Antitubercular nitrofuran isoxazolines with improved pharmacokinetic properties

A series of tetracyclic nitrofuran isoxazoline anti-tuberculosis agents was designed and synthesized to improve the pharmacokinetic properties of an initial lead compound, which had potent anti-tuberculosis activity but suffered from poor solubility, high protein binding and rapid metabolism. In this study, structural modifications were carried on the outer phenyl and piperidine rings to introduce solubilizing and metabolically blocking functional groups. The compounds generated were evaluated for their in vitro antitubercular activity, bacterial spectrum of activity, solubility, permeability, microsomal stability and protein binding. Pharmacokinetic profiles for the most promising candidates were then determined. Compounds with phenyl morpholine and pyridyl morpholine outer rings were found to be the most potent anti-tuberculosis agents in the series. These compounds retained a narrow antibacterial spectrum of activity, with weak anti-Gram positive and no Gram negative activity, as well as good activity against non-replicating Mycobacterium tuberculosis in a low oxygen model. Overall, the addition of solubilizing and metabolically blocked outer rings did improve solubility and decrease protein binding as designed. However, the metabolic stability for compounds in this series was generally lower than desired. The best three compounds selected for in vivo pharmacokinetic testing all showed high oral bioavailability, with one notable compound showing a significantly longer half-life and good tolerability supporting its further advancement.     

Exploring structure-promiscuity relationships using dual-site promiscuity cliffs and corresponding single-site analogs

Currently available volumes of compounds and biological activity data enable large-scale analyses of compound promiscuity (multi-target activity). To aid in the exploration of structure-promiscuity relationships, promiscuity cliffs (PCs) were introduced previously. In analogy to activity cliffs, PCs were defined as pairs of structurally analogous compounds with large differences in the number of targets they are active against. Hence, PCs reveal small chemical modifications that are implicated in promiscuity. As introduced originally, PCs were identified by applying the matched molecular pair formalism and were thus confined to changes at a single substitution site. Herein, PCs with multiple substitution sites are introduced and a pilot study on a large collection of protein kinase inhibitors is reported, which provide excellent test cases for promiscuity analysis. For dual-site PCs (dsPCs), which dominated the distribution of multi-site PCs, an extended data structure was generated comprising a dsPC and two single-site analogs accounting for individual substitutions. Using a canonical representation, extended dsPCs are intuitive and easy to interpret from a chemical perspective. The analog quartet representing an extended dsPC is rich in structure-promiscuity relationship information and makes it possible to evaluate the potential interplay of chemical modifications implicated in promiscuity. Furthermore, extended dsPCs provide insights into possible experimental causes of apparent differences in analog promiscuity such as varying test frequencies. Hence, the newly introduced PC format should be of interest for exploring origins of compound promiscuity in medicinal chemistry and for formulating experimentally testable target hypotheses for analogs.     

Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs

As part of an effort to develop stable and replicable unnatural base pairs, we have evaluated a large number of unnatural nucleotides with predominantly hydrophobic nucleobases. Despite its limited aromatic surface area, a nucleobase analog scaffold that has emerged as being especially promising is the simple phenyl ring. Modifications of this scaffold with methyl and fluoro groups have been shown to impact base pair stability and polymerase recognition, suggesting that nucleobase shape, hydrophobicity and electrostatics are important. To further explore the impact of heteroatom substitution within this nucleobase scaffold, we report the synthesis, stability and polymerase recognition of nucleoside analogs bearing single bromo- or cyano-derivatized phenyl rings. Both modifications are found to generally stabilize base pair formation to a greater extent than methyl or fluoro substitution. Moreover, polymerase recognition of the unnatural base pairs is found to be very sensitive to both the position and nature of the heteroatom substituent. The results help identify the determinants of base pair stability and efficient replication and should contribute to the effort to develop stable and replicable unnatural base pairs.     

Rapid method for construction of yeast artificial chromosome human DNA libraries involving the trapping of cells in agarose films

A simple method for the molecular cloning of fragments of more than one hundred kilobase pairs of exogenous DNA, by the encapsulation of cells in agarose beads, was reported previously for the construction of a human genomic DNA library in a yeast artificial chromosome (YAC) vector (in situ YAC construction) [1]. The efficiency of this procedure is impaired by the step in which agarose beads that contain human DNA fragments are melted before transformation. The incomplete solubility of the ligated human DNA fragment-YAC vector often results in lower than desirable frequencies of transformation. To overcome this problem we have developed a new improved method that involves use of an agarose film. The technical manipulations involved in the construction of clones of very large segments of human DNA are discussed.     

ADMET rules of thumb II: A comparison of the effects of common substituents on a range of ADMET parameters

A systematic analysis of data generated in key in vitro assays within GSK has been undertaken to identify what impact a range of common substituents have on a range of ADMET parameters. These include; P450 1A2, 2C9, 2C19, 2D6 and 3A4 inhibition, hERG inhibition, phosphate buffer solubility and artificial membrane permeability. We do this by identifying all matched molecular pairs, differing by the replacement of a hydrogen atom with a list of predefined substituents.For each substituent we calculate the mean difference in the ADMET parameter for all the matched molecular pairs identified, making a statistical assessment of the difference, as well as assessing the diversity for each example to ensure that the results can be generalized. We also relate the change in activity observed for each substituent to differences in their molecular properties in an effort to identify any structural alerts.     

Design and synthesis of 1,5-diarylbenzimidazoles as inhibitors of the VEGF-receptor KDR

1,5-Diarylbenzimidazoles have been identified as potent inhibitors of KDR kinase activity. The series was developed with a goal of finding compounds with optimal drug-like properties. This communication describes structural modifications in the series that enhance solubility, lower protein binding, and provide compounds with excellent potency and pharmacokinetic profiles.     

Laccase-catalyzed decolorization of the synthetic azo-dye diamond black PV 200 and of some structurally related derivatives

The kinetics of laccase-catalyzed transformation of the azo-dye Diamond Black PV 200 (CI Mordant Black 9) and various related synthesized derivatives were analyzed for dependence on pH and substrate structure. The reaction mixture of Diamond Black PV 200 was analyzed by HPLC/MS–MS and it was shown that upon laccase oxidation, reactive chinoid fragments of lower molecular weight were formed. These may further oligomerize as indicated by the appearance of a number of compounds with increased molecular weight. The pH optimum for the decolorization was pH 5 for Diamond Black PV 200 which did not change significantly when the substitution pattern of its basic structure was varied. Biodegradability, however, was strongly dependent on the structure of the dyes.     

Laccase-catalyzed decolorization of the synthetic azo-dye diamond black PV 200 and of some structurally related derivatives

The kinetics of laccase-catalyzed transformation of the azo-dye Diamond Black PV 200 (CI Mordant Black 9) and various related synthesized derivatives were analyzed for dependence on pH and substrate structure. The reaction mixture of Diamond Black PV 200 was analyzed by HPLC/MS-MS and it was shown that upon laccase oxidation, reactive chinoid fragments of lower molecular weight were formed. These may further oligomerize as indicated by the appearance of a number of compounds with increased molecular weight. The pH optimum for the decolorization was pH 5 for Diamond Black PV 200 which did not change significantly when the substitution pattern of its basic structure was varied. Biodegradability, however, was strongly dependent on the structure of the dyes.     

Bioactive Compounds with Added Value Prepared from Terpenes Contained in Solid Wastes from the Olive Oil Industry

Starting from solid wastes from two‐phase olive‐oil extraction, the pentacyclic triterpenes oleanolic acid and maslinic acid were isolated. These natural compounds were transformed into methyl olean‐12‐en‐28‐oate ( 5 ), which then was transformed into several seco‐C‐ring triterpene compounds by chemical and photolytic modifications. The triene seco‐products were fragmented through several oxidative procedures to produce, simultaneously, cis‐ and trans‐decalin derivatives, both potential synthons for bioactive compounds. The chemical behavior of the isolated fragments was investigated, and a suitable approach to several low‐molecular‐weight terpenes was performed. These are interesting processes for the value‐addition to solid waste from the olive‐oil industry.     

The biological equilibrium of base pairs

Summary An inherent feature of double-stranded DNA is the possible replacement of any base pair by another one upon replication. A replication-dependent substitution mutation of a matched base pair requires the temporary formation of a mismatched base pair (mispair). A functionally complementary pair of mispairs is ascribed to each of the four types of substitution mutations. Provided that all types of mispairs can be formed, a dynamic biological equilibrium between the four matched base pairs must exist in all DNA, which is directly related to the formation and stability of the corresponding eight mispairs in vivo. Each nucleotide position in a genome can therefore be described as a system of six dynamic equilibria between the four matched base pairs. After a sufficient number of replications, these equilibrium states will express an overall mutation-selection balance for each individual base pair. In a thermodynamic context, the mispairs represent intermediate states on the transformation pathway between the matched base pairs. Catalysts change the stability and probability of formation of intermediate states. Mutagenic proteins are proposed as hypothetical substitution mutation catalysts in vivo. Functionally, they would be capable of recognizing a particular DNA sequence, tautomerizing a nucleotide base thereof, and hence efficiently inducing a specific misincorporation. Phenomenologically such catalysts would accelerate the rates of substitution mutations and provide pathways for directional mutation pressure. Present address until March 31 1990: University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, Great Britain     

Cytotoxic and antitumoral properties in a series of new, ring D modified, olivacine analogues

The present study describes the synthesis and pharmacological profiles of new olivacine related compounds, possessing a modified D ring. The impact of this modification has been evaluated with respect to the cytotoxic and in vivo antitumoral effects of these molecules and in comparison with parent S 16020-2 previously prepared and investigated in our laboratory. The D ring size and number of nitrogen atoms as well as the position of the aminoalkyl substituent have a profound impact on the cytotoxic and antitumoral profiles. Thus out of the prepared pyrazinocarbazole compounds, 2 is devoid of any substantial cytotoxic and antitumoral activities while the pyrimidocarbazole 3 has a similar profile compared to 1 (S 16020-2). L1210 and P388 in vivo antitumoral effects are lost for both imidazocarbazoles 4 and 5, but the former conserves an in vivo antitumoral effect on B16 melanoma, this effect being the largest in the series. Structural similarities and differences amongst the studied compounds could be evidenced by calculation of global properties such as molecular electrostatic potentials (MEP maps) and partition coefficients (logP), thus adding information on the impact of chemical changes on these two parameters known to influence biological behavior.     

Design, synthesis, and biological evaluation of a novel series of bisintercalating DNA-binding piperazine-linked bisanthrapyrazole compounds as anticancer agents

A series of bisintercalating DNA binding bisanthrapyrazole compounds containing piperazine linkers were designed by molecular modeling and docking techniques. Because the anthrapyrazoles are not quinones they are unable to be reductively activated like doxorubicin and other anthracyclines and thus they should not be cardiotoxic. The concentration dependent increase in DNA melting temperature was used to determine the strength of DNA binding and the bisintercalation potential of the compounds. Compounds with more than a three-carbon linker that could span four DNA base pairs achieved bisintercalation. All of the bisanthrapyrazoles inhibited human erythroleukemic K562 cell growth in the low to submicromolar concentration range. They also strongly inhibited the decatenation activity of topoisomerase IIα and the relaxation activity of topoisomerase I. However, as measured by their ability to induce double strand breaks in plasmid DNA, the bisanthrapyrazole compounds did not act as topoisomerase IIα poisons. In conclusion, a novel group of bisanthrapyrazole compounds were designed, synthesized, and biologically evaluated as potential anticancer agents.     

Relating the structure,activity, and physical properties of ultrashort-acting benzodiazepine receptor agonists

The ultrashort-acting benzodiazepine (USA BZD) agonists reported previously have been structurally modified to improve aqueous solubility. Lactam-to-amidine modifications, replacement of the C5-haloaryl ring, and annulation of heterocycles are presented. These analogues retain BZD receptor potency and full agonism profiles.     

Thiazolidinone CFTR inhibitors with improved water solubility identified by structure-activity analysis

The thiazolidinone 3-[(3-trifluoromethyl)phenyl]-5-[(4-carboxyphenyl)methylene]-2-thioxo-4-thiazolidinone (CFTR(inh)-172) inhibits cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel conductance with submicromolar affinity and blocks cholera toxin-induced intestinal fluid secretion. Fifty-eight CFTR(inh)-172 analogs were synthesized to identify CFTR inhibitors with improved water solubility, exploring modifications in its two phenyl rings, thiazolidinone core, and core-phenyl connectors. Greatest CFTR inhibition potency was found for 3-CF(3) and polar group-substituted-phenyl rings, and a thiazolidinone core. Two compounds with approximately 1muM CFTR inhibition potency and solubility >180 microM (>10-fold more than CFTR(inh)-172) were identified: Tetrazolo-172, containing 4-tetrazolophenyl in place of 4-carboxyphenyl, and Oxo-172, containing thiazolidinedione in place of the thiazolidinone core. These water soluble thiazolidinone analogs had low cellular toxicity. The improved water solubility of Tetrazolo- and Oxo-172 make them potential lead candidates for therapy of secretory diarrheas and polycystic kidney disease.     

Synthesize and characterization of organic-soluble acylated chitosan

Acylated chitosan was synthesized by reaction of chitosan and stearoyl chloride. The chemical structures and physical properties of the prepared compounds were confirmed by Fourier transform infrared (FT-IR), ¹H Nuclear Magnetic Resonance (¹H NMR) spectroscopy, X-ray diffraction (XRD) and Thermogravimetric (TG) techniques. The degree of substitution (DS) was calculated by ¹H NMR and ranged from 1.8 to 3.8. The synthesized compounds exhibited an excellent solubility in organic solvents. XRD analysis showed that they had high crystalline structure. TG results demonstrated that thermal stability of the prepared compounds was lower than that of chitosan, the weight loss decreased with increase of DS. This procedure could be a facile method to prepare organic-soluble chitosan derivatives.     

Design,synthesis, and SAR of cis-1,2-diaminocyclohexane derivatives as potent factor Xa inhibitors. Part I: Exploration of 5–6 fused rings as alternative S1 moieties

A series of cis-1,2-diaminocyclohexane derivatives were synthesized with the aim of optimizing previously disclosed factor Xa (fXa) inhibitors. The exploration of 5–6 fused rings as alternative S1 moieties resulted in two compounds which demonstrated improved solubility and reduced food effect compared to the clinical candidate, compound A. Herein, we describe the synthesis and structure–activity relationship (SAR), together with the physicochemical properties and pharmacokinetic (PK) profiles of some prospective compounds.     

Impact of black soldier fly larvae meal on the chemical and nutritional characteristics of rainbow trout fillets

The present research studied the effect of a dietary inclusion with Hermetia illucens larvae meal (Hi) on rainbow trout’s fillets chemical composition. The effect of Hi inclusion in diets on rainbow trout chemical characteristics was evaluated. Trout were fed three different diets: control (C, no Hi inclusion), 25% and 50% of substitution of fish meal with Hi (Hi25 and Hi50, respectively). Fillets were analysed to quantify proximate composition, carbohydrates percentage, colour parameters, nucleotides concentration, fatty acids profile, volatile organic compounds (VOCs) and myofibrillar and sarcoplasmic concentrations. Diets did not affect proximate composition. Contrariwise, Hi50 diet decreased fillet yellowness and both substitution percentages affected negatively adenosine monophosphate concentration. Saturated fatty acids, mostly C12 : 0, increased their contents in relation with Hi inclusion at the expense of monounsaturated and polyunsaturated (both n-3 and n-6) fatty acids. Less modifications were reported in VOCs as only heptanal and octanal concentrations were affected, no new compounds appeared in relation with Hi inclusion. No modifications in proteins patterns were shown even if myofibrillar content decreased in trout fed Hi50. The results highlighted that chemical modifications occurred in fillets were related to the chemical composition of the H. illucens meal and to the percentage of inclusion in the diet. Substitution of fish meal with a precisely percentage of H. illucens meal could be a potential future solution in order to decrease the quantity of fish meal used in aquafeeds.     

4-Aminopyrimidines as novel HIV-1 inhibitors

A series of 4-aminopyrimidines (1) was identified as novel HIV inhibitors of unknown molecular target. Structural modifications were carried out to establish its SAR and identify the linking site for target identification. A number of analogs were found to possess single digit inhibitory activity for HIV replication. Several analogs with various potential linkers, including a biotinated analog, also exhibited excellent potency, and could serve as tools for the identification of novel anti-HIV targets.