N,N'-bis[4-(N-alkylamidino)phenyl]homopiperazines as anti-Pneumocystis carinii agents.

The synthesis, anti-Pneumocystis carinii activity and DNA binding properties of eight new N,N'-bis[4-(N-alkylamidino)phenyl]homopiperazines are reported. Compounds 2 and 8 were the most potent and caused about 70% inhibition of Pneumocystis carinii growth in a cell culture model at 1 microM concentrations.

Synthesis of a reported calpain inhibitor isolated from Streptomyces griseus.

The reported diketopiperazine calpain inhibitor, cis-L-L-3,6-bis-(4-hydroxybenzyl)-1,4-dimethylpiperazine-2,5-dione 1, and its analogues 3 and 4 were synthesized from the corresponding amino acids. The previously assigned structure of 1 is confirmed but neither synthetic 1 nor its N-methylphenylalanine analogues 3 and 4 inhibit porcine erythrocyte calpain I.

Trypanocidal activity of dicationic compounds related to pentamidine.

Eight dicationic compounds related to pentamidine were studied for trypanocidal activity in seven trypanosome isolates. In vitro studies revealed that diamidines are more potent than diimidazolines. For example, 2 (a diamidine) and 4 (a diimidazoline) inhibited the growth of KETRI 243 with IC50 values of 2.3 and 900 nM, respectively. Introduction of polar groups into the linker decreased the effectiveness of the compounds against drug-resistant trypanosomes. In compounds with a 2-butene linker between the cationic groups, trans-isomers were more potent than cis-isomers. The cis- and trans-buteneamidines cured infection caused by Trypanosoma brucei brucei (EATRO Lab 110) and protected mice against infection by Trypanosoma brucei rhodesiense isolates, some of which are resistant to diamidines and melarsoprol.

Significance of hydrogen bonding at the S(1)' subsite of calpain I.

alpha-Ketohydroxamates were synthesized as bioisosteres of alpha-ketoamides. The alpha-ketohydroxamates were generally more potent than the corresponding alpha-ketoamides. The potency of the compounds suggests that hydrogen bonding and steric bulk of substituents on the nitrogen atom of the ketoamide moiety influence calpain inhibition.

Synthesis and calpain inhibitory activity of alpha-ketoamides with 2,3-methanoleucine stereoisomers at the P2 position.

A series of novel ketoamides incorporating all four 2,3-methanoleucine stereoisomers at the P2 position was synthesized. The compounds displayed a wide variation in Ki values for inhibition of calpain I depending on the configuration of the P2 methanoleucine residue. However, similar variation in cathepsin B inhibition was not observed suggesting that the S2 pocket of calpain I is more stereosensitive than that of cathepsin B.

A survey of calpain inhibitors.

Calpain is unique among the cysteine protease family of enzymes in that it combines thiol protease activity with calmodulin-like activity. Despite its wide spread distribution the exact physiological function(s) of calpain is yet to be deciphered. The enzyme is however, implicated in a number of pathophysiological conditions. Due to the potential of calpain as a therapeutic target a number of inhibitors have been described for the enzyme. In this article we have grouped calpain inhibitors into those derived from natural sources, and those derived from chemical synthesis. Additionally, an overview of functional groups that have been used as warheads of calpain inhibitors is presented along with a discussion of the structure activity relationship studies of the address region of peptidyl calpain inhibitors. Recent work in this area has led to a better understanding of the structural requirements for tight binding of inhibitors to the active site of calpain. A discussion of peptidomimetic calpain inhibitors, nonpeptide calpain inhibitors, and selectivity of some calpain inhibitors are also presented. The recent disclosure of the crystal structure of a nonpeptide calpain inhibitor bound to a hydrophobic pocket on the calcium-binding domain of calpain has opened the door to future development of potent cell permeable nonpeptide calpain inhibitors.

Asymmetric synthesis of 2,3-methanoleucine stereoisomers from common intermediates.

2,3-Methanoamino acids are useful probes for studying the bioactive conformation of peptides and for investigating the effect of local conformational constraints on the activity of peptidomimetics. We synthesized all four stereoisomers of Cbz-protected 2, 3-methanoleucine for incorporation into peptidomimetic inhibitors of calpain. While the synthesis of 2,3-methanoamino acids has been previously reported, our procedure offers a versatile route in which the pair of diastereomers of each geometric isomer was synthesized from a common intermediate.

Unprecedented crystallization and X-ray crystal structure of racemic N(alpha)-(t-butyloxycarbonyl)-L-L-phenylalanine N-methoxy-N-methylamide.

Weinreb amide 3 was synthesized using isobutyl chloroformate, carbonyldiimidazole, or ethylcarbodiimide as the coupling agent in the reaction of Boc-phenylalanine with O,N-dimethylhydroxylamine hydrochloride. An optically active oil was isolated along with an optically inactive solid irrespective of the type of coupling agent used. Single crystal X-ray analysis of the solid revealed that it is a racemate. The molecular packing of the crystals reflect the stability of the racemate as opposed to an enantiomerically pure solid.

Novel bisbenzamidines and bisbenzimidazolines as noncompetitive NMDA receptor antagonists.

A series of novel bisbenzamidines and bisbenzimidazolines with different linkers connecting the aromatic groups was tested in vitro for NMDA receptor antagonist activity. IC50 values for these compounds ranged from 1.2 to >200 microM. The bisbenzamidine with a homopiperazine ring as the central linker was found to be the most potent NMDA receptor antagonist among all the pentamidine analogues tested so far.

Peptidomimetic probes and molecular modeling suggest that Alzheimer's gamma-secretase is an intramembrane-cleaving aspartyl protease.

The amyloid beta-protein (Abeta), implicated in the pathogenesis of Alzheimer's disease (AD), is a proteolytic metabolite generated by the sequential action of beta- and gamma-secretases on the amyloid precursor protein (APP). The two main forms of Abeta are 40- and 42-amino acid C-terminal variants, Abeta40 and Abeta42. We recently described a difluoro ketone peptidomimetic (1) that blocks Abeta production at the gamma-secretase level [Wolfe, M. S., et al. (1998) J. Med. Chem. 41, 6-9]. Although designed to inhibit Abeta42 production, 1 also effectively blocked Abeta40 formation. Various amino acid changes in 1 still resulted in inhibition of Abeta40 and Abeta42 production, suggesting relatively loose sequence specificity by gamma-secretase. The alcohol counterparts of selected difluoro ketones also lowered Abeta levels, indicating that the ketone carbonyl is not essential for activity and suggesting that these compounds inhibit an aspartyl protease. Selected compounds inhibited the aspartyl protease cathepsin D but not the cysteine protease calpain, corroborating previous suggestions that gamma-secretase is an aspartyl protease with some properties similar to those of cathepsin D. Also, since the gamma-secretase cleavage sites on APP are within the transmembrane region, we consider the hypothesis that this region binds to gamma-secretase as an alpha-helix and discuss the implications of this model for the mechanism of certain forms of hereditary AD.

In vitro antimicrobial activity of aromatic diamidines and diimidazolines related to pentamidine.

Geometric isomers of pentamidine analogues were screened for antimicrobial activity in vitro. cis isomers demonstrated good antibacterial activity compared to their trans counterparts. Both isomers were moderately active against opportunistic pathogens that afflict AIDS patients with minimum inhibitory concentrations in the range of 3.12-12.5 microg/mL.

Synthesis and radioprotective effects of adamantyl substituted 1,4-dihydropyridine derivatives.

A series of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic acid diesters substituted at the N-1 and/or C-4 positions of the dihydropyridine ring was synthesized. The in vitro cytotoxicity and in vitro and in vivo radioprotective efficacy of these agents were evaluated in Chinese hamster (V-79) cells and CD2F1 male mice, respectively. Compounds with at least one adamantyl substituent afforded better radioprotection than those without this substituent. Substitution of an aromatic ring at the C-4 position of the dihydropyridine ring did not enhance the radioprotectant action of the compounds.

Synthesis and antimicrobial activity of 6,7-annulated pyrido[2,3-d]pyrimidines.

Four new 6H-indeno[2',1':5,6]pyrido[2,3-d]pryimidines (10-13) were synthesized via cyclocondensation reactions involving chlorovinyl aldehyde 1 or ketoaldehyde 3 and appropriately substituted 6-aminopyrimidines. The regiochemistry of the compounds was established by 1H NMR and 13C NMR spectral data as well as X-ray crystal data. Compounds 10 and 11 and previously reported homologues 14 and 15 were screened for antimicrobial activity. Moderate antimicrobial activity was observed for some of these compounds. Compound 14 was especially active against Staphylococcus aureus. Crystal data for 13 (C14H7N3Cl2) follows: monoclinic space group, P21/n; Unit cell dimensions, a = 7.284(1) A, b = 12.800(1) A, c = 13.108(1) A, beta = 93.98(1) degree, V = 1219.2(2) A3, Z = 4.

Pentamidine congeners. 3. Crystal structure and molecular modeling studies of trans-1,4-bis(4-amidinophenoxy)-2-butene.

X-ray diffraction was used to confirm the geometry of trans-1,4-bis(4-amidinophenoxy)-2-butene dihydrochloride dihydrate (trans-butenamidine). trans-Butenamidine is a semirigid analogue of pentamidine that has demonstrated good anti-Pneumocystis carinii activity in rats. Molecular modeling studies revealed that unlike pentamidine or propamidine, trans-butenamidine does not discriminate between AT and TA sequences in its binding to the minor groove of DNA. Crystal data: [C18H22N4O2(2+)][Cl(-)]2[H2O]2, triclinic space group, P1, a = 9.443(1) A, b = 11.400(1) A, c = 11.919(1) A, alpha = 62.19(1) degree, beta = 81.10(1) degree, gamma = 72.19(1) degree, V = 1080.3(3) A3, Z = 2, R = 0.054 for 1149 observed reflections with I > 3 sigma (1).

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.

Sequence-selective binding to DNA of cis- and trans- butamidine analogues of the anti-Pneumocystis carinii pneumonia drug pentamidine.

Footprinting experiments using both DNase I and methidium propyl-EDTA.Fe(II) have been used to investigate the sequence selectivity in binding to DNA of pentamidine and four butamidine analogues active against the Pneumocystis carinii pathogen, which afflicts patients with acquired immunodeficiency syndrome. In common with pentamidine, the butamidine drugs, which contain cis- or trans-1,4-but-2-ene linkers and either bis(amidine) or bis(imidazolidine) terminal groups, bind selectively to DNA sequences composed of at least 4 consecutive A.T base pairs. None of the drugs tolerates the presence of a G.C base pair within the binding site. Consistently in the DNase I and methidium propyl-EDTA.Fe(II) footprinting experiments, the cis-isomers produce stronger footprints than do the trans-isomers, despite their similar hydrogen-bonding potentialities. The present experimental data support the view that the conformation of the drug plays a determining role in the binding reaction. Starting from the known structure of a pentamidine-oligonucleotide complex, it is possible to rationalize the different capacities of the cis- and trans-butamidine analogues to recognize defined DNA sequences in terms of the radius of curvature of the molecule and the distance between the positively charged terminal groups. Together, these features constitute critical factors favoring (cis-conformation) or hampering (trans-conformation) the fitting of the drugs into the minor groove of DNA. In terms of structure-activity relationships, the AT-specific recognition of DNA by this series of butamidine derivatives cannot be directly correlated with their potencies against Pneumocystis carinii pneumonia.

Structure, DNA minor groove binding, and base pair specificity of alkyl- and aryl-linked bis(amidinobenzimidazoles) and bis(amidinoindoles).

A series of bis(amidinobenzimidazoles) and bis(amidinoindoles) with varied linking chains connecting the aromatic groups and various modifications to the basic amidino groups have been prepared. The calf thymus (CT) DNA and nucleic acid homopolymer [poly(dA).poly(dT),poly(dA-dT).poly-(dA-dT), and poly(dG-dC).poly(dG-dC)] binding properties of these compounds have been studied by thermal denaturation (delta Tm) and viscosity. The compounds show a greater affinity for poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) than for poly(dG-dC).poly(dG-dC). Viscometric titrations indicate that the compounds do not bind by intercalation. Molecular modeling studies and the biophysical data suggest that the molecules bind to the minor groove of CT DNA and homopolymers. Analysis of the shape of the molecules is consistent with this mode of nucleic acid binding. Compounds with an even number of methylenes connecting the benzimidazole rings have a higher affinity for DNA than those with an odd number of methylenes. Molecular modeling calculations that determine the radius of curvature of four defined groups in the molecule show that the shape of the molecule, as a function of chain length, affects the strength of nucleic acid binding. Electronic effects from cationic substituents as well as hydrogen bonding from the imidazole nitrogens also contribute to the nucleic acid affinity. The bis(amidinoindoles) show no structurally associated differential in nucleic acid base pair specificity or affinity.

Synthesis and biological activity of 5,11-methylenetetrahydro-5- deazahomofolic acid.

The synthesis of 5,11-methylene-5-deazatetrahydrohomofolate (5), a stable, semirigid mimic of 5,10-methylenetetrahydrofolate (4) is reported as a potential inhibitor of thymidylate synthases (TS). The key intermediate 3-amino-1-oxo-tetrahydropyrimido[4,5-c] [2,6]naphthyridine (6) was obtained by the regiospecific cyclocondensation of 2,4,6-triaminopyrimidine with ethyl 1-benzyl-3-oxo-4-piperidinecarboxylate followed by halogenation (of the resulting lactam 9) and catalytic hydrogenolysis. Selective reduction of 6 followed by arylation with tert-butyl p-fluorobenzoate, saponification, and coupling with diethyl L-glutamate followed by saponification afforded the target compound 5. The title compound was tested as an inhibitor of the growth of Manca human lymphoma cells and also as an inhibitor of TS from Manca cells and Lactobacillus casei and was found to be inactive. In addition, compound 5 also failed to inhibit glycinamide ribonucleotide formyltransferase from L. casei and from Manca cells.