Amidine Moiety Research Articles

Overcoming strong retention barriers of A- and V-series nerve agents on silica sorbents

The present study explores the potential of silica solid phase extraction for gas chromatography mass spectrometric analyses of A- and V-series nerve agents. Owing to the presence of basic amidine and amine moieties, these analyte undergo strong ionic interactions with inherently acidic silica surfaces, producing poor recoveries. Subtle optimizations in the elution composition empowered the analytes to overcome the retention barriers from sorbent surfaces. Acetone containing 10 % (v/v) NH4OH effectively minimized strong analyte-sorbent interactions allowing good to excellent recoveries. Recoveries for A-series agents ranged from 88 to 96 %. VX, which is reported to be poorly recoverable from such sorbent matrices offered best data so far, reaching up to 74 % under optimized conditions. The method detection limits for the selected analytes in mass spectrometric analysis ranged from 47 to 171 ng/ml. Strong affinities of analytes towards silica sorbent were further exploited to expand the scope of analysis and establish the method's efficacy for a wide range of organic matrices. The applicability of the method to the real world applications was also validated in blind spiking exercises in diverse organic liquid samples received in 48th, 50th and 52nd proficiency tests conducted by the Organization for the Prohibition of Chemical Weapons (OPCW).

A Hydroxylamine‐Mediated Amidination of Lysine Residues That Retains the Protein's Positive Charge

AbstractLysine‐specific peptide and protein modification strategies are widely used to study charge‐related functions and applications. However, these strategies often result in the loss of the positive charge on lysine, significantly impacting the charge‐related properties of proteins. Herein, we report a strategy to preserve the positive charge and selectively convert amines in lysine side chains to amidines using nitriles and hydroxylamine under aqueous conditions. Various unprotected peptides and proteins were successfully modified with a high conversion rate. Moreover, the reactive amidine moiety and derived modification site enable subsequent secondary modifications. Notably, positive charges were retained during the modification. Therefore, positive charge‐related protein properties, such as liquid‐liquid phase separation behaviour of α‐synuclein, were not affected. This strategy was subsequently applied to a lysine rich protein to develop an amidine‐containing coacervate DNA complex with outstanding mechanical properties. Overall, our innovative strategy provides a new avenue to explore the characteristics of positively charged proteins.

A Hydroxylamine-Mediated Amidination of Lysine Residues That Retains the Protein's Positive Charge.

Lysine-specific peptide and protein modification strategies are widely used to study charge-related functions and applications. However, these strategies often result in the loss of the positive charge on lysine, significantly impacting the charge-related properties of proteins. Herein, we report a strategy to preserve the positive charge and selectively convert amines in lysine side chains to amidines using nitriles and hydroxylamine under aqueous conditions. Various unprotected peptides and proteins were successfully modified with a high conversion rate. Moreover, the reactive amidine moiety and derived modification site enable subsequent secondary modifications. Notably, positive charges were retained during the modification. Therefore, positive charge-related protein properties, such as liquid-liquid phase separation behaviour of α-synuclein, were not affected. This strategy was subsequently applied to a lysine rich protein to develop an amidine-containing coacervate DNA complex with outstanding mechanical properties. Overall, our innovative strategy provides a new avenue to explore the characteristics of positively charged proteins.

3,6-Disubstituted derivatives of 1,2,4,5-tetrazine with pyridinyl amidine moieties and condensed systems on their basis: synthesis, docking, and antibacterial activity

3,6-Disubstituted derivatives of 1,2,4,5-tetrazine with pyridinyl amidine moieties and condensed systems on their basis: synthesis, docking, and antibacterial activity

Sulfonamido, amido heterocyclic adducts of tetrazole derivatives as BACE1 inhibitors: in silico exploration.

Alzheimer's disease is a neurodegenerative disorder accounting for 60-80% of dementia cases and is accompanied by a high mortality rate in patients above 70years of age. The formation of senile plaques composed of amyloid-β protein is a hallmark of Alzheimer's disease. Beta-site APP cleaving enzyme 1 (BACE1) is a proteolytic enzyme involved in the degradation of amyloid precursor protein, which further degrades to form toxic amyloid-β fragments. Hence, inhibition of BACE1 was stated to be an effective strategy for Alzheimer's therapeutics. Keeping in mind the structures of different BACE1 inhibitors that had reached the clinical trials, we designed a library of compounds (total 164) based on a substituted 5-amino tetrazole scaffold which was an isosteric replacement of the cyclic amidine moiety, a common component of the BACE1 inhibitors which reached the clinical trials. The scaffold was linked to different structural moieties with the aid of an amide or sulfonamide bond to design some novel molecules. Molecular docking was initially performed and the top 5 molecules were selected based on docking scores and protein-ligand interactions. Furthermore, molecular dynamic simulations were performed for these molecules (3g, 7k, 8n, 9d, 9g) for 100ns and MM-GBSA calculations were performed for each of these complexes. After critical evaluation of the obtained results, three potential molecules (9d, 8n, and 7k) were forwarded for prolonged stability studies by performing molecular dynamic simulations for 250ns and simultaneous MM-GBSA calculations. It was observed that the compounds (9d, 8n, and 7k) were forming good interactions with the amino acid residues of the catalytic site of the enzyme with multiple non-covalent interactions. In MD simulations, the compounds have shown better stability and better binding energy throughout the runtime.

Improved synthesis and evaluation of preclinical pharmacodynamic parameters of a new monocyclic β-lactam DPI-2016

Monocyclic β-lactams are stable to a number of β-lactamases and are the focus of researchers for the development of antibacterial drugs, particularly against Enterobacterales. We recently synthesized and reported the bactericidal activity of diverse series of aztreonam appended with amidine moieties as siderophores. One of the derivatives exhibiting the highest MIC value in vitro was selected for further preclinical studies. The compound DPI-2016 was reassessed for its synthetic routes and methods that were improved to find the maximum final yields aimed at large-scale synthesis. In addition, the results of the pharmacological studies were determined with reference to aztreonam. It has been found that the compound DPI-2016 showed comparable or slightly improved ADMET as well as pharmacokinetic parameters to aztreonam. It is estimated that the compound could be a potential lead for further clinical evaluation.

Synthesis and Coordination Behavior of a Hybrid Phosphanylferrocene Amidine Ligand

AbstractThe combination of different donor moieties often results in unconventional coordination behavior. This contribution describes the synthesis of a new hybrid ligand, phosphanylferrocene amidine Ph2PfcN=CHNMe2 (1; fc=ferrocene‐1,1′‐diyl), and its coordination behavior toward the light platinum metals. Reacting compound 1 with [PdCl2(MeCN)2] produced the chelate complex [PdCl2(1‐κ2P,N)] and the bis (phosphane) complex trans‐[PdCl2(1‐κP)2], depending on the ligand‐to‐metal stoichiometry. Halide removal from [PdCl2(1‐κ2P,N)] with Na[BARF] afforded the chloride‐bridged dimer [Pd2(μ‐Cl)2(1‐κ2P,N)2][BARF]2, which was presumably in equilibrium with the mononuclear κ3‐complex [PdCl(1‐κ3Fe,P,N)][BARF] in solution (BARF=tetrakis [3,5‐bis(trifluoromethyl)phenyl]borate). The reactions of 1 with the isoelectronic precursors [(arene)MCl(μ‐Cl)]2 (M/arene=Ru(II)/p‐cymene, and Rh(III)/C5Me5) generated the respective bridge‐cleavage products [(arene)MCl2(1‐κP)], which transformed into the P,N‐chelate complexes [(arene)MCl(1‐κ2P,N)][BARF] when treated with Na[BARF] as a chloride scavenger. All this suggests preferential coordination the phosphane moiety to soft metal ions, while the coordination of the amidine moiety can be induced through changing the reaction stoichiometry or by generating a vacant coordination site at the metal ion. The compounds were characterized using a combination of standard spectroscopic methods (multinuclear NMR, IR, and ESI MS) and single‐crystal X‐ray crystallography, and compounds 1 and 3 were further studied by cyclic voltammetry.

Computationally design aspects of superbasic amidine-arsinine 1-oxide binary frameworks

Novel Brønsted superbases (1–10) were designed on the basis of arsinine 1-oxide core by changing the species of proton absorption site, type and situation of electron-donating substituents in the gas phase and CH3CN medium. The conjugate acids of the designed structures are stabilized through positive charge distribution and/or formation of an intramolecular hydrogen bond. To explore the various structural aspects of the designed molecules for reaching the higher basicity values in gas phase and solution phase in CH3CN solvent, proton affinity (PA), gas phase basicity (GB), pKa, and Nucleus-IndependentChemicalShifts 1 Å above the arsinine 1-oxide ring center along with zz axis (NICS(1)zz) parameters as well as natural bond orbital (NBO) charges calculated and obtained for each structure. The basicity strength of proposed structures was evaluated using B3LYP/6–311 + G(d,p) level of theory. The protonation of all designed structures was studied from both possible sites in gas and CH3CN phase and PA, GB, pKa, and NICS(1)zz values were calculated for each case. It was found that most designed compounds demonstrate superbasicity characteristics and especially amidine-arsinine 1-oxide core structure including two phosphazene electron donating groups (10) shows highest superbasicity properties. The most important finding of the study was the considerable synergistic effect between amidine and arsinine 1-oxide moieties for creating remarkable basicity strength. Aromaticity alterations of the arsinine 1-oxide ring also was monitored during protonation process.

Cyclizations of Alkenyl(Alkynyl)-Functionalized Quinazolinones and their Heteroanalogues: a Powerful Strategy for the Construction of Polyheterocyclic Structures.

Quinazolin-4-one, its heteroanalogues, and derivatives represent an outstandingly important class of compounds in modern organic, medicinal, and pharmaceutical chemistry, as these molecular structures are noted for their wide synthetic and pharmacological potential. In the last years, ever-increasing research attention has been paid to quinazolinone derivatives bearing alkenyl and alkynyl substituents on the pyrimidinone nucleus. The original structural combination of synthetically powerful endocyclic amidine (or amidine-related) and exocyclic unsaturated moieties provides a driving force for cyclizations, which offer an efficient toolkit to construct a variety of fused pyrimidine systems with saturated N- and N,S-heterocycles. In this connection, the present review article is mainly aimed at systematic coverage of the progress in using alkenyl(alkynyl)quinazolinones and their heteroanalogues as convenient bifunctional substrates for regioselective annulation of small- and medium-sized heterocyclic nuclei. Much attention is paid to elucidating the structural and electronic effects of reagents on the regio- and stereoselectivity of the cyclizations as well as to clarifying the relevant reaction mechanisms.

Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria.

The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.

Novel hydroxy- and amidino-substituted benzimidazoles and benzothiazoles as antibacterial and antiproliferative agents.

Aim: The aim was synthesis of novel benzazoles bearing amidino and 2-hydroxyphenyl substituents to explore their biological activity. Methods: Condensation of 5-substituted salicylaldehydes and intermediatesgave new benzazoles by previously published and developed procedures, which were tested for antibacterial and antiproliferative activity in vitro. Results: The best antibacterial activity showed benzimidazole with 2-imidazolinyl group 27 and benzothiazole with an unsubstituted amidine 48 (minimum inhibitory concentration8μg/ml). Benzothiazole 53 proved most potent at inhibiting proliferation of all cancer cells (IC50: 1.2-2.0μM). Conclusion: Most active compounds have been recognized as lead compounds for additional optimization to improve their biological activity. The type of amidine moiety markedly influenced the biological activity. Benzothiazoles showed improved antiproliferative activity in comparison to benzimidazoles.

An Efficient Approach for the Synthesis and Antitumor Evaluation of Novel Azo- and Anil-Linked with 3-Aminopyrazolo[3,4-b]pyridine.

In this project, an effective procedure for constructing a new combination of pyrazolo[3,4-b]pyridine was depicted through the coupling of diazonium salt 2 of heterocyclic amine 1 with active methylene, enamine, and amidine moieties such as 3, 5, 7, and 9 at 0-5 °C in pyridine to afford hydrazinylhydrazonoyl derivatives 4, and diazenylheterocyclic derivatives 6, 8, and 10, respectively. Also, aminopyrazolo[3,4-b]pyridine 1 condensed with different aryl or heteroaryl aldehydes in EtOH/AcOH gave the corresponding aldimine 14, 15, 16. Compound 15 was cyclized via refluxing in DMF for 6 h to afford 18, while the transformation of compound 16 with an alkyl halide afforded 19a, b. The synthesized compounds, explicated by spectral data and elemental analysis, were examined for their antitumor activities. The in vitro cytotoxic activity of new pyrazolo[3,4-b]pyridines against the A2780CP, MCF-7, and HepG-2 cell lines was evaluated using the reference doxorubicin. Compounds 15 and 19a exhibited high reactivity against the A2780CP cell lines, with IC50 values of 35 and 17.9 μM, respectively. Also, compound 28 had the cytotoxic potential for A2780CP and MCF-7 cell lines, with IC50 values of 14.5, and 27.8 μM, respectively.

Amidinoquinoxaline N-oxides: synthesis and activity against anaerobic bacteria.

We present herein an in-depth study on the activity of amidinoquinoxaline N-oxides 1 against Gram-positive and Gram-negative anaerobic bacteria. Based on 5-phenyl-2,3-dihydropyrimidoquinoxaline N-oxide 1a, the selected structural variations included in our study comprise the substituents α- to the N-oxide function, the benzofused ring, substitution and quaternization of the amidine moiety, and the amidine ring size. Compounds 1 showed good to excellent antianaerobic activity, evaluated as the corresponding CIM50 and CIM90 values, and an antimicrobial spectrum similar to metronidazole. Six out of 13 compounds 1 had CIM90 values significantly lower than the reference drug. Among them, imidazoline derivatives 1i-l were the most active structures. Such compounds were synthesized by base-promoted ring closure of the corresponding amidines. The N-oxides under study showed no significant cytotoxicity against RAW 264.7 cells, with high selectivity indexes. Their calculated ADME properties indicate that the compounds are potentially good oral drug candidates. The antianaerobic activity correlated satisfactorily with the electron affinity of the compounds, suggesting that they may undergo bioreductive activation before exerting their antibacterial activity.

Al and Zn phenoxy-amidine complexes for lactide ROP catalysis.

We report the synthesis of a new generation of phenoxy-amidine ligands based on an aryloxy moiety possessing an ortho-N-linked trisubstituted amidine. The reaction of the phenol-amidine proligands with aluminum and zinc alkyls gave mono- or bis-ligated complexes depending on the metal/ligand ratio used. The solid-state structure of four proligands and thirteen Zn and Al complexes has been determined by X-Ray diffraction analysis. The mono-ligated complexes present an aryloxy-bridged dimeric structure, which is retained in solution in the case of Zn complexes but not with aluminum according to DOSY NMR experiments. Bis(ligated) Al and Zn complexes exhibit fluxional behaviour in solution attributed to coordination-decoordination of the amidine moiety and the rotation around the amidine C-NR'2 and C-Ar bonds. These complexes were tested for the ROP of rac-lactide in solution and under bulk conditions. In both cases, the most performant catalysts are Zn complexes featuring a phenoxy-amidine ligand with a pendant additional dimethylamino arm.

YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis.

YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.

Phenoxy-Amidine Ligands: Toward Lactic Acid-Tolerant Catalysts for Lactide Ring-Opening Polymerization

The replacement of the imine functionality in the ubiquitous phenoxy-imine (FI) ligands by a more robust and donor N,N,N′-trisubstituted amidine function was examined and gave rise to the synthesis of five new phenoxy-amidine (FA) ligands (L1–L5). The solid-state structure of four proligands has been determined by X-ray diffraction analysis and showed that the amidine moiety is in a trans-configuration. The reaction of the phenol-amidine proligands with AlMe3 afforded mononuclear (L1–L5)AlMe2 (1a–5a). A similar alkane elimination route was used from ZnEt2 and led to dinuclear [(L1–L5)ZnEt]2 complexes (1b–5b) or to homoleptic (L2/L4)2Zn complexes (2b′, 4b′) depending on the metal/ligand ratio used. The structure of these complexes has been determined by NMR spectroscopy (1H, 13C, HMBC, HSQC, DOSY, and NOESY experiments) and X-ray diffraction study for seven of them. The crystal structure of the Al complexes showed FA ligands coordinated in a chelate fashion via the O atom of the aryloxy group and the imino-N atom, indicating that the amidine function has undergone trans–cis isomerization upon coordination. A similar chelating coordination mode was observed for the FA ligands with Zn metal ions. These complexes were used as initiators for the ring-opening polymerization of rac-lactide. FA–Zn complexes gave the best performance, affording polylactic acid with a narrow molecular weight distribution and heterotactic bias (Pr up to 0.75). Remarkably, some of these complexes were able to tolerate the presence of a large amount of lactic acid to the point of using it as a co-initiator during the polymerization reaction.

Triflamidation of Allyl-Containing Substances:Unusual Dehydrobromination vs. Intramolecular Heterocyclization.

Allyl halides with triflamide under oxidative conditions form halogen-substituted amidines. Allyl cyanide reacts with triflamide in acetonitrile or THF solutions in the presence of NBS to give the products of bromotriflamidation with a solvent interception, whereas in CH2Cl2 two regioisomers of the bromotriflamidation product without a solvent interception were obtained. The formed products undergo base-induced dehydrobromination to give linear isomers with the new C=C bond conjugated either with the nitrile group or the amidine moiety or alkoxy group. Under the same conditions, the reaction of allyl alcohol with triflamide gives rise to amidine, which was prepared earlier by the reaction of diallyl formal with triflamide. Unlike their iodo-substituted analogs, bromo-substituted amidines successfully transform into imidazolidines under the action of potassium carbonate.

CO2-Switchable Single-Chain Polymeric Nanoparticles Enable Gas-Controllable Reaction Separation for Asymmetric Catalysis in Water

Water-soluble single-chain polymeric nanoparticles (SCPNs), which isolated catalytic sites within a hydrophobic interior, made water-incompatible organometallic catalysis highly efficient in water. However, it is still a great challenge to conveniently control their hydrophilicity, so as to combine reactivity and recovery of the catalytic SCPNs in aqueous systems. Herein, we have developed a series of catalytic SCPNs, which possessed CO2-switchable hydrophilic/hydrophobic behavior, to realize the gas-controlled reaction and separation for asymmetric sulfa-Michael addition (SMA) in water. A novel series of CO2-switchable random copolymers were thus synthesized by copolymerization of CO2-responsive amidine derivatives with hydrophobic chiral salen FeIII monomers via reversible addition-fragmentation chain transfer polymerization. Characterization suggested their CO2-controlled self-collapse behavior in water due to CO2-switched change in hydrophilicity/hydrophobicity of the amidine moiety. The resultant CO2-switchable SCPNs provided hydrophobic, catalytic compartments for asymmetric SMA in water upon CO2 addition, giving various chiral β-keto sulfides with almost quantitative yields (90–98%) and high enantioselectivities (93–99%). When CO2 is removed by N2 bubbling, they were collapsed and spontaneously precipitated from the aqueous system for steady reuse. The gas-controlled reaction-separation approach provides an energy-efficient way to combine reactivity and recovery of catalytic SCPNs in aqueous systems, which should be quite practical in large-scale industrial applications.

Synthesis and insecticidal activity of novel 1,2,4‐triazole containing amidine moiety

AbstractUnder the guidance of molecular hybridization, a series of compounds containing neonicotinoid and amidine fragments were designed and synthesized. The biological activities were evaluated againstPlutella xylostellaandAphis gossypii. Most of these compounds showed good activities withAphis gossypiiat the concentration of 500 μg/ml. The Structure–activity relationship analysis showed length and size of the alkyl group on the 1,2,4‐triazole skeleton have a significant impact on the insecticidal activity.

Protonation-Induced Antiaromaticity in Octaaza[8]circulenes: Cyclooctatetraene Scaffolds Constrained with Four Amidine Moieties.

The switching of cyclic π-conjugation pathways using external stimuli is an attractive research topic in the field of organic chemistry. Here, we synthesized C4h -symmetric octaaza[8]circulenes with four peripherally arranged amidine moieties that exhibit enhanced antiaromaticity upon protonation. Titration experiments with methanesulfonic acid revealed the formation of the tetraprotonated forms of the octaaza[8]circulenes in solution. Single-crystal X-ray diffraction analyses and theoretical calculations indicated that the contribution of the 8π antiaromatic character of the octaaza[8]circulenes is enhanced by the delocalization of charge through the protonation of the pyridine rings.