Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry

The binding of a series of benzoxazole analogs with different amide- and ester-linked side chains to duplex DNA in the absence and presence of divalent metal cations is examined. All ligands were found to form complexes with Ni2+, Cu2+, and Zn2+, with 2:1 ligand/metal cation binding stoichiometries dominating for ligands containing shorter side chains (2, 6, 7, and 8), while 1:1 complexes were the most abundant for ligands with long side chains (9, 10, and 11). Ligand binding with duplex DNA in the absence of metal cations was assessed, and the long side-chain ligands were found to form low abundance complexes with 1:1 ligand/DNA binding stoichiometries. The ligands with the shorter side chains only formed DNA complexes in the presence of metal cations, most notably for 7 and 8 binding to DNA in the presence of Cu2+. The binding of long side-chain ligands was enhanced by Cu2+ and to a lesser degree by Ni2+ and Zn2+. The cytotoxicities of all of the ligands against the A549 lung cancer and MCF7 breast cancer cell lines were also examined. The ligands exhibiting the most dramatic metal-enhanced DNA binding also demonstrated the greatest cytotoxic activity. Both 7 and 8 were found to be the most cytotoxic against the A549 lung cancer cell line and 8 demonstrated moderate cytotoxicity against MCF7 breast cancer cells. Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds.     

Effects of coordinating metal ions on the mediated inhibition of trypsin by bis(benzimidazoles) and related compounds

The presence of the Zn2+ ion dramatically enhances the inhibition of trypsin and tryptase by amidine-modified benzimidazole inhibitors via coordination to both the catalytically active Ser195 hydroxyl and His57 imidazole residues of the enzyme and the nitrogens of the amidine-modified benzimidazole inhibitor (Janc, J. W.; Clark, J. M.; Warne, R. L.; Elrod, K. C.; Katz, B. A.; Moore, W. R. Biochemistry 2000, 39, 4792-4800). Some new 5-amidino-2-substituted benzimidazoles were synthesized and compared to known related molecules to explore systematically the metal-mediated inhibition of bovine trypsin as a function of coordinating groups and metal ions. These compounds take advantage of the favorable interaction between the amidine group on one side of the inhibitor and the Asp189 carboxylate in the binding pocket of the enzyme. The 5-amidino-2-substituted benzimidazoles all demonstrated similar inhibition constants (Ki) of 20-50 microM in the absence of metal ions. In the presence of Zn2+, inhibition increased to varying extents, depending upon the group substituted at the 2 position of the benzimidazole. The largest increase in inhibition in the presence of Zn2+ was seen with (5-amidino-2-benzimidazolyl)-2-benzimidazolylmethane with an apparent inhibition constant (Ki') of 0.37 +/- 0.06 nM, giving a 59,000-fold increase in inhibition when Zn2+ is present. Other metal ions, including Mn2+, Sc3+, and Hg2+, also increased the inhibition by several of the benzimidazole derivatives synthesized. The compound bis(2-benzimidazolyl)methane (BBIM) was also examined because it lacks the amidine group that provides a favorable hydrogen-bonding interaction with Asp189 in the binding pocket of trypsin. In the absence of metal ions, BBIM did not have a detectable affinity for trypsin; however, in the presence of Zn2+, a Ki' of 127 +/- 3 nM was observed. This result demonstrates that an affinity for the enzyme in the absence of metal ions is not required for potent metal-mediated inhibition, greatly expanding the possibilities for metal mediation of nonmetalloenzymes.     

Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole)

Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co²⁺, Ni²⁺, and Cu²⁺ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.     

A facile and efficient addition reaction of nitrogen‐containing heterocyclic compounds with DMAD under neat conditions

A simple and efficient method was developed for the reaction of dimethyl acetylenedicarboxylate with benzothiazole, isoquinoline, quinoline, 3‐bromopyridine, pyridine, benzoxazole, benzimidazole, and 5,6‐dimethyl benzimidazole for the high‐yield synthesis of the related heterocyclic products ( 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ) in very short reaction time under neat procedure. The reaction of isoquinoline, 3‐bromopyridine, and pyridine afforded to diastereomeric mixtures of products 2 , 4 , and 5 , respectively. However, only one isomer of products 1 , 3 , 6 , 7 , and 8 were identified from the reaction of benzothiazole, quinoline, benzoxazole, benzimidazole, and 5,6‐dimethyl benzimidazole, respectively. Benzotriazole afforded to product 9 under these conditions. For comparison, the reactions were examined in different reaction mediums and/or under microwave irradiation. J. Heterocyclic Chem., (2011).     

New Wide Rim Phosphomethylated Calix[4]arenes in Extraction of Americium and Europium

A new series of the cone-shaped tetraalkoxycalix[4]arenes substituted at the wide rim with four phosphomethyl groups have been synthesized by the Arbuzov, Michaelis–Becker and Aterthon–Todd reactions of the chloromethyl or phenylhydrophosphinylmethylcalix[4]arenes. Their binding properties towards Eu³⁺ and Am³⁺ cations were investigated by the liquid–liquid extraction method. Due to the ‘calixarene effect’ the tetraphosphorylated calixarenes are more effective extractants for the metal cations than their acyclic analogs or some industrial extractants such as trialkylphosphinoxides, carbamoylphosphinoxide, bis-2-diethylhexyl phosphoric acid.     

Design,Synthesis, In Vitro Antimicrobial,Antioxidant Evaluation,and Molecular Docking Study of Novel Benzimidazole and Benzoxazole Derivatives

A series of novel 2‐substituted benzimidazole and benzoxazole derivatives as a potential antimicrobial and antioxidant agent were synthesized via coupling of N‐methyl‐o‐phenylenediamine or 2‐amino‐phenol with aromatic aldehyde and acid in the presence of polyphosphoric acid as an efficient catalyst as well as solvent by conventional method in short reaction times with excellent yield. The newly synthesized benzimidazole and benzoxazole derivatives were evaluated for antimicrobial and antioxidant activity and exhibited excellent to good activities compared to the standard drugs. Furthermore, the theoretical predictions based on molecular docking against microbial DNA gyrase could provide an insight into the plausible mechanism of action and establish a link between the observed antimicrobial activity and the binding affinity shedding light on specific thermodynamic (bonded and nonbonded) interactions governing the activity. Furthermore, the synthesized compounds were analyzed for absorption, distribution, metabolism, and excretion properties and exhibited potential properties to build up as good oral drug candidates.     

丙二胺缩乙酰丙酮单席夫碱、咪唑金属配合物的XPS与电子结构分析

对6个丙二胺缩乙酰丙酮单席夫碱、咪唑（苯并咪唑）金属配合物进行了XPS分析，得到了配合物在生成过程中金属离子M(Cu^2 、Ni^2 、Co^2 ）的2p轨道、配位体N原子的1s轨道能级的变化道；观察到咪唑或苯并咪唑配位后，其环上另一个非配位的胺N原子向亚胺型N原子状态过渡。     

Influence of metal cations on the intramolecular hydrogen-bonding network and pKa in phosphorylated compounds

The binding of the most common metal cations of cytoplasm (Li+, Na+, K+, Mg2+ and Ca2+) to a model molecule having an intramolecular hydrogen-bonding network, myo-inositol-2-monophosphate, was studied using first principles. A strong correlation between the conformation of metal inositol phosphate complexes with the type of metal cation, degree of deprotonation state, and the surrounding environment has been observed. On the basis of the hydrogen-bonding network analysis of the cation-phosphate complexes (Mn+-Ins(2)P1), the alkali cations show little effect on the conformational preference while the conformational preference for the binding of the alkaline earth cations is pH-dependent and solvent-dependent. For example, these calculations predict that Mg2+-Ins(2)P1(0) and Mg2+-Ins(2)P1(2-) favor the 1a/5e form while Mg2+-Ins(2)P1(1-) favors the 5a/1e conformation. The Ca2+-Ins(2)P1(2-) complex prefers the 1a/5e conformation in the gas phase and in a nonpolar protein environment, but inverts to the 5a/1e conformation upon entering the polar aqueous phase. The binding affinities of the cations and the pK(a) values for the cation-phosphate complexes are derived from thermodynamical analysis.     

Electronic structure, 1H NMR spectra,and reactivity in certain tricyclic heteroaromatic systems

The simple MO LCAO method was used for calculations on 4H-imidazo[5,1-b]benzimidazole, imidazo[5,1-b]benzoxazole, imidazo[5,1-b]benzothiazole, and a number of their derivatives. Inclusion of the unshared pairs of the hetero atoms at positions 4 and 9 in the -electron system has a considerable effect on the stability of compounds of this type. The ¹H NMR spectra were recorded for 4-methyl-imidazo[5,1-b]benzimidazole and imidazo[5,1-b]benzoxazole derivatives, and a similarity was found between the chemical shifts of the imidazole ring protons and the -electron densities at the adjacent carbon atoms. Calculation of a series of models for the cations and measurements of the basicity constants show protonation of 4-methylimidazo[5,1-b]benzimidazole takes place at the nitrogen atom in position 2. The calculated values for the electronic structure and reactivity indices in the investigated series of tricyclic systems were compared with their chemical properties.     

Crystal and electronic structures of magnesium(II), copper(II), and mixed magnesium(II)-copper(II) complexes of the quinoline half of styrylquinoline-type HIV-1 integrase inhibitors

A new target in AIDS therapy development is HIV-1 integrase (IN). It was proven that HIV-1 IN required divalent metal cations to achieve phosphodiester bond cleavage of DNA. Accordingly, all newly investigated potent IN inhibitors contain chemical fragments possessing a high ability to chelate metal cations. One of the promising leads in the polyhydroxylated styrylquinolines (SQLs) series is (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinoline carboxylic acid (1). The present study focuses on the quinoline-based progenitor (2), which is actually the most probable chelating part of SQLs. Conventional and synchrotron low-temperature X-ray crystallographic studies were used to investigate the chelating power of progenitor 2. Mg2+ and Cu2+ cations were selected for this purpose, and three types of metal complexes of 2 were obtained: Mg(II) complex (4), Cu(II) complex (5) and mixed Mg(II)-Cu(II) complexes (6 and 7). The analysis of the crystal structure of complex 4 indicates that two tridentate ligands coordinate two Mg2+ cations, both in octahedral geometry. The Mg-Mg distance was found equal to 3.221(1) A, in agreement with the metal-metal distance of 3.9 A encountered in the crystal structure of Escherichia coli DNA polymerase I. In 5, the complex is formed by two bidentate ligands coordinating one copper ion in tetrahedral geometry. Both mixed Mg(II)-Cu(II) complexes, 6 and 7 exhibit an original arrangement of four ligands linked to a central heterometallic cluster consisting of three octahedrally coordinated magnesium ions and one tetrahedrally coordinated copper ion. Quantum mechanics calculations were also carried out in order to display the electrostatic potential generated by the dianionic ligand 2 and complex 4 and to quantify the binding energy (BE) during the formation of the magnesium complex of progenitor 2. A comparison of the binding energies of two hypothetical monometallic Mg(II) complexes with that found in the bimetallic magnesium complex 4 was made.     

Microwave assisted one pot synthesis of 2-ethylamino benzimidazole,benzoxazole and benzothiazole derivatives

A rapid and efficient one-pot method for the synthesis of 2-ethylamino benzimidazole, benzoxazole, and benzothiazole derivatives has been described. The reaction of o-phenylenediamines or o-aminophenols or 2-mercaptoanilines with EDC.HCl under microwave irradiation afforded the corresponding 2-ethylamino benzimidazole, benzoxazole and benzothiazole derivatives in excellent yields.     

Photoinduced formation of a cryptand from a coronand: an unexpected switch in cation binding affinity

Aza-crown ethers 2 and 3 with anthracene-containing pendant arms have been synthesised and characterised. Both compounds bind Group 1 metal cations in solution, forming complexes of 1:1 stoichiometry. The properties of compound 2 and its complexes have been studied by a range of techniques, including NMR, UV and fluorescence spectroscopy and X-ray crystallography. The pendant arms can adopt either a cis or a trans geometry, the cis geometry favoured with larger cations. The geometry of the complex affects the fluorescence properties of the system, with larger cations giving higher excimer/monomer ratios. Upon irradiation at lambda>300 nm, coronand 2 forms the cryptand 5 through a reversible intramolecular [4pi+4pi] cycloaddition reaction. The rates of the forward and reverse reactions of this photochromic process are cation dependent; in particular the rate of the thermal reverse reaction is decreased by smaller cations and increased by larger cations, especially Rb(+). The metal binding constants in methanol for 2 and 5 have been determined, revealing that the cryptand 5 binds Na(+) and Rb(+) more weakly than crown ether 2 by over two orders of magnitude.     

Synthesis and Protonation Features of 24-, 27- and 32-membered Macrocyclic Polyamines

Three macrocyclic polyamines [24]ane-N₆ 1 , [32]ane-N₈ 2 and [27]ane-N₆O₃ 3 of ring size 24, 32 and 27, respectively, have been synthesized. They contain either trimethylenediamine of ethylenediamine units. The acyclic analog 4 , as the reference compound, was also prepared. Compounds 1–3 are macrocyclic analogs of natural polyamines and are potential ligands for metal cations as well as, when protonated, for anions. The protonation constants of compounds 1–4 have been determined. They are high enough for compounds 1–4 to be fully protonated in a pH-range close to neutrality, as required for binding of anions of weak acids. The effect of structural features on the protonation constants are briefly discussed in relation to the design of macrocyclic polyamine ligands.     

苹果酸酶结合域定点突变对烟酰胺腺嘌呤二核苷酸类似物催化性能的影响

通过对苹果酸酶(ME)辅酶结合域L310、Q401、L404饱和位点突变库与辅酶烟酰胺腺嘌呤二核苷酸(NAD⁺)类似物库的高通量筛选,研究了苹果酸酶结合域位点对NAD⁺及其类似物(B1~B7)催化活性的影响。 结果表明,突变后酶ME-Q401H/L404T对类似物B4的k_cat/K_m是野生型酶的50倍;突变后酶ME-L310M/Q401N对类似物B4的k_cat/K_m是野生型酶的16倍,对类似物B3的k_cat/K_m是野生型酶的5倍,因此通过对结合域定点突变,NAD⁺类似物的催化活性得到提高。     

Complexation and Transport of Alkali and Alkaline Earth Metal Cations by p-tert-Butyldihomooxacalix[4]arene Tetraketone Derivatives

The binding properties of three p-tert-butyldihomooxacalix[4]arene tetraketone derivatives (tert-butyl 2b, adamantyl 2c and phenyl 2d) in the cone conformation and one derivative (methyl 2a) in a partial cone conformation, towards alkali and alkaline earth metal cations have been established by extraction studies of metal picrates from water into dichloromethane, stability constant measurements in methanol and acetonitrile, and by ¹H NMR spectrometry. Transport experiments of metal picrates through a dichloromethane membrane were also performed. The results are compared to those obtained with closely-related calix[n]arene derivatives (n = 4 and 5) and discussed in terms of the substituents, size and conformational effects. Methylketone 2a is a poor binder for all the cations studied, due to its partial cone conformation. Ketones 2b, 2c and 2d show high extraction and complexation levels for the alkali cations, with similar profiles and preference for K⁺ and Na⁺ (plateau selectivity). Towards alkaline earth cations, these ketones show a strong peak selectivity for Ba²⁺ in extraction, but a plateau selectivity for Ca²⁺, Sr²⁺ and Ba²⁺ in complexation. The nature of the substituent attached to the ketone function has some influence on their binding properties, with phenylketone 2d being a slightly weaker binder than ketones 2b and 2c. ¹H NMR titrations confirm the formation of 1:1 complexes between the ketones and the cations studied, also indicating that they should be located inside the cavity defined by the phenoxy and carbonyl oxygen atoms. Ketones 2b, 2c and 2d show transport rates that do not follow, in general, the same trends observed in extraction and complexation.     

Organic heterocyclic-based colorimetric and fluorimetric chemosensors for the detection of different analytes: a review (from 2015 to 2022)

Heterocyclic organic compounds, also called heterocycles, are any major class of organic compounds having at least one atom other than carbon in the ring. Due to their excellent electronic and structural features, these compounds exhibit a wide range of biological and nonbiological applications. Among these, indole, benzimidazole, benzothiazole, and benzoxazole are versatile organic heterocyclic compounds widely used in different fields. They show a wide range of applications in polymer, coordination chemistry, pharmacy, dyes, food packages, medicine, and industries. These compounds contain heteroatoms like S-, N-, and O-, through which they interact with metal ions, anions, and neutral species, giving measurable analytical signals that can be used as fluorimetric and colorimetric chemosensors for detecting different analytes in biological, agricultural and environmental samples. This review summarizes indole, benzimidazole, benzothiazole, and benzoxazole-based fluorimetric and colorimetric chemosensors for detecting metal ions, anions, and neutral species. Furthermore, the recognition mechanisms have been discussed in detail, which could help researchers to design efficient, highly selective, and sensitive chemosensors to recognize and determine heavy metal cations.     

Synthesis and Antimicrobial Activities of Novel 2‐[substituted‐1H‐pyrazol‐4‐yl] Benzothiazoles,Benzoxazoles, and Benzimidazoles

In an endeavor to find a new class of antimicrobial agents, a series of novel substituted benzimidazole, benzoxazole, and benzothiazole derivatives 6 containing pyrazole moiety have been synthesized by reaction of 3‐aryl‐4‐formyl pyrazole 4 with substituted phenylenediamine or o‐aminophenol or o‐aminothiophenol 5 . Reaction of phenyl hydrazine or 2‐hydrazinopyridine 1 with substituted acetophenones 2 gave the corresponding hydrazones 3 , which on Vilsmeier–Haack reaction with POCl₃–DMF gave substituted 3‐aryl‐4‐formyl pyrazoles 4 . All final compounds 6a , 6b , 6c , 6d , 6e , 6f , 6g , 6h , 6i , 6j , 6k were evaluated for in vitro antibacterial activities against Escherichia coli and Staphylococcus aureus strains and in vitro antifungal activity against Candida albicans and Aspergillus niger strains by using serial dilution method. The antimicrobial activities were expressed as the minimum inhibitory concentration in µg/mL. The compound containing benzimidazole and benzoxazole moiety gave better antibacterial and antifungal activities than benzothiazole compounds.     

Mercury ions complexation with a series of heterocyclic derivatives of 3-hydroxychromone: spectral effects and prospects for ultrasensitive Hg2+ probing

Complexation of three 3-hydroxychromone derivatives bearing a nitrogen-containing heterocyclic moiety in the position 2 of the chromone bicycle - benzimidazole, quinoline, and 2,5-diphenyloxazole, with mercury(II) ions is reported. Formation of chelate complexes with the metal cations coordinated with the cavity formed by 3-OH and 4-C═O groups was shown, as well as the possibility of side moiety heteroatom participation in binding of metal ions. High sensitivity to mercury of 2,5-diphenyloxazole-substituted 3-hydroxychromone was elucidated, allowing to detect Hg(2+) below the maximum permissible concentration for drinking water. This makes the above-mentioned compound a prospective basis for development of sensors for ultralow mercury concentration detection in water. Unusual fluorescence ignition of 2-(quinolin-2-yl)-3-hydroxychromone at low Hg(2+) concentrations, rarely observed for heavy metals ions complexation with organic fluorescent ligands, was discussed.     

Metal ion extraction by cone p-tert-butylcalix[4]arene-1,3-crown-5 with two N-(X)sulfonyl carbamoylmethoxy side arms and -1,3-monothiacrown-5 analogues

Four cone p-tert-butylcalix[4]arene-1,3-monothiacrown-5 ligands each with two N-(X)sulfonyl carbamoylmethoxy side arms are synthesized for comparison with analogs having only oxygen heteroatoms in the crown ether ring. Solvent extractions of hard alkali metal and alkaline earth metal cations, intermediate Pb²⁺, and soft Hg²⁺ from aqueous solutions into chloroform by these ligands are utilized to probe the effects of sulfur replacement in the crown ether ring on metal ion complexation.