A proposed common spatial pharmacophore and the corresponding active conformations of some peptide leukotriene receptor antagonists

Summary Molecular modeling studies were carried out by a combined use of conformational analysis and 3D-QSAR methods to identify molecular features common to a series of hydroxyacetophenone (HAP) and non-hydroxyacetophenone (non-HAP) peptide leukotriene (pLT) receptor antagonists. In attempts to develop a ligand-binding model for the pLT receptor, the Apex-3D program was used to identify biophoric structural patterns that are common to 13 diverse sets of compounds showing different levels of biological activity. A systematic conformational analysis was carried out to obtain sterically accessible conformations for these flexible compounds. Apex-3D was then utilized to propose common biophoric regions based on the selection of one of several conformations (MOPAC-minimized AM1) from each compound's data set that best fits the biophoric pattern and the resulting superimposition with all the other data-set compounds. Apex-3D identified three common biophoric features important for activity: one as the hydroxyl, acetyl, carbonyl and carboxyl groups, which mimic the acid-binding region of an agonist, the other as the hydrogen-bond donating site, and the third part is represented by a plane in which lipophilic aromatic groups align. The structure-activity relationships were then assessed by using the 3D-QSAR model. A common biophore model is proposed from the Apex-3D analysis which may be useful in designing new pLT antagonists. Molecular volumes and electrostatic potential similarities were also calculated in order to obtain the important structural requirements for the activity.     

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.     

Synthesis,Structural Characterization,and In Vitro and In Silico Antifungal Evaluation of Azo-Azomethine Pyrazoles (PhN2(PhOH)CHN(C3N2(CH3)3)PhR,R = H or NO2)

The azo-azomethine imines, R¹-N=N-R²-CH=N-R³, are a class of active pharmacological ligands that have been prominent antifungal, antibacterial, and antitumor agents. In this study, four new azo-azomethines, R¹ = Ph, R² = phenol, and R³ = pyrazol-Ph-R’ (R = H or NO₂), have been synthesized, structurally characterized using X-ray, IR, NMR and UV–Vis techniques, and their antifungal activity evaluated against certified strains of Candida albicans and Cryptococcus neoformans. The antifungal tests revealed a high to moderate inhibitory activity towards both strains, which is regulated as a function of both the presence and the location of the nitro group in the aromatic ring of the series. These biological assays were further complemented with molecular docking studies against three different molecular targets from each fungus strain. Molecular dynamics simulations and binding free energy calculations were performed on the two best molecular docking results for each fungus strain. Better affinity for active sites for nitro compounds at the “meta” and “para” positions was found, making them promising building blocks for the development of new Schiff bases with high antifungal activity.     

Synthesis of Novel Thiazole Derivatives Bearing β-Amino Acid and Aromatic Moieties as Promising Scaffolds for the Development of New Antibacterial and Antifungal Candidates Targeting Multidrug-Resistant Pathogens

Rapidly growing antimicrobial resistance among clinically important bacterial and fungal pathogens accounts for high morbidity and mortality worldwide. Therefore, it is critical to look for new small molecules targeting multidrug-resistant pathogens. Herein, in this paper we report a synthesis, ADME properties, and in vitro antimicrobial activity characterization of novel thiazole derivatives bearing β-amino acid, azole, and aromatic moieties. The in silico ADME characterization revealed that compounds 1–9 meet at least 2 Lipinski drug-like properties while cytotoxicity studies demonstrated low cytotoxicity to Vero cells. Further in vitro antimicrobial activity characterization showed the selective and potent bactericidal activity of 2a–c against Gram-positive pathogens (MIC 1–64 µg/mL) with profound activity against S. aureus (MIC 1–2 µg/mL) harboring genetically defined resistance mechanisms. Furthermore, the compounds 2a–c exhibited antifungal activity against azole resistant A. fumigatus, while only 2b and 5a showed antifungal activity against multidrug resistant yeasts including Candida auris. Collectively, these results demonstrate that thiazole derivatives 2a–c and 5a could be further explored as a promising scaffold for future development of antifungal and antibacterial agents targeting highly resistant pathogenic microorganisms.     

Molecular modeling and 3D-QSAR studies in 2-aziridinyl-and 2,3-bis(aziridinyl)-1,4-naphthoquinonyl sulfonate and acylate derivatives as potential antimalarial agents

Malaria is still continuing to be one of the most dreadful diseases of the tropical countries particularly due to the development of resistance to the existing antimalarials. From observed, antimalarial activity of 2-aziridinyl- and 2,3-bis(aziridinyl)-1,4-naphthoquinonyl sulfonate and acylate derivatives acting through redox cycling mechanism, molecular modeling and three dimensional-quantitative structure activity relationship (3D-QSAR) studies have been carried out on a set of 63 compounds to identify important pharmacophors. Among several 3D-QSAR models generated, three models with correlation coefficient r > 0.82, match > 0.60 and chance = 0.00 have shown two common biophoric sites: one being the oxygen atom at position 1 of the naphthoquinone ring in terms of pi-population, charge and electron donating ability while the second being the center of the phenyl ring in terms of its 6pi-electrons. In addition to these sites, the models also share two common secondary sites: one positively contributing H-acceptor site while the second site contributing negatively in terms of steric refractivity. All these models showed good agreement between the experimental, calculated and predicted antimalarial activities.     

Molecular Modeling and 3D-QSAR Studies in 2-Aziridinyl-and 2,3-Bis(Aziridinyl)-1,4-Naphthoquinonyl Sulfonate and Acylate Derivatives as Potential Antimalarial Agents

Abstract

Malaria is still continuing to be one of the most dreadful diseases of the tropical countries particularly due to the development of resistance to the existing antimalarials. From observed, antimalarial activity of 2-aziridinyl- and 2,3-bis(aziridinyl)-1,4-naphthoquinonyl sulfonate and acylate derivatives acting through redox cycling mechanism, molecular modeling and three dimensional-quantitative structure activity relationship (3D-QSAR) studies have been carried out on a set of 63 compounds to identify important pharmacophors. Among several 3D-QSAR models generated, three models with correlation coefficient r > 0.82, match > 0.60 and chance = 0.00 have shown two common biophoric sites: one being the oxygen atom at position 1 of the naphthoquinone ring in terms of π-population, charge and electron donating ability while the second being the center of the phenyl ring in terms of its 6π-electrons. In addition to these sites, the models also share two common secondary sites: one positively contributing H-acceptor site while the second site contributing negatively in terms of steric refractivity. All these models showed good agreement between the experimental, calculated and predicted antimalarial activities.     

氟喹诺酮C-3均三唑硫醚酮缩氨基硫脲衍生物的合成及抗肿瘤活性

为发现氟喹诺酮由抗菌活性向抗肿瘤活性转化的结构修饰方法,基于生物电子等排药物设计原理,用唑杂环作为氧氟沙星(1)C-3羧基的等排体、硫醚酮缩氨基硫脲为其功能侧链修饰基,设计合成C-3均三唑硫醚酮缩氨基硫脲目标化合物(6a~6g),其结构经元素分析和光谱数据确证。 体外抗肿瘤活性结果表明,中间体C-3均三唑硫醚酮(5a~5g)和目标化合物(6a~6g)的活性均强于母体氧氟沙星的活性,其中缩氨基硫脲的活性强于相应硫醚酮的活性,尤其是苯环含硝基和氟原子目标化合物的活性与对照药阿霉素的活性相当。 因此,功能缩氨基硫脲链修饰的均三唑作为C-3羧基的等排体有利于提高氟喹诺酮的抗肿瘤活性。     

Design synthesis and biological evaluation of 3-substituted triazole derivatives

Based on the active site of lanosterol 14α-demethylase of azole antifungal agents,sixteen 1-(1H-1,2,4-triazole-1-yl)- 2-(2,4- difluorophenyl)-3-(N-n-butyl-N-1-substitutedbenzyl-4-methylene-1H-1,2,3-triazole)-2-propanols have been designed,synthesized and evaluated as antifungal agents.Results of preliminary antifungal tests against eight human pathogenic fungi in vitro showed that some of the compounds exhibited excellent activities with broad spectrum.     

Probing structure and functional dynamics of (large) proteins with aromatic rings: L-GFT-TROSY (4,3)D HCCH NMR spectroscopy

NMR assignment of aromatic rings in proteins is a prerequisite for obtaining high-quality solution structures of proteins and for studying the dynamics and folding of their molecular cores. Here we present sensitive PFG-PEP L-GFT-(TROSY) (4,3)D HCCH NMR for identification of aromatic spin systems based on four-dimensional (4D) spectral information which can be rapidly obtained with high digital resolution. The G-matrix Fourier Transform (GFT) experiment relies on newly introduced longitudinal relaxation (L-)optimization for aromatic protons and is optimally suited for both sensitivity and sampling limited data collection, making it particularly attractive for NMR-based structural genomics. Applications are presented for 21 and 13 kDa proteins HR41 and MaR11, targets of the Northeast Structural Genomics Consortium for which data collection is, respectively, sensitivity and sampling limited. Complete assignment of aromatic rings enabled high-quality NMR structure determination, and nearly complete analysis of aromatic proton line widths allowed one to assess the flipping of most rings in HR41. Specifically, the ring of Tyr90 flips very slowly on the seconds time scale, thereby proving the absence of fast larger-amplitude motional modes which could allow the ring to flip. This indicates remarkable rigidity of the substructure in which the ring is embedded. Tyr90 is conserved among ubiquitin-conjugating enzymes E2, to which HR41 belongs, and is located in spatial proximity to the interface between E2 and ubiquitin protein ligase E3. Hence, the conformational rigidity and/or the slow motional mode probed by the ring might be of functional importance.     

苯酰胺类D2受体显像剂的共平面效应

苯酰胺类化合物是多巴胺Ｄ2受体的拮抗剂,它不仅与Ｄ2受体的亲和力高,而且产生的锥体外副反应极轻,是一类很有应用潜力的抗精神病药物.放射性同位素(123Ｉ等)标记的苯酰胺类化合物可作为多巴胺Ｄ2受体显像剂用于临床诊断疾病.近年来,相继报导了一系列高亲和力的该类化合物,其中,123ＩＩＢＺＭ等已用于临床诊断疾病[1].本文在前文[2]苯酰胺类Ｄ2受体显像剂结构效应的研究基础上,利用ＳＹＢＹＬ6.4软件,研究了该类化合物分子的不同构象以及空间结构与结合活性之间的关系,证实了前文提出的由于分子内氢键形成六元共平面假想Ａ环、Ｂ环等是影响…     

Unsymmetrical Trifluoromethyl Methoxyphenyl β-Diketones: Effect of the Position of Methoxy Group and Coordination at Cu(II) on Biological Activity

Copper(II) complexes with 1,1,1-trifluoro-4-(4-methoxyphenyl)butan-2,4-dione (HL1) were synthesized and characterized by elemental analysis, FT-IR spectroscopy, and single crystal X-ray diffraction. The biological properties of HL1 and cis-[Cu(L1)₂(DMSO)] (3) were examined against Gram-positive and Gram-negative bacteria and opportunistic unicellular fungi. The cytotoxicity was estimated towards the HeLa and Vero cell lines. Complex 3 demonstrated antibacterial activity towards S. aureus comparable to that of streptomycin, lower antifungal activity than the ligand HL1 and moderate cytotoxicity. The bioactivity was compared with the activity of compounds of similar structures. The effect of changing the position of the methoxy group at the aromatic ring in the ligand moiety of the complexes on their antimicrobial and cytotoxic activity was explored. We propose that complex 3 has lower bioavailability and reduced bioactivity than expected due to strong intermolecular contacts. In addition, molecular docking studies provided theoretical information on the interactions of tested compounds with ribonucleotide reductase subunit R2, as well as the chaperones Hsp70 and Hsp90, which are important biomolecular targets for antitumor and antimicrobial drug search and design. The obtained results revealed that the complexes displayed enhanced affinity over organic ligands. Taken together, the copper(II) complexes with the trifluoromethyl methoxyphenyl-substituted β-diketones could be considered as promising anticancer agents with antibacterial properties.     

含氮杂茂配体的类茂配合物NpCpTiCl_2催化乙烯聚合研究

茂金属催化烯烃聚合时不仅须大量甲基铝氧烷(MAO)作助催化剂,而且其稳定性较差,结构修饰困难,这都一定程度上限制了茂金属催化剂的发展.近几年来,将非环戊二烯类配体与IVB 族金属作用形成的配合物应用于催化烯烃聚合的研究大量出现[1],其中非环戊二烯配体有脒化物[2,3]、酰胺基[4,5]、NFDA3唑啉[6]、卟啉[7 ]、烷氧基[8]、芳氧基[9～11]、和β-二酮[12,13]、8-羟基喹啉[14～16]等.这些非茂配合物均可催化乙烯或丙烯聚合,但活性都较低.我们曾制备了含配位原子为氧或氮的非环戊二烯基配体的半茂配合物,即茂金属中一个环戊二烯基配体被非环戊二烯基配体取代,使金属中心与一个茂和一个非茂配体配位而形成的桥连或非桥连型的配合物[17,18].这类配合物不仅稳定性好,而且消耗的助催化剂量较少,活性高,对所得聚合物的结构有一定的控制作用.桥连型半茂配合物以“限制几何构型”催化剂为代表[16,19～20 ],非桥连型半茂配合物的报道较少,如CpTi(OiPr)Me2和CpTi(OAr)X2 [21 ,22].我们选择氮杂茂类配体为非环戊二烯阴离子配体,氮杂茂环以一价阴离子的形式与金属中心钛配位,与另一个环戊二烯阴离子形成类茂型配合物.这种类茂配合物易于制备, 稳定性好,而且消耗的助催化剂量较小.     

Molecular and electronic structure, magnetotropicity and absorption spectra of benzene-trinuclear copper(I) and silver(I) trihalide columnar binary stacks

The molecular and electronic structures, stabilities, bonding features, magnetotropicity and absorption spectra of benzene-trinuclear Cu(I) and Ag(I) trihalide columnar binary stacks with the general formula [c-M(3)(μ(2)-X)(3)](n)(C(6)H(6))(m) (M = Cu, Ag; X = halide; n, m ≤ 2) have been investigated by means of electronic structure calculation methods. The interaction of c-M(3)(μ(2)-X)(3) clusters with one and two benzene molecules yields 1:1 and 1:2 binary stacks, while benzene sandwiched 2:1 stacks are formed upon interaction of two c-M(3)(μ(2)-X)(3) clusters with one benzene molecule. In all binary stacks the plane of the alternating c-M(3)(μ(2)-X)(3) and benzene components adopts an almost parallel orientation. The separation distance between the centroids of the benzene and the proximal c-M(3)(μ(2)-X)(3) metallic cluster found in the range 2.97-3.33 ? at the B97D/Def2-TZVP level is indicative of a π···π stacking interaction mode, for the centroid separation distance is very close to the sum of the van der Waals radii of Cu···C (3.10 ?) and Ag···C (3.44 ?). Energy decomposition analysis (EDA) at the SSB-D/TZP level revealed that the dominant term in the c-M(3)(μ(2)-X)(3)···C(6)H(6) interaction arises from dispersion and electrostatic forces while the covalent interactions are predicted to be negligible. On the other hand, charge decomposition analysis (CDA) illustrated very small charge transfer from C(6)H(6) toward the c-M(3)(μ(2)-X)(3) clusters, thus reflecting weak π-base/π-acid interactions which are further corroborated by the respective electrostatic potentials and the fact that the total dipole moment vector points to the center of the metallic ring of the c-M(3)(μ(2)-X)(3) cluster. The absorption spectra of all aromatic columnar binary stacks simulated by means of TD-DFT calculations showed strong absorptions in the UV region. The main features of the simulated absorption spectra are thoroughly analyzed, and assignments of the contributing electronic transitions are given. The magnetotropicity of the binary stacks evaluated by the NICS(zz)-scan curves indicated an enhancement of the diatropicity of the inorganic ring upon interaction with the aromatic benzene molecule. Noteworthy is the slight enhancement of the diatropicity of the benzene ring, particularly in the region between the interacting rings, probably due to the superposition (coupling) of the diamagnetic ring currents of the interacting aromatic ring systems.     

Selective (15)N-labeling and analysis of (13)C-(15)N J couplings as an effective tool for studying the structure and azide-tetrazole equilibrium in a series of tetrazolo[1,5-b][1,2,4]triazines and tetrazolo[1,5-a]pyrimidines

Two general methods for the selective incorporation of an (15)N-label in the azole ring of tetrazolo[1,5-b][1,2,4]triazines and tetrazolo[1,5-a]pyrimidines were developed. The first approach included treatment of azinylhydrazides with (15)N-labeled nitrous acid, and the second approach was based on fusion of the azine ring to [2-(15)N]-5-aminotetrazole. The synthesized compounds were studied by (1)H, (13)C, and (15)N NMR spectroscopy in both DMSO and TFA solution, in which the azide-tetrazole equilibrium is shifted to tetrazole and azide forms, respectively. Incorporation of the (15)N-label led to the appearance of (13)C-(15)N J coupling constants (J(CN)), which can be measured easily using either 1D (13)C spectra with selective (15)N decoupling or with amplitude modulated 1D (13)C spin-echo experiments with selective inversion of the (15)N nuclei. The observed J(CN) patterns permit unambiguous determination of the type of fusion between the azole and azine rings in tetrazolo[1,5-b][1,2,4]triazine derivatives. Joint analysis of J(CN) patterns and (15)N chemical shifts was found to be the most efficient way to study the azido-tetrazole equilibrium.     

含嘧啶环的1,3,4-噁二唑Mannich碱的合成及生物活性

以芳香酸为原料, 通过酯化、 肼解及环化反应制得中间体5-芳基取代-1,3,4-噁二唑-2-硫酮(C1~C3), 然后中间体与甲醛和取代氨基嘧啶(D1~D5)发生Mannich反应得到一系列新型含有嘧啶环的1,3,4-噁二唑类衍生物(E1~E15). 所得目标化合物的结构经元素分析、 IR及 ¹H NMR确认. 初步的生物活性测定结果表明, 大部分目标化合物对植物病原菌有很好的抑制作用, 其中化合物E3和E8的抑菌效果优于对照药三唑酮.     

Design,synthesis and SAR study of novel sulfonylurea derivatives containing arylpyrimidine moieties as potential anti-phytopathogenic fungal agents

Three series of novel sulfonylureas (SUs) 9-11 containing aromatic-substituted pyrimidines were designed and synthesized. The 3D-QASR and molecular docking studies showed that SUs should be considered as potential antiphytopathogenic fungal agents.     

Design,synthesis and SAR study of novel sulfonylurea derivatives containing arylpyrimidine moieties as potential anti-phytopathogenic fungal agents

Acetohydroxyacid synthase(AHAS) was considered as a promising target for antifungal agents.Herein,three series of novel sulfonylureas(SUs) 9-11 containing aromatic-substituted pyrimidines were designed and synthesized according to pharmacophore-combination and bioisosterism strategy.The in vitro fungicidal activities against ten phytopathogenic fungi indicated that most of the title compounds exhibited broad-spectrum and excellent fungicidal activities.Based on the preliminary fungicidal activities,a CoMFA model was constructed and the 3 D-QSAR analysis indicated that either a bulky group around the 5-position of the pyrimidine ring or electropositive group around the 2-position of the benzene ring would be favour to fungicidal activities.In order to study interaction mechanism,10 k was automatically docked into yeast AHAS and it further indicated that bearing bulky groups-aryl at the pyrimidine ring was critical to enhance antifungal activities.It revealed that the antifungal activity of derivatives 9-11 probably results from the inhibition of fungal AHAS.Thus,the present results strongly showed that SUs should be considered as lead compounds or model molecules to develop novel antiphyt o pathogenic fungal agents.     

1-[2-(N-甲基-N-取代苄基)氨基-2-(4-叔丁基苯基)乙基]-1H-1,2,4-三唑类化合物的合成及抗真菌活性

根据氮唑类和苄胺类抗真菌药物的构效关系和作用机理,设计合成了23种1-[2-(N-甲基-N-取代苄基)氨基-2-(4-叔丁基苯基)乙基]-1H-1,2,4-三唑类化合物,其结构经元素分析、红外光谱及核磁共振谱分析证实.体外抑菌实验结果表明:目标化合物对常见的9种致病真菌均有一定活性,对浅表真菌活性优于深部真菌,其中化合物3,4,6,10,12,14和15对羊毛样小孢子菌具有较强的活性.     

Synthesis,Characterization, and Molecular Docking Study of Some Novel Imidazole Derivatives as Potential Antifungal Agents

The azole pharmacophore is still regarded as a viable lead structure for the synthesis of more effective antifungal agents. In this study, two novel series of imidazole derivatives containing dithiocarbamate (5a–5g) and (benz)azolethiol (6a–6n) side chains that are structurally related to the famous antifungal azole pharmacophore were synthesized, and the structures of them were characterized by spectral (IR, ¹H NMR, ¹³C NMR, and MS spectra) analyses. The synthesized compounds were screened in vitro antifungal activity against pathogenic strains fungi. Theoretical ADME (absorption, distribution, metabolism, and excretion) predictions were calculated for final compounds. A molecular docking study of the most active compound with target “lanosterol 14α‐demethylase” (CYP51) was performed to unravel the mode of antifungal action. Compound 5e , which features imidazole and 4‐methoxybenzyl piperazine scaffolds, showed the most promising antifungal activity with an MIC₅₀ value of 0.78 μg/mL against C. krusei. Effect of the compound 5e against ergosterol biosynthesis was observed by LC–MS–MS method, which is based on quantification of ergosterol level in C. krusei.     

1—[2—（N—甲基—N—取代苄基）氨基—2—（4—叔丁基苯基）乙？…

根据氮唑类和苄胺类抗真菌药物的构效关系和作用机理,设计合成了２３种１－「２－（Ｎ－甲基－Ｎ－取代苄基）氨基－２－（４－叔丁基苯基）乙基」－１Ｈ－１,２,４－三唑类化合物,其结构经元素分析、红外光谱及核磁共振谱分析 证实。体外抑菌实验结果表明：目标化合物对常见的９种致病真菌均有一定活性,对浅表真菌活性优于深部真菌,其中化合物３,４,６,１０,１２,１４和１５对羊毛样小孢菌具有较强的活性。