Novel benzoyl nitrogen mustard derivatives of pyrazole analogues of distamycin A: synthesis and antileukemic activity

An improved 4'-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA

Nucleic acid crosslinkers that covalently join complementary strands of DNA/RNA have applications in both pharmaceuticals and as biochemical probes. Psoralen is a popular crosslinking moiety that reacts with double stranded DNA and RNA upon exposure to longwave UV light. The commercially available compound EZ-link psoralen-PEG3-biotin has been used in numerous studies to crosslink DNA and double-stranded RNA for genome-wide investigations. Here we present a new probe, AP3B, which uses the psoralen derivative, 4'-aminomethyltrioxsalen, to crosslink and biotinylate nucleic acids. We show that AP3B is 4 to 5 times more effective at labeling DNA in cells and produces a comparable number of crosslinks with over 100 times less compound and less exposure to UV light in vitro than EZ-link psoralen-PEG3-biotin.

An overview of recent advances in duplex DNA recognition by small molecules

As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.

Multicomponent reactions: a sustainable tool to 1,2- and 1,3-azoles

The present review outlines the recent advancements and pioneering efforts on the synthesis of 1,2/1,3-azoles employing a multicomponent strategy.

Synthesis and biological activity of benzamide DNA minor groove binders

A range of di- and triaryl benzamides were synthesised to investigate the effect of the presence and nature of a polar sidechain, bonding and substitution patterns and functionalisation of benzylic substituents. These compounds were tested for their antiproliferative activity as well as their DNA binding activity. The most active compounds in all assays were unsymmetrical triaryl benzamides with a bulky or alkylating benzylic substituent and a polar amino sidechain.

Sulphur promoted C(sp3)–C(sp2) cross dehydrogenative cyclisation of acetophenone hydrazones with aldehydes: efficient synthesis of 3,4,5-trisubstituted 1H-pyrazoles

The first-time sulfur-promoted CDC approach involving acetophenone hydrazones and aldehydes has been developed for the synthesis of substituted pyrazoles.

One-pot three-component approach to the synthesis of polyfunctional pyrazoles

A simple, multicomponent, and straightforward reaction of vinyl azide, aldehyde, and tosylhydrazine affords the construction of 3,4,5-trisubstituted 1H-pyrazoles regioselectively in the presence of base with moderate to excellent yields. A range of functionality could be tolerated in this methodology, and a possible mechanism is proposed.

N-{3-[Bis(2-hydroxy-ethyl)amino-meth-yl]-5-nitro-phen-yl}benzamide

The title compound, C₁₈H₂₁N₃O₅, was prepared by the reaction of 3-benzamido-5-nitro­benzyl methane­sulfonate with diethano­lamine and is an inter­mediate in the synthesis of DNA minor-groove-binding polybenzamide agents capable of being conjugated to additional biologically active species. The asymmetric unit contains two independent mol­ecules, which differ only in the orientations of the hydroxy­ethyl groups. In the crystal structure, inter­molecular N—H⋯O and O—H⋯O hydrogen bonds link mol­ecules into one-dimensional chains.

Ethyl 4-amino-3-methyl-benzoate

The asymmetric unit of the title compound, C₁₀H₁₃NO₂, contains two mol­ecules which are linked via an N—H⋯N hydrogen bonds to form a dimer. These dimers are further linked via N—H⋯O inter­molecular hydrogen bonds.

Cytokinetics and mechanism of action of AKO4: a novel nitrogen mustard targeted to bcr-abl

The "combi-targeting" concept seeks to design molecules to not only block tyrosine kinase (TK) activity but also to induce DNA damage. Here we design AK04, a molecule that combines the pharmacophore chlorambucil with that of STI-571 (Gleevec). The results showed that although a less potent abl TK inhibitor than STI571, AK04 was capable of significantly blocking bcr-abl phosphorylation not only in a purified abl assay but also in the bcr-abl+ K562 cells. In contrast to STI571 and like chlorambucil, it induced a dose-dependent increase in DNA damage in these cells. More importantly, AK04 was 12-32-fold more potent than chlorambucil in all bcr-abl+ cells of our cell panel. In the isogenic human megakaryocytic Mo7e and Mo7/bcr-abl cells, AK04 selectively killed the bcr-abl transfectants. Flow cytometry revealed that despite being a five-fold less potent inhibitor of bcr-abl than STI-571, it induced a significant dose-dependent increase in levels of cell death by apoptosis in KU812 cells 24 h post-treatment. Under these conditions, chlorambucil did not induce any significant level of apoptosis. These results suggest that AK04 is a nitrogen mustard with binary bcr-abl/DNA targeting effects, a property that may account for its superior potency when compared with the classical mustard chlorambucil.

Cinnamoyl nitrogen mustard derivatives of pyrazole analogues of tallimustine modified at the amidino moiety: design, synthesis, molecular modeling and antitumor activity studies

The design, synthesis and in vitro activities of a series of cinnamoyl nitrogen mustard pyrazole analogues of tallimustine 8-13, in which the amidino moiety has been replaced by moieties of different physico-chemical features are described, and the structure-activity relationships are discussed. In spite of the relevance of these modifications on the amidino moiety, these derivatives showed significant growth inhibitory activity against mouse leukemia L1210 cells. A selected series of compounds have been evaluated for their sequence selective alkylating properties and cytotoxicity against human K562 leukemia cells. Therefore, the presence of the amidino moiety, and in general of a basic moiety, is not an absolute requirement for biological activity. Our preliminary results indicated that the compounds of this series have a pattern of alkylation similar to that of tallimustine, but they seem to be less reactive overall in alkylating naked DNA.

Hybridized particle swarm algorithm for adaptive structure training of multilayer feed-forward neural network: QSAR studies of bioactivity of organic compounds

The multilayer feed-forward ANN is an important modeling technique used in QSAR studying. The training of ANN is usually carried out only to optimize the weights of the neural network and without paying attention to the network topology. Some other strategies used to train ANN are, first, to discover an optimum structure of the network, and then to find weights for an already defined structure. These methods tend to converge to local optima, and may also lead to overfitting. In this article, a hybridized particle swarm optimization (PSO) approach was applied to the neural network structure training (HPSONN). The continuous version of PSO was used for the weight training of ANN, and the modified discrete PSO was applied to find appropriate the network architecture. The network structure and connectivity are trained simultaneously. The two versions of PSO can jointly search the global optimal ANN architecture and weights. A new objective function is formulated to determine the appropriate network architecture and optimum value of the weights. The proposed HPSONN algorithm was used to predict carcinogenic potency of aromatic amines and biological activity of a series of distamycin and distamycin-like derivatives. The results were compared to those obtained by PSO and GA training in which the network architecture was kept fixed. The comparison demonstrated that the HPSONN is a useful tool for training ANN, which converges quickly towards the optimal position, and can avoid overfitting in some extent.

Synthesis and antitumor evaluation of some new substituted amidino-benzimidazolyl-furyl-phenyl-acrylates and naphtho[2,1-b]furan-carboxylates

The multistep synthesis of a series of substituted amidino-benzimidazolyl-furyl-phenyl-acrylic acid's esters and substituted amidino-benzimidazolyl-naphtho[2,1-b]furan-carboxylic acid's esters is described starting from corresponding 3-(2-furyl)-2-phenyl-acrylic acids. The new compounds were tested on the cytostatic activities against malignant cell lines: pancreatic carcinoma (MiaPaCa2), breast carcinoma (MCF7), cervical carcinoma (HeLa), laryngeal carcinoma (Hep2), colon carcinoma (HT 29), melanoma (HBL), and human fibroblasts cell line (WI38). All compounds inhibited the proliferation of tumor cell lines. Inhibitory effect of examined compounds depended on concentration, but without significant difference among the type of tumor cells. The compounds 2 and 5 exerted very low inhibitory effect on the growth of human fibroblasts. Unsubstituted derivative 8 has not inhibited any tested cell lines.

Cellulose beads: a new versatile solid support for microwave- assisted synthesis. Preparation of pyrazole and isoxazole libraries

The synthesis of libraries of substituted pyrazoles and isoxazoles has been developed via in situ generation of polymer-bound enaminones. The synthetic protocol makes use of commercially available aniline cellulose, a low-cost and versatile biopolymer, under very mild conditions. This new support allowed us to carry out reactions in polar solvents under both conventional heating and MW irradiation without degradation of the polymer. The reaction between cellulose-bound enaminone and hydroxylamine or hydrazines to afford the target heterocycles in high yields directly in solution is the key step. The support can be conveniently recycled.

The discovery of a new potential anticancer drug: a case history

DNA minor groove binders (MGB) represent a class of anticancer agents whose DNA sequence specificity was hypothesized to lead to high selectivity of action. Tallimustine (TAM), a benzoyl nitrogen mustard derivative of distamycin A (DST), showed excellent antitumor activity in preclinical tests, but also a severe myelotoxicity. Novel nitrogen mustard, nitrogen half-mustard and sulfur mustard derivatives of DST showing excellent activity were recently identified and SAR reported. In particular nitrogen half-mustard and sulfur mustard derivatives, as one-arm alkylating agents, represent interesting structural novelties. A further new class of cytotoxic anticancer agents is that of alpha-halogenoacrylamido derivatives of DST-like oligopeptides, which show an activity profile substantially improved in comparison to TAM. In particular brostallicin (PNU-166196), alpha-bromo-acrylamido tetra-pyrrole derivative ending with a guanidino moiety, showed high cytotoxic potency and myelotoxicity dramatically reduced in comparison to TAM and other MGB. Brostallicin binds to the minor groove but appears unreactive in classical in vitro DNA alkylation assays. About the apparent lack of DNA alkylation we speculated that an intracellular nucleophile, e.g. glutathione (GSH), could activate the reactivity of the compound leading to alkylation of DNA in vivo. Evidence of both covalent interaction of brostallicin with plasmidic DNA in the presence of GSH and of enhanced cytotoxicity in cancer cells characterized by high levels of GSH were obtained. Brostallicin was selected for clinical development and is now undergoing Phase II studies.

Development of distamycin-related DNA binding anticancer drugs

The relatively low therapeutic index of the clinically used alkylating agents is probably related to the fact that these compounds cause DNA damage in a relatively unspecific manner, mainly involving guanine-cytosine rich stretches of DNA present in virtually all genes, therefore inducing unselective growth inhibition and death, both in neoplastic and in highly proliferative normal tissues. These considerations explain why in the last twenty years there has been an increasing interest in the identification of compounds which can target DNA with a much higher degree of sequence specificity than that of conventional alkylators. Minor groove binders (MGBs) are one of the most widely studied class of alkylating agents characterised by a high level of sequence specificity. The prototype of this class of drugs is distamycin A which is an antiviral compound able to interact, non-covalently, in theminor groove of DNA in A-T rich regions. It is not cytotoxic against tumour cells and thus has been used as a carrier for targeting cytotoxic alkylating moieties in theminor groove of DNA. The benzoyl mustard derivative of distamycin A, tallimustine, was found to be able to alkylate the N(3) of adenine in theminor groove of DNA only in the target hexamer 5'-TTTTGA or 5'-TTTTAA. Tallimustine was investigated in the clinic and was not successful because it causes severe bone marrow toxicity. The screening of other distamycin derivatives, which maintain antitumour activity and exhibit much lower toxicity against human bone marrow cells than tallimustine led to the identification of brostallicin (PNU-166196) which is currently under early clinical investigation. Although MGBs which bind DNA in A-T rich regions have not fulfilled the expectations, it is too early to draw definitive conclusions on this class of compounds. The peculiar bone-marrow toxicity observed in the clinic both with tallimustine or with CC-1065 derivatives is not necessarily a feature of all MGBs, as indicated by recent evidence obtained with brostallicin and other structurally unrelated MGBs (e.g., ET-743).

A new class of cytotoxic DNA minor groove binders: α-halogenoacrylic derivatives of pyrrolecarbamoyl oligomers

DNA minor groove binders represent a class of cytotoxic antitumor agents whose DNA sequence specificity may lead to a high selectivity of action. Tallimustine, benzoyl nitrogen mustard derivative of distamycin A, showed excellent antitumor activity in preclinical tests but also a severe myelotoxicity. Novel nitrogen mustard derivatives of distamycin showing improved activity profile were recently identified. In particular, cinnamic nitrogen mustard and cinnamic ethyl half-mustard analogs of tallimustine showed increased potency and more favorable cytotoxicity/myelotoxicity ratio. However a series of alpha-halogenoacrylamido derivatives of distamycin-like frames showed an activity profile substantially improved in comparison to tallimustine. In particular PNU-166196, alpha-bromo-acrylamido derivative of four pyrrole distamycin-like frame ending with a guanidino moiety, showed high cytotoxic potency even on tumor cell lines resistant to alkylating agents and camptothecin, broad antitumor activity and myelotoxicity dramatically reduced in comparison to tallimustine. This compound was found to bind to minor groove TA-rich sequences but appeared unreactive in classical in vitro DNA alkylation assays. With respect to the apparent lack of DNA alkylation we speculated that an intracellular reactive nucleophilic species, e.g. glutathione (GSH), could activate the reactivity of the compound leading to alkylation of DNA in vivo. Recent evidence of both covalent interaction of PNU-166196 with plasmidic DNA in the presence of GSH and of enhanced cytotoxicity in tumor cells characterized by high levels of GSH were obtained. PNU-166196, in view of its excellent activity profile and its outstanding favorable cytotoxicity/myelotoxicity ratio, was selected for clinical development and is undergoing phase I studies.