to gain preliminary information concerning the importance of the nitrogen location on the tropane ring system, the receptor binding affinity of 8-methyl-8-azabicyclo[3.2.1]octan-3 beta-ol benzoate (5, beta-tropacocaine) was compared to that of the isomeric 6-methyl-6-azabicyclo[3.2.1]octan-3 beta-ol benzoate (4d). The fact that both compounds have similar binding affinities for the cocaine receptor suggests that 3 beta-(benzoyloxy)-6-methyl-6-azabicyclo[3.2.1] octane-2-carboxylic acid methyl ester, which is isomeric with cocaine, may possess binding potency similar to cocaine.     

Hydroxyethylene sulfones as a new scaffold to address aspartic proteases: design, synthesis, and structural characterization

Hydroxyethylene sulfones were developed as novel scaffolds against aspartyl proteases. A diastereoselective synthesis has been established to introduce the required side chain decoration with desired stereochemistry. Depending on the substitution of the hydroxyethylene sulfone core, micro- to submicromolar inhibition of HIV-1 protease is achieved for the S-configuration at P1 and R-configuration at the hydroxy-group-bearing backbone atom. This stereochemical preference is consistent with the S,R configuration of amprenavir. The racemic mixture of the most potent derivative (K(i) = 80 nM) was separated by chiral HPLC, revealing the S,R,S-enantiomer to be more active (K(i) = 45 nM). Docking studies suggested this isomer as the more active one. The subsequently determined crystal structure with HIV-1 protease, cocrystallized from a racemic mixture, exclusively reveals the S,R,S-enantiomer accommodated to the binding pocket. The transition state mimicking hydroxy group of the inhibitor is centered between both catalytic aspartates, while either its carbonyl or sulfonyl group forms H-bonds to the structurally conserved water mediating interactions between ligand and Ile50NH/Ile50NH' of both flaps. Biological testing of the stereoisomeric hydroxyethylene sulfones against cathepsin D and beta-secretase did not reveal significant inhibition. Most likely, the latter proteases require inverted configuration at the hydroxy group.     

Effects of KB-2796, a new calcium antagonist, and other diphenylpiperazines on [3H]nitrendipine binding

The effect of KB-2796, a new diphenylpiperazine calcium antagonist, on [3H]nitrendipine ([3H]NTD) binding was investigated in synaptosomal membranes prepared from the guinea pig cerebral cortex. KB-2796 inhibited [3H]NTD binding in a dose-dependent manner with an IC50 value of 86 nM. In this respect, KB-2796 was the most potent among the diphenylpiperazine derivatives tested. Saturation binding data indicated that this inhibition resulted from a decrease in the binding affinity without changes in the maximal number of binding sites. KB-2796, however, significantly increased the dissociation rate constant of [3H]NTD from radiolabeled membranes. This finding suggests that KB-2796 inhibits [3H]NTD binding by a negative heterotropic allosteric mechanism. Other diphenylpiperazines tested also showed similar inhibitory properties. Diphenylpiperazines may act at a site, which is different from the 1,4-dihydropyridine binding site, on the voltage-dependent calcium channel.     

DNA binding by epipodophyllotoxins and N-acyl anthracyclines: implications for mechanism of topoisomerase II inhibition

Previous evidence suggests that epipodophyllotoxins, such as etoposide and teniposide, and the N-acyl anthracycline AD41 inhibit topoisomerase II resealing even though they apparently do not bind to DNA. Using experimental conditions designed to detect limited numbers of DNA binding sites, we now report that both epipodophyllotoxins and the N-acyl anthracyclines AD41 and AD32 bind to DNA. Binding was greater to kinetoplast DNA than to pUC18 plasmid DNA. There was also greater etoposide binding to single-stranded DNA than to double-stranded linear or supercoiled DNA. Based on binding competition experiments, etoposide and teniposide appear to have equal affinity for DNA, in spite of the fact that the latter is more potent as a topoisomerase inhibitor. This suggests that the difference in the drugs relates to protein interaction. There are 3- to 7-fold more binding sites for AD41 than for AD32, depending on the DNA substrate employed, and both drugs, unlike adriamycin, exhibit saturation of binding sites over a concentration range of 0-50 microM when kinetoplast DNA is the substrate. Evidence for DNA intercalation by AD41 is provided by the observation that the drug introduces positive supercoils into covalently closed plasmid DNA. Based on these data, a hypothesis is proposed that would provide a general mechanism whereby intercalating agents and epipodophyllotoxins alter topoisomerase function and presumably exert their antitumor effects.     

HIV-1 IN strand transfer chelating inhibitors: a focus on metal binding

Most active and selective strand transfer HIV-1 integrase (IN) inhibitors contain chelating functional groups that are crucial feature for the inhibition of the catalytic activities of the enzyme. In particular, diketo acids and their derivatives can coordinate one or two metal ions within the catalytic core of the enzyme. The present work is intended as a contribution to elucidate the mechanism of action of the HIV-IN inhibitors by studying the coordinative features of H?L1 (L-708,906), an important member of the diketo acids family of inhibitors, and H?L?, a model for S-1360, another potent IN inhibitor. Magnesium(II) and manganese(II) complexes of H?L1 and H?L2 were isolated and fully characterized in solution and in the solid state. The crystal structures of the manganese complex [Mn(HL?)?(CH?OH)?]·2CH?OH were solved by X-ray diffraction analysis. Moreover, the speciation models for H?L? with magnesium(II) and manganese(II) ions were performed and the formation constants of the complexes were measured. M(HL?)? (M = Mg2+, Mn2+) was the most abundant species in solution at physiological pH. All the synthesized compounds were tested for their anti-IN activity, showing good results both for the ligand and the corresponding complexes. From analysis of the speciation models and of the biological data we can conclude that coordination of both metal cofactors could not be strictly necessary and that inhibitors can act as complexes and not only as free ligands.     

Neuropeptide Y receptor in pig spleen: binding characteristics, reduction of cyclic AMP formation and calcium antagonist inhibition of vasoconstriction

Specific, high-affinity binding sites for 125I-porcine neuropeptide Y (NPY) were demonstrated in membranes from the pig spleen. The equilibrium dissociation constant (KD) of the receptor 125I-NPY complex was 532 +/- 87 pM and the maximal number of specific binding sites (Bmax) 23 +/- 3 fmol/mg protein. The Scatchard plot for 125I-NPY binding under equilibrium conditions showed a best-fit to a straight line, whereas the dissociation appeared biphasic. 125I-NPY binding was unaffected by adrenoceptor antagonists and was inhibited by the guanosine triphosphate (GTP) analogue guanylylimidodiphosphate, suggesting regulation by a GTP binding protein. A series of NPY analogues showed a good correlation between binding, inhibition of forskolin-induced cyclic adenosine monophosphate (cAMP) formation and vasoconstrictor activity in vivo. A large carboxyl terminal portion of NPY and the carboxyl terminal amide were essential for binding, inhibition of cAMP formation and vasoconstrictor effects. The NPY fragment 13-36, which has been reported to act only on prejunctional NPY receptors, showed only a 10-fold lower potency than NPY-(1-36) both in binding to splenic membranes and vasoconstrictor activity in vivo. Phenylephrine increased phosphatidyl inositol turnover whereas NPY-(1-36) or -(13-36) did not induce formation of inositol phosphates. The calcium antagonists felodipine and nifedipine attenuated the splenic vasoconstrictor response to NPY in vivo but not the NPY-evoked inhibition of cAMP accumulation or the specific binding of 125I-NPY.(ABSTRACT TRUNCATED AT 250 WORDS)     

6-Chloropyridazin-3-yl derivatives active as nicotinic agents: synthesis,binding, and modeling studies

3,8-Diazabicyclo[3.2.1]octane (1), 2,5-diazabicyclo[2.2.1]heptane (2), piperazine (3), and homopiperazine (4) derivatives, substituted at one nitrogen atom with the 6-chloro-3-pyridazinyl group while the other nitrogen atom was either unsubstituted or mono- or dimethylated, were synthesized and tested for their affinity toward the neuronal nicotinic acetylcholine receptors (nAChRs). All of the compounds had K(i) values in the nanomolar range. A molecular modeling study allowed location of their preferred conformations, the energies of which were recalculated in water with a continuum solvent model. Some of the compounds showed, in their populated conformations, only pharmacophoric distances longer than the values taken into consideration by the Sheridan model for nAChRs receptors. Thus, this SAR study gives support to the hypothesis that these longer distances are still compatible with affinity for alpha4beta2 receptors in the nanomolar range.     

Impact of binding mechanism on selective inhibition of histone deacetylase isoforms

Industrialized drug screening campaigns usually deliver hundreds of compounds that are active on a particular pharmaceutical target. In light of high failure rates of drug candidates due to unforeseeable off‐target toxicity, the early identification of the most promising compounds with high potential for target selectivity is an urgent need to improve the quality of lead compounds and lower attrition rates in the drug development process. The reliable prediction of the selectivity of active substances for a target protein is a challenging task. A comprehensive study of the binding kinetics, thermodynamics, and selectivity of chemically related ligands of histone deacetylase (HDAC) like amidohydrolase from Pseudomonas aeruginosa (HDAH_pa) reveals one general binding mechanism for all analyzed compounds consisting of a preceding conformational selection step followed by an optional subsequent induced fit. Depending on the chemical structure, the ligands bind to one or two of at least three protein conformations with different rate constants. Although these kinetic and mechanistic differences hamper the predictability of selectivity for the HDAC inhibitors, we demonstrate that the enthalpy‐weighted binding constant is a useful metric to predict isoform selectivity of inhibitors against HDAC enzymes and relatively robust toward different but related binding mechanisms.     

Oxime amides as a novel zinc binding group in histone deacetylase inhibitors: synthesis, biological activity, and computational evaluation

Several oxime containing molecules, characterized by a SAHA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new α-oxime amide derivatives do not select between class I and class II HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile.     

2-Methoxyestradiol and analogs as novel antiproliferative agents: analysis of three-dimensional quantitative structure-activity relationships for DNA synthesis inhibition and estrogen receptor binding

2-Methoxyestradiol (2-MEO), a metabolite of estrogen, is an attractive lead compound for the development of novel antitumor and anti-inflammatory agents, because it embodies antiproliferative and antiangiogenic activities in one molecule. However, the affinity of 2-MEO for the estrogen receptor would lead to undesirable side effects. As a prelude to the design of 2-MEO-like compounds with an optimal activity profile, we assayed 2-MEO and a series of analogs for their ability to cause G(1) cell-cycle arrest (by measuring inhibition of DNA synthesis in human cultured airway smooth muscle) and to inhibit binding of [(3)H]estradiol at the estrogen receptor (ER; from rat uterine smooth muscle). One compound, a diacetoxy enediol derivative, was identified with reasonable potency for DNA synthesis (pIC(50) = 5.97) but showed negligible affinity for the ER (pIC(50) < 5). Three-dimensional quantitative structure-activity relationships were developed for these activities using comparative molecular field analysis (CoMFA) techniques. Comparison of optimized CoMFA models revealed distinct structural requirements for DNA synthesis inhibition and ER binding. For example, DNA synthesis inhibition is enhanced by electropositive substitutions in the 2-position below the plane of the steroid A-ring, whereas ER binding is favored by electronegative substitution in this position. Similarly, DNA synthesis inhibition correlates negatively with increased steric bulk in regions clustered around the A and B rings; changes in steric bulk in these regions has little correlation with ER binding. These observations will guide the design of new analogs with improved potency for desired characteristics (e.g., DNA synthesis inhibition) with minimal unwanted activities (e.g., ER binding).