The Supramolecular Self-Assembly of Aminoglycoside Antibiotics and their Applications

Aminoglycosides, a class of antibiotics that includes gentamicin, kanamycin, neomycin, streptomycin, tobramycin and apramycin, are derived from various streptomyces species. Despite the significant increase in the antibacterial resistant pathogens, aminoglycosides remain an important class of antimicrobial drugs due to their unique chemical structure which offers a broad spectrum of activity. The modification of antibiotics and their subsequent use in supramolecular chemistry is rarely reported. Given the importance of aminoglycosides, here we give a brief overview on the modification of 4,5- and 4,6-disubstituted deoxystreptamine classes of aminoglycosides through supramolecular chemistry and their potential for real world applications. We also make the case that the work in this area is gaining momentum, and there are significant opportunities to meet the challenges of modern antibiotics through the modification of aminoglycosides by harnessing the advantages of supramolecular chemistry.     

Design and Synthesis of 2,2′‐Diindolylmethanes to Selectively Target Certain G‐Quadruplex DNA Structures

G‐quadruplex (G4) structures carry vital biological functions, and compounds that selectively target certain G4 structures have both therapeutic potential and value as research tools. Along this line, 2,2′‐diindolylmethanes have been designed and synthesized in this work based on the condensation of 3,6‐ or 3,7‐disubstituted indoles with aldehydes. The developed class of compounds efficiently stabilizes G4 structures without inducing conformational changes in such structures. Furthermore, the 2,2′‐diindolylmethanes target certain G4 structures more efficiently than others and this G4 selectivity can be altered by chemical modifications of the compounds.     

分子动力学模拟研究A1408G突变对核糖体16S rRNA片段的影响

利用分子动力学模拟方法, 研究了原核生物核糖体小亚基中的16S rRNA片段与氨基糖苷类抗生素巴龙霉素复合物结构的柔性. 结果表明, 16S rRNA片段中的1408位点的腺嘌呤(A)突变为鸟嘌呤(G), 改变了与tRNA中反密码子环识别相关的2个腺嘌呤A1492和A1493的空间构象, 阻碍了氨基糖苷类抗生素与核糖体的结合, 从而影响原核生物蛋白转录过程. 模拟结果与实验测定的晶体结构相吻合, 可为基于核糖体16S rRNA的药物分子设计提供较可靠的结构信息.     

依文思蓝-氨基糖苷类抗生素的显色反应及其分析应用

在pH 2 .0～ 7.0的条件下 ,依文思蓝 (EB)与硫酸新霉素 (NEO)、硫酸卡那霉素 (KANA)、硫酸庆大霉素(GEN)和硫酸妥布霉素 (TOB)等氨基糖苷类抗生素反应生成蓝色离子缔合物 ,最大显色波长位于 672～ 676nm ;不同体系的线性范围从 0～ 9.0至 0～ 1 2 .0mg L ;摩尔吸光系数 (ε)在 1 .75× 1 0 4 ～ 3 .3 0× 1 0 4 L·mol- 1 ·cm- 1之间 ;最大褪色波长位于 61 6～ 62 0nm的区间。用褪色光度法测定时 ,线性范围从 0～ 6.0mg L至 0～ 1 4.0mg L;摩尔吸光系数 (ε)从 1 .2 2× 1 0 4 至 4.63× 1 0 4 L·mol- 1 ·cm- 1 。当用双波长叠加法时 ,ε值在 (2 .97～ 7.93 )× 1 0 4 L·mol- 1 ·cm- 1 之间。探讨了适宜的反应条件及主要的分析化学性质。该方法用于市售药物及尿液中氨基糖苷类抗生素含量的测定 ,结果满意     

镧-依文思蓝-氨基糖苷类抗生素的显色反应及其分析应用

分光光度法;镧-依文思蓝-氨基糖苷类抗生素的显色反应及其分析应用     

滂胺天蓝-氨基糖苷类抗生素的显色反应及其分析应用

在 pH2.0～7.0的条件下 ,滂胺天蓝(PSB)与硫酸卡那霉素(KANA)、硫酸庆大霉素(GEN)和硫酸新霉素(NEO)等氨基糖苷类抗生素反应生成蓝色离子缔合物 ,最大显色波长位于686～690nm ,线性范围分别为0～14.0、0～12.5、0～14.0mg/L ,摩尔吸光系数(ε)分别为1.53×104、1.12×104、1.47×104L/(mol·cm) ;最大褪色波长位于620～622nm ,线性范围分别为0～14.0、0～12.0、0～14.0mg/L ,摩尔吸光系数(ε)分别为1.41×104、1.43×104、2.42×104L/(mol·cm) ;当用双波长叠加法测定时 ,ε值分别为2.94×104、2.55×104、3.89×104L/(mol·cm) ;探讨了适宜的反应条件 ;该法用于市售药物中氨基糖苷类抗生素含量的测定 ,结果令人满意     

Rapid Potentiometric Determination of Aminoglycoside Antibiotics in Drug Dosage Forms and Biological Fluids Using Ion-Selective Electrodes

Ion-selective electrodes with plasticized membranes based on ion pairs of gentamycin and kanamycin with tetraphenylborate and Acid Chrome Black Special were proposed. The physicochemical properties of the ionophores and the properties of membranes on based on these compounds were studied. Procedures were developed for determining aminoglycoside antibiotics in pharmaceutical dosage forms, serum, and saliva from patients with infectious pathologies.__________Translated from Zhurnal Analiticheskoi Khimii, Vol. 60, No. 6, 2005, pp. 592–597.Original Russian Text Copyright © 2005 by E. Kulapina, Baraguzina, O. Kulapina.Presented at the VI All-Russia Conference (with international participation) on Electrochemical Methods of Analysis (EMA-2004, Ufa, May 23–27, 2004).     

Aminoglycoside complexation with a DNA.RNA hybrid duplex: the thermodynamics of recognition and inhibition of RNA processing enzymes

Spectroscopic and calorimetric techniques were employed to characterize and contrast the binding of the aminoglycoside paromomycin to three octamer nucleic acid duplexes of identical sequence but different strand composition (a DNA.RNA hybrid duplex and the corresponding DNA.DNA and RNA.RNA duplexes). In addition, the impact of paromomycin binding on both RNase H- and RNase A-mediated cleavage of the RNA strand in the DNA.RNA duplex was also determined. Our results reveal the following significant features: (i) Paromomycin binding enhances the thermal stabilities of the RNA.RNA and DNA.RNA duplexes to similar extents, with this thermal enhancement being substantially greater in magnitude than that of the DNA.DNA duplex. (ii) Paromomycin binding to the DNA.RNA hybrid duplex induces CD changes consistent with a shift from an A-like to a more canonical A-conformation. (iii) Paromomycin binding to all three octamer duplexes is linked to the uptake of a similar number of protons, with the magnitude of this number being dependent on pH. (iv) The affinity of paromomycin for the three host duplexes follows the hierarchy, RNA.RNA > DNA.RNA > DNA.DNA. (v) The observed affinity of paromomycin for the RNA.RNA and DNA.RNA duplexes decreases with increasing pH. (vi) The binding of paromomycin to the DNA.RNA hybrid duplex inhibits both RNase H- and RNase A-mediated cleavage of the RNA strand. We discuss the implications of our combined results with regard to the specific targeting of DNA.RNA hybrid duplex domains and potential antiretroviral applications.     

Synthesis and Biological Evaluation of Iodinated Fidaxomicin Antibiotics

Fidaxomicin ( 1 , tiacumicin B, lipiarmycin A3) is a marketed antibiotic that is used in the treatment of Clostridium difficile infections. Based on the analysis of a cryo-EM structure of fidaxomicin binding to its target enzyme (RNA-polymerase), a cation-π interaction of the aromatic moiety with an arginine residue was identified. Therefore, the variation of the substituents and concurrently changing the electronic properties of the aryl moiety represents an interesting strategy in the search for new fidaxomicin analogs. Herein, we report the first semisynthetic access to new fidaxomicin analogs with varying halogen substituents through a Pd-catalyzed hydrodechlorination reaction. Subsequent iodination gave access to the first iodo-fidaxomicin derivatives, which matched or improved antibacterial properties compared to fidaxomicin against Mycobacterium tuberculosis and Staphylococcus aureus ATCC 29213.     

高效液相色谱-电喷雾离子阱质谱法分析6种氨基糖甙类抗生素

采用高效液相色谱-电喷雾离子阱质谱(HPLC-MSn)联用,分离和鉴定6种氨基糖甙类抗生素及其中的杂质,并探讨这6种结构相似的氨基糖甙类抗生素的质谱裂解规律。采用Agilent SB-C18(250 mm×4.6mm,5μm)色谱柱,流动相为0.05mol/L三氟乙酸溶液-甲醇(90∶10)和0.05 mol/L五氟丙酸溶液-甲醇(65∶35);在正离子检测方式下,用电喷雾离子阱质谱法对阿司米星、异帕米星、大观霉素、威替米星、奈替米星、西索米星及其杂质进行多级质谱分析。异帕米星、威替米星、奈替米星、西索米星及其杂质在二级质谱分析时,均可发生B环(脱氧链霉胺)与C环(氨基葡萄糖)之间的糖苷键断裂,生成脱去C环的碎片离子,并进一步发生A环(氨基葡萄糖)与B环之间的糖苷键断裂,生成A环或B环的碎片离子。鉴定了6种氨基糖甙类抗生素中7个杂质的结构。     

16S,20S-环氧孕甾-3S-醇乙酸酯的合成及其区域选择性环氧开环取代反应

提供了一种将剑麻皂甙元降解产物孕甾三醇转化为16S,20S-环氧孕甾-3S-醇乙酸酯（4b）的合成方法,并系统地考察了其在不同条件下的环氧开环反应.研究发现16S,20S-环氧孕甾-3S-醇乙酸酯可选择性地被转化为20R-溴代孕甾-3S,16S-二醇二乙酸酯、20R-溴代孕甾-3S,16S-二醇-3-乙酸酯、20R-氯...     

Design,Synthesis, and Antibacterial Evaluation of Novel Ocotillol Derivatives and Their Synergistic Effects with Conventional Antibiotics

The improper use of antibiotics has led to the development of bacterial resistance, resulting in fewer antibiotics for many bacterial infections. Especially, the drug resistance of hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) is distinctly serious. This research designed and synthesized two series of 3-substituted ocotillol derivatives in order to improve their anti-HA-MRSA potency and synergistic antibacterial activity. Among the synthesized compounds, 20–31 showed minimum inhibitory concentration (MIC) values of 1–64 µg/mL in vitro against HA-MRSA 18–19, 18–20, and S. aureus ATCC29213. Compound 21 showed the best antibacterial activity, with an MIC of 1 μg/mL and had synergistic inhibitory effects. The fractional inhibitory concentration index (FICI) value was 0.375, when combined with chloramphenicol (CHL) or kanamycin (KAN). The structure–activity relationships (SARs) of ocotillol-type derivatives were also summarized. Compound 21 has the potential to be developed as a novel antibacterial agent or potentiator against HA-MRSA.     

Structure and Function of the Ribosomal Frameshifting Pseudoknot RNA from Beet Western Yellow Virus

Many viruses reprogram ribosomes to produce two different proteins from two different reading frames. So‐called ?1 frameshifting often involves pairwise alignment of two adjacent tRNAs at a ‘slippery' sequence in the ribosomal A and P sites such that an overlapping codon is shifted upstream by one base relative to the zero frame. In the majority of cases, an RNA pseudoknot located downstream stimulates this type of frameshift. Crystal structures of the frameshifting RNA pseudoknot from Beet Western Yellow Virus (BWYV) have provided a detailed picture of the tertiary interactions stabilizing this folding motif, including a minor‐groove triplex and quadruple‐base interactions. The structure determined at atomic resolution revealed the locations of several magnesium ions and provided insights into the role of structured water stabilizing the RNA. Systematic in vitro and in vivo mutational analyses based on the structural results revealed specific tertiary interactions and regions in the pseudoknot that drastically change frameshifting efficiency. Here, we summarize recent advances in our understanding of pseudoknot‐mediated ribosomal frameshifting on the basis of the insights gained from structural and functional studies of the RNA pseudoknot from BWYV.     

Aminoglycoside microarrays to explore interactions of antibiotics with RNAs and proteins

RNA is an important target for drug discovery efforts. Several clinically used aminoglycoside antibiotics bind to bacterial rRNA and inhibit protein synthesis. Aminoglycosides, however, are losing efficacy due to their inherent toxicity and the increase in antibiotic resistance. Targeting of other RNAs is also becoming more attractive thanks to the discovery of new potential RNA drug targets through genome sequencing and biochemical efforts. Identification of new compounds that target RNA is therefore urgent, and we report here on the development of rapid screening methods to probe binding of low molecular weight ligands to proteins and RNAs. A series of aminoglycosides has been immobilized onto glass microscope slides, and binding to proteins and RNAs has been detected by fluorescence. Construction and analysis of the arrays is completed by standard DNA genechip technology. Binding of immobilized aminoglycosides to proteins that are models for study of aminoglycoside toxicity (DNA polymerase and phospholipase C), small RNA oligonucleotide mimics of aminoglycoside binding sites in the ribosome (rRNA A-site mimics), and a large (approximately 400 nucleotide) group I ribozyme RNA is detected. The ability to screen large RNAs alleviates many complications associated with binding experiments that use isolated truncated regions from larger RNAs. These studies lay the foundation for rapid identification of small organic ligands from combinatorial libraries that exhibit strong and selective RNA binding while displaying decreased affinity to toxicity-causing proteins.     

Synthesis of Selectively Protected Chitobiose and Chitotriose Derivatives from one Precursor. Versatile Building Blocks for Oligosaccharide Synthesis

Abstract

The inner core region of cell surface N-glycoproteins consists of a chitobiose substructure², containing β-(1,4)-linked disaccharides of glucosamine. Such carbohydrate structures are also found as repeating units of the bacterial cell wall peptidoglycan³ and in novel tetra- and pentasaccharide plant hormones, which are nodulation factors on legume roots.⁴ Since the first synthesis of a chitobiose derivative in 1966 by Paulsen,⁵ approaches to these compounds have relied mainly on the oxazoline method.⁶ The coupling reactions of aminosugar chlorides,⁷ bromides,⁸ acetates⁹ and trichloroacetimidates¹⁰ to suitable glycosyl acceptors have also been described. Most of these syntheses¹¹ require two completely different coupling partners; only in very few examples could the glycosyl donor and acceptor be obtained from the same starting material.¹² During our investigations into the stereocontrolled synthesis of glucosamine oligosaccharides, we required an economical synthetic route to protected derivatives of chitotriose. For the purpose of easy oligomerization, the anomeric protecting group of every building block had to be exchangeable selectively with the activating group for the next glycosylation. In this paper, we report an efficient approach to chitobiose and chitotriose from a single precursor. Furthermore, the hydroxyl groups at C-1, C-3, C-4, C-6 of these oligosaccharides are differentially protected. This protecting group scenario allows a specific access to any of these functionalities by regioselective deblocking. The N-phthalimide group was chosen out of several possible amino protecting groups to ensure β-selectivity and simultaneous activation in the coupling.¹³