Dynamic combinatorial chemistry with hydrazones: libraries incorporating heterocyclic and steroidal motifs

Synthesis, characterization, and anticancer evaluation of novel 4-hydrazinothiazole analogs

Single-step synthesis of novel 4-hydrazinothiazole derivatives 6a-e was achieved under mild conditions using the sequential four-components method involving isothiocyanate, aminoguanidine, carbonyl adduct, and α-haloketone derivatives. Deprotection of these hydrazinothiazoles was influenced by acylation, providing a novel group of diacylated molecular structures with a broader scope for the design of thiazolyl-containing drugs 7a and 7b. FTIR, 1 H/13 C NMR, LC-MS spectroscopy, and CHN elemental analyses were used to study the compound chemical structures. Using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay on human periodontal ligament fibroblast (HPDLF) cells, the 4-hydrazinothiazole derivatives were screened for cytotoxicity in an in vitro cytotoxicity investigation. The 4-hydrazinothiazole compound 6b bearing an isopropylidene-hydrazino group demonstrated strongly potent cytotoxicity against CAKI1 (IC50  = 1.65 ± 0.24 μM) and A498 (IC50 of 0.85 ± 0.24 μM). Furthermore, the chloroacetyl-containing thiazole compound 7a displayed efficient inhibition of growth against the test cell lines CAKI1 and A498 at low micromolar concentrations, IC50 0.78 and 0.74 μM, respectively.

Membrane-active substituted triazines as antibacterial agents against Staphylococcus aureus with potential for low drug resistance and broad activity

A library of new naphthalimide-triazine analogues was synthesized as broad-spectrum antibacterial agents to overcome drug resistance. Bioactivity assay reveals that derivative 8e, with benzylamine in its structure, exhibits strong antibacterial properties against multi-drug resistance Staphylococcus aureus at a concentration of 1.56 μg/ml. It was also found to be better than chloromycin and amoxicillin. The active compound 8e efficiently inhibits the development of drug resistance within 11 passages. In addition, compound 8e inhibits the formation of biofilms in S. aureus and acts rapidly in bactericidal efficacy. Furthermore, mechanistic studies reveal that compound 8e effectively destroys the cytoplasmic membrane of bacteria, leading to leakage of intercellular protein content and loss in metabolic activity. Compound 8e binds to HSA readily with a binding constant of 1.32 × 10⁵ M^-1, indicating that the compound could be delivered to the target site effectively. Compound 8e can also form a supramolecular complex with DNA to obstruct DNA replications. These results suggest that analogue 8e could be further developed as a potential antibacterial agent. Furthermore, the cytotoxicity of all the synthesized compounds was evaluated against 60 human cancer cell lines to test their potential for anticancer agents.

Copper-Catalyzed Radical Hydrazono-Phosphorylation of Alkenes

An efficient copper-catalyzed radical hydrazono-phosphorylation of alkenes with hydrazine derivatives and diarylphosphine oxides is described. The reaction provides a general and convenient method toward the synthesis of diverse β-hydrazonophosphine oxides in satisfactory yields. Based on conducted mechanistic experiments, a mechanism involving Ag-catalyzed oxidative generation of phosphinoyl radicals and subsequent addition to alkenes followed by Cu-assisted hydrazonation is proposed. Moreover, the practicability of the reaction is successfully demonstrated by its successful application on a gram scale.

Copper-Catalyzed Stereoselective Radical Phosphono-hydrazonation of Alkynes

A copper-catalyzed stereoselective phosphono-hydrazonation of terminal alkynes with alkyl carbazates and diarylphosphine oxides is described. This methodology provides facile access to a variety of β-hydrazonophosphine oxides in satisfactory yields. The reaction proceeds under mild conditions and exhibits good functional group tolerance. A mechanism featuring persulfate-mediated oxidative generation of phosphinoyl radicals and copper-assisted hydrazonation is proposed.

Development and Validation of a Liquid Chromatographic Method for Aroylhydrazones at Hydrolytic Conditions

Background:

The indole-containing aroylhydrazone derivatives 3a-c with potent antimycobacterial activity against a referent strain M. tuberculosis H37Rv and low cytotoxicity were evaluated for their stability via the precise and accurate HPLC analytical method in aqueous media of different pH (2.0, 7.0, 9.0 and 12.0).

Objective:

The study describes the development and validation of a simple and reliable HPLC-UV procedure for the determination of aroylhydrazone derivatives and their hydrolytic stability. Additionally, to recognize if hydrolysis leads to generating undesired products, the degradation processes were identified.

Method:

The separation was achieved with a LiChrosorb®RP-18 (250 x 4.6 mm) column, at ambient temperature with isocratic mode with mobile phase containing mixture of component A (acetonitrile) and component B (0.001M NaH2PO4, with 5 mM 1-heptane sulfonic acid sodium salt, adjusted to pH 3.0) in a ratio 60:40 (v/v). The flow rate was 1.0 ml/min and the eluent was monitored at 297 nm. The proposed method was validated as per ICH guidelines.

Result:

The obtained results showed that the compounds were sensitive to hydrolytic decomposition in aqueous media, resulting in the splitting of the hydrazone bond. Rapid hydrolysis of substances was observed in the acid medium. The elevated temperature significantly accelerated the hydrolytic reaction. Relatively slow hydrolysis of 3a-c was observed in a neutral solution and aqueous solutions buffered to pH 9. The hydrolysis of 3a-c in neutral, alkaline and strong alkaline medium followed the pseudo- first-order reaction rate and showed a linear dependence of lnC versus time.

Conclusion:

A validated high-performance liquid chromatographic assay for the determination of the hydrolytic stability of a series of aroylhydrazones was developed and optimized for the first time. The methods devised are successfully applicable to the development of pharmaceutical formulations.

pKa Modulation of Pyrrolidine-Based Catalytic Polymers Used for the Preparation of Glycosyl Hydrazides at Physiological pH and Temperature

Inspired by the ability of enzymes to use the surrounding hydrophobic and/or polarizable groups to modulate the pK_a of a given amino acid, we designed a series of soluble polymers able to decrease the basicity of pyrrolidine (from 11.2 to 8.6 pK_a units), which clearly increases its aminocatalytic activity at physiological pH in C═N bond formation reactions via ion iminium activation. Other parameters such as charge density, hydrophobic/hydrophilic balance, and aggregation state have been studied as important factors in the catalytic activity of the polymers for a given substrate. To demonstrate the utility of our approach, an optimal pyrrolidine-based catalytic polymer has been used for the formation of C-N bonds between hydrazides and free sugars as the model system for the preparation of glycoconjugates.

Structure-activity relationships (SAR) of triazine derivatives: Promising antimicrobial agents

The emergence of drug resistance has created unmet medical need for the development of new classes of antibiotics. Innovation of new antibacterial agents with new mode of action remains a high priority universally. Triazines are six-membered, nitrogen-containing heterocyclic scaffold with a wide range of pharmaceutical properties such as antibacterial, antifungal, anticancer, antioxidants, antitubercular, antimalarial, anti-HIV, anticonvulsant, anti-inflammatory, antiulcer, and analgesic activities. The present review focuses on the recent developments in the area of medicinal chemistry to discover various chemical structures as potential antimicrobial agents and their structure-activity relationships (SAR) studies are also discussed for further rational design of this kind of derivatives.

Synthesis of Macrocycles Derived from Substituted Triazines

A triazine ring derivatized with morpholine, an N-alkyl-N'-BOC-hydrazine (alkyl=isopropyl or benzyl) and the diethylacetal of glycinylpropionaldehyde undergoes spontaneous dimerization in good yields upon acid-catalyzed deprotection. The resulting 24-member macrocycles can be characterized by NMR spectroscopy, mass spectrometry, and single crystal X-ray diffraction. In the solid state, both homodimers adopt a taco-like conformation. Although each shows π-π stacking between the triazine rings, different patterns of hydrogen bonds emerge. The crystal structure of the isopropyl dimer shows that it includes two molecules of trifluoracetic acid per macrocycle. The trifluoroacetate anion charge balances the protonated triazines, which engage in bifurcated hydrogen bonds with the carbonyl acceptor of the distant glycine. This carbonyl also forms a hydrogen bond with the NH of the proximate glycine. The crystal structure of the benzyl derivative does not include trifluoracetic acid. Instead, two hydrogen bonds form, each between a glycine NH and the lone pair of the C=N nitrogen of the hydrazine group. In the solid state, both molecules present the alkyl side chains and morpholine groups in close proximity. A heterodimer is accessible in approximately statistical yields-along with both homodimers-by mixing the two protected monomers prior to subjecting them to deprotection.

Specific dsDNA recognition by a mimic of the DNA binding domain of the c-Myc/Max transcription factor

We here report on the synthesis of the first mimic of the DNA binding domain of the c-Myc/Max-bHLH-ZIP transcription factor able to selectively recognize its cognate E-box sequence 5'-CACGTG-3' through the major groove of the double-stranded DNA. The designed peptidosteroid conjugate was shown to be effective as DNA binder in the presence of excess competitor DNA.

Oximes and Hydrazones in Bioconjugation: Mechanism and Catalysis

The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.

Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung

Proteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.

Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery

Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.

A DFT Approach to the Mechanistic Study of Hydrozone Hydrolysis

Hydrazone chemistry is widely utilized in biomedical field as a means of bioconjugation protocol, especially in drug delivery field due to pH labile nature of this linkage. In the light of kinetics studies, the generally accepted mechanism for the hydrolysis of hydrazones involves two main steps, namely, nucleophilic addition of water molecule to the hydrazone molecule to form carbinolamine intermediate and subsequent decomposition of this intermediate into the hydrazine and aldehyde/ketone moieties. Hydrolysis of hydrazones is catalyzed in the acidic environments and is thought to proceed through several proton transfer steps. To the best of our knowledge, in the literature no detailed theoretical study has been reported related to the mechanism of hydrolysis. In this study, we evaluated the proposed mechanism with DFT calculations with M06-2X functional at the 6-311+g(d,p) level including conductor-like polarizable continuum model solvation model. We also analyzed possible proton transfer pathways and assessed energetics of each step.

Exploring thermodynamically downhill nanostructured peptide libraries: from structural to morphological insight

Biocatalytic evolution of thermodynamically downhill nanostructured peptide libraries in hydrogel states are envisaged.

Fast alpha nucleophiles: structures that undergo rapid hydrazone/oxime formation at neutral pH

Hydrazones and oximes are widely useful structures for conjugate formation in chemistry and biology, but their formation can be slow at neutral pH. Kinetics studies were performed for a range of structurally varied hydrazines, and a surprisingly large variation in reaction rate was observed. Structures that undergo especially rapid reactions were identified, enabling reaction rates that rival orthogonal cycloaddition-based conjugation chemistries.

Dynamic thiol exchange with β-sulfido-α,β-unsaturated carbonyl compounds and dithianes

A reversible covalent bond exchange of thiols, β-sulfido-α,β-unsaturated carbonyls, and dithianes has been studied in DMSO and D(2)O/DMSO mixtures. The equilibrium between thiols and β-sulfido-α,β-unsaturated carbonyls is obtained within a few hours, while the equilibration starting with the β-dithiane carbonyls and thiols requires a few days. This time scale makes the system ideal for utilization in dynamic combinatorial chemistry.

Bivalent enzyme inhibitors discovered using dynamic covalent chemistry

A bivalent dynamic covalent chemistry (DCC) system has been designed to selectively target members of the homodimeric glutathione-S-transferase (GST) enzyme family. The dynamic covalent libraries (DCLs) use aniline-catalysed acylhydrazone exchange between bivalent hydrazides and glutathione-conjugated aldehydes and the bis-hydrazides act as linkers to bridge between each glutathione binding site. The resultant DCLs were found to be compatible and highly responsive to templating with different GST isozymes, with the best results coming from the M and Schistosoma japonicum (Sj) class of GSTs, targets in cancer and tropical disease, respectively. The approach yielded compounds with selective, nanomolar affinity (K(i) =61 nM for mGSTM1-1) and demonstrates that DCC can be used to simultaneously interrogate binding sites on different subunits of a dimeric protein.

Probing the mechanism and dynamic reversibility of trianglimine formation using real-time electrospray ionization time-of-flight mass spectrometry

RATIONALE

The [3+3]-cyclocondensation reactions of chiral (1R,2R)-1,2-diaminocyclohexane with aromatic or aliphatic bis-aldehydes to form trianglimine macrocycles were reported a decade ago and were believed to proceed through a stepwise mechanistic pathway; however, no intermediates were ever isolated or detected and characterized.

METHODS

We investigated the mechanism of the [3+3]-cyclocondensation reaction using a selection of dialdehyde starting materials using real-time electrospray ionization time-of-flight mass spectrometry.

RESULTS

We observed up to a maximum of 16 reaction intermediates along the reaction pathway, more than for any other multistep reaction reported. We also probed the dynamic reversibility of trianglimines using selected small dynamic combinatorial libraries and showed that trianglimine formation is indeed fully reversible.

CONCLUSIONS

This study represents a significant contribution towards understanding the mechanism of trianglimine formation and its potential applicability can be extended to include other cascade reactions.

Dynamic multicomponent hemiaminal assembly

A simple approach to generating in situ metal-templated tris-(2-picolyl)amine-like multicomponent assemblies with potential applications in molecular recognition and sensing is reported. The assembly is based on the reversible covalent association between di-(2-picolyl)amine and aldehydes. Zinc ion is best for inducing assembly among the metal salts investigated, whereas 2-picolinaldehyde is the best among the heterocyclic aldehydes studied. Although an equilibrium constant of 6.6×10(3) M(-1) was measured for the assembly formed by 2-picolinaldehdye, di-(2-picolyl)amine, and zinc triflate, the equilibrium constants for other systems are in the 10(2) M(-1) range. X-ray structural analysis revealed that zinc adopts trigonal-bipyramidal geometry within the assembled ligand. The diversity and equilibrium of the assemblies are readily altered by simply changing concentrations, varying components, or adding counteranions.

From static to dynamic: escaping kinetic traps in hydrazone-based dynamic combinatorial libraries

Thermodynamic control over kinetically-trapped mixtures of hydrazone-based macrocycles is achieved by addition of an aromatic monohydrazide to generate dynamic combinatorial libraries (DCLs) of linear and macrocyclic oligomers.