Synthesis, biological evaluation, and molecular modeling studies of rebeccamycin analogues modified in the carbohydrate moiety

A new series of indolocarbazole glycosides containing disaccharides were synthesized and their in vitro antiproliferative activity was evaluated against three human cancer cell lines (A2780, H460, and GLC4). Cytotoxicity appeared to be remarkably affected by the regio- and stereochemical features of the disaccharide moiety. In vivo antitumor activity of the compounds studied, two of which having IC(50)<100 nm, was determined using ovarian cancer cell line A2780 xenografted on nude mice. One compound showed an efficacy similar to that of the reference compound edotecarin, though with a lower long-lasting activity. The topoisomerase I inhibitory properties of some compounds were also examined. Molecular dynamics simulations of the ternary topoisomerase I-DNA-ligand complexes were performed to analyze the structural features of topoisomerase I poisoning with this class of indolocarbazoles. A plausible explanation of their biological behavior was provided. These theoretical results were compared with the recently published crystal structure of an indolocarbazole monosaccharide bound to the covalent human topoisomerase I-DNA complex.     

All Ag Nanoparticles Are Not the Same: Covalent Interactions between Ag Nanoparticles and Nitrile Groups Help Combat Drug- and Ag-Resistant Bacteria

Antimicrobial resistance has long been viewed as a lethal threat to global health. Despite the availability of a wide range of antibacterial medicines all around the world, organisms have evolved a resistance mechanism to these therapies. As a result, a scenario has emerged requiring the development of effective antibacterial drugs/agents. In this article, we exclusively highlight a significant finding reported by Zbořil and associates (Adv. Sci. 2021, 2003090). The authors construct a covalently bounded silver-cyanographene (GCN/Ag) with the antibacterial activity of 30 fold higher than that of free Ag ions or typical Ag nanoparticles (AgNPs). Ascribed to the strong covalent bond between nitrile and Ag, an immense cytocompatibility is shown by the GCN/Ag towards healthy human cells with a minute leaching of Ag ions. Firm interactions between the microbial membrane and the GCN/Ag are confirmed by molecular dynamics simulations, which rule out the dependence of antibacterial activity upon the Ag ions alone. Thus, this study furnishes ample scope to unfold next-generation hybrid antimicrobial drugs to confront infections arising from drug and Ag-resistant bacterial strains.     

In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB

Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.     

Synthesis and Evaluation of N‐Phenylpyrrolamides as DNA Gyrase B Inhibitors

ATP‐competitive inhibitors of DNA gyrase and topoisomerase IV are among the most interesting classes of antibacterial drugs that are unrepresented in the antibacterial pipeline. We developed 32 new N‐phenylpyrrolamides and evaluated them against DNA gyrase and topoisomerase IV from E. coli and Staphylococcus aureus. Antibacterial activities were studied against Gram‐positive and Gram‐negative bacterial strains. The most potent compound displayed an IC₅₀ of 47 nm against E. coli DNA gyrase, and a minimum inhibitory concentration (MIC) of 12.5 μm against the Gram‐positive Enterococcus faecalis. Some compounds displayed good antibacterial activities against an efflux‐pump‐deficient E. coli strain (MIC=6.25 μm ) and against wild‐type E. coli in the presence of efflux pump inhibitor PAβN (MIC=3.13 μm ). Here we describe new findings regarding the structure–activity relationships of N‐phenylpyrrolamide DNA gyrase B inhibitors and investigate the factors that are important for the antibacterial activity of this class of compounds.     

镧-磺基水杨酸-8-羟基喹啉三元配合物合成、表征及其抑菌性

合成了一种镧-磺基水杨酸-8-羟基喹啉三元配合物,采用摩尔电导率、红外光谱、紫外光谱、荧光光谱和热重分析手段进行表征,并研究了该三元配合物对常见的大肠杆菌、金黄色葡萄球菌和真菌黑曲霉的抑菌活性。结果表明:该三元配合物对大肠杆菌、金黄色葡萄球菌、黑曲霉菌都具有良好的抑菌效果。织物经该配合物的整理后,也具有了较强的抗菌作用。     

Discovery of Mono‐ and Disubstituted 1H‐Pyrazolo[3,4]pyrimidines and 9H‐Purines as Catalytic Inhibitors of Human DNA Topoisomerase IIα

Human DNA topoisomerase IIα (htIIα) is a validated target for the development of anticancer agents. Based on structural data regarding the binding mode of AMP‐PNP (5′‐adenylyl‐β,γ‐imidodiphosphate) to htIIα, we designed a two‐stage virtual screening campaign that combines structure‐based pharmacophores and molecular docking. In the first stage, we identified several monosubstituted 9H‐purine compounds and a novel class of 1H‐pyrazolo[3,4]pyrimidines as inhibitors of htIIα. In the second stage, disubstituted analogues with improved cellular activities were discovered. Compounds from both classes were shown to inhibit htIIα‐mediated DNA decatenation, and surface plasmon resonance (SPR) experiments confirmed binding of these two compounds on the htIIα ATPase domain. Proposed complexes and interaction patterns between both compounds and htIIα were further analyzed in molecular dynamics simulations. Two compounds identified in the second stage showed promising anticancer activities in hepatocellular carcinoma (HepG2) and breast cancer (MCF‐7) cell lines. The discovered compounds are suitable starting points for further hit‐to‐lead development in anticancer drug discovery.     

Towards Catalytic Antibiotics: Redesign of Aminoglycosides To Catalytically Disable Bacterial Ribosomes

The emergence of multidrug-resistant pathogens that are resistant to the majority of currently available antibiotics is a significant clinical problem. The development of new antibacterial agents and novel approaches is therefore extremely important. We set out to explore the potential of catalytic antibiotics as a new paradigm in antibiotics research. Herein, we describe our pilot study on the design, synthesis, and biological testing of a series of new derivatives of the natural aminoglycoside antibiotic neomycin B for their potential action as catalytic antibiotics. The new derivatives showed significant antibacterial activity against wild-type bacteria and were especially potent against resistant and pathogenic strains including Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus. Selected compounds displayed RNase activity even though the activity was not as high and specific as we would have expected. On the basis of the observed chemical and biochemical data, along with the comparative molecular dynamics simulations of the prokaryotic rRNA decoding site, we postulate that the rational design of catalytic antibiotics should involve not only their structure but also a comprehensive analysis of the rRNA A-site dynamics.     

Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study

We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.     

Natural Compounds as Therapeutic Agents: The Case of Human Topoisomerase IB

Natural products are widely used as source for drugs development. An interesting example is represented by natural drugs developed against human topoisomerase IB, a ubiquitous enzyme involved in many cellular processes where several topological problems occur due the formation of supercoiled DNA. Human topoisomerase IB, involved in the solution of such problems relaxing the DNA cleaving and religating a single DNA strand, represents an important target in anticancer therapy. Several natural compounds inhibiting or poisoning this enzyme are under investigation as possible new drugs. This review summarizes the natural products that target human topoisomerase IB that may be used as the lead compounds to develop new anticancer drugs. Moreover, the natural compounds and their derivatives that are in clinical trial are also commented on.     

Ligand- and Structure-Based Approaches of Escherichia coli FabI Inhibition by Triclosan Derivatives: From Chemical Similarity to Protein Dynamics Influence

Enoyl-acyl carrier protein reductase (FabI) is the limiting step to complete the elongation cycle in type II fatty acid synthase (FAS) systems and is a relevant target for antibacterial drugs. E. coli FabI has been employed as a model to develop new inhibitors against FAS, especially triclosan and diphenyl ether derivatives. Chemical similarity models (CSM) were used to understand which features were relevant for FabI inhibition. Exhaustive screening of different CSM parameter combinations featured chemical groups, such as the hydroxy group, as relevant to distinguish between active/decoy compounds. Those chemical features can interact with the catalytic Tyr156. Further molecular dynamics simulation of FabI revealed the ionization state as a relevant for ligand stability. Also, our models point the balance between potency and the occupancy of the hydrophobic pocket. This work discusses the strengths and weak points of each technique, highlighting the importance of complementarity among approaches to elucidate EcFabI inhibitor's binding mode and offers insights for future drug discovery.     

Evaluation of Interactions of Selected Olivacine Derivatives with DNA and Topoisomerase II

Olivacine and ellipticine are model anticancer drugs acting as topoisomerase II inhibitors. Here, we present investigations performed on four olivacine derivatives in light of their antitumor activity. The aim of this study was to identify the best antitumor compound among the four tested olivacine derivatives. The study was performed using CCRF/CEM and MCF-7 cell lines. Comet assay, polarography, inhibition of topoisomerase II activity, histone acetylation, and molecular docking studies were performed. Each tested compound displayed interaction with DNA and topoisomerase II, but did not cause histone acetylation. Compound 2 (9-methoxy-5,6-dimethyl-1-({[1-hydroxy-2-(hydroxymethyl)butan-2-yl]amino}methyl)-6H-pyrido[4,3-b]carbazole) was found to be the best candidate as an anticancer drug because it had the highest affinity for topoisomerase II and caused the least genotoxic damage in cells.     

Graphene defect polarity dynamics

Topological defects in graphene, such as dislocations and grain boundaries, can produce out-of-plane buckling defects, which can bulge either up or down and, therefore, introduce two different polarities (namely, “up” and “down”). These defects have strong effects on graphene properties. We perform very long-time-scale, temperature accelerated molecular dynamics simulations of these topological defects and observe that they are able to flip polarity through concerted motion of multiple carbon atoms without breaking any covalent bonds; the simulations reveal the polarity flipping transition pathway. Polarity flipping has activation barriers ranging from 0.80 to 1.55 eV – several times lower than those of breaking covalent bonds (e.g., Stone–Wales bond rotations) and implies that flipping can occur over seconds or years, depending on the defect structure. The simulations further show that when multiple defects are present, polarity flipping can propagate through the defects system leading to interesting and complex higher-order polarity changes.     

A novel homogenous assay for topoisomerase II action and inhibition

Topoisomerase II is the only enzyme able to cleave and religate double-stranded DNA; this makes it essential for many vital functions during normal cell growth. Increased expression of topoisomerase II is a common occurrence in neoplasia, and different topoisomerase II inhibitors have indeed been proven to be powerful anticancer drugs. For this reason, the topoisomerase II catalytic cycle has attracted strong interest, but only a few techniques contributing to studies in this field have emerged. All of the currently used conventional methods to elucidate the action and inhibition of topoisomerase II require separation steps and are therefore unsatisfactory in terms of sensitivity, speed, and throughput. Here, for the first time, we present an assay that works in homogenous solution. The assay is based on dual-color fluorescence cross-correlation spectroscopy (DC-FCCS) and allows monitoring of topoisomerase II action and, especially, detection and discrimination of different topoisomerase II inhibitor classes. The effectiveness of our new assay was confirmed by measuring the effects of a catalytic inhibitor (novobiocin) and a topoisomerase poison (m-AMSA) with bacteriophage T4 topoisomerase as a model system, thus showing the strategy to be easy, fast, and extremely sensitive. Further development of the DC-FCCS-based assay and subsequent application in high-throughput drug screening of new anticancer drugs is proposed and discussed.     

Discovery of Benzimidazole–Quinolone Hybrids as New Cleaving Agents toward Drug‐Resistant Pseudomonas aeruginosa DNA

A series of benzimidazole–quinolone hybrids as new potential antimicrobial agents were designed and synthesized. Bioactive assays indicated that some of the prepared compounds exhibited potent antibacterial and antifungal activities. Notably, 2‐fluorobenzyl derivative 5 b (ethyl 7‐chloro‐6‐fluoro‐1‐[[1‐[(2‐fluorophenyl)methyl]benzimidazol‐2‐yl]methyl]‐4‐oxo‐quinoline‐3‐carboxylate) showed remarkable antimicrobial activity against resistant Pseudomonas aeruginosa and Candida tropicalis isolated from infected patients. Active molecule 5 b could not only rapidly kill the tested strains, but also exhibit low toxicity toward Hep‐2 cells. It was more difficult to trigger the development of bacterial resistance of P. aeruginosa against 5 b than that against norfloxacin. Molecular docking demonstrated that 5 b could effectively bind with topoisomerase IV–DNA complexes, and quantum chemical studies theoretically elucidated the good antimicrobial activity of compound 5 b . Preliminary experimental reaction mechanism exploration suggested that derivative 5 b could not intercalate into DNA isolated from drug‐resistant P. aeruginosa, but was able to cleave DNA effectively, which might further block DNA replication to exert powerful bioactivities. In addition, compound 5 b is a promising antibacterial agent with membrane disruption abilities.     

双水杨醛缩邻苯二胺-Ce（Ⅲ）配合物的生物活性研究

合成了一种salen稀土金属双水杨醛缩邻苯二胺ce（Ⅲ）配合物,其结构用紫外光谱、红外光谱、核磁共振及电喷雾质谱进行表征。用纸片法测定配合物对大肠杆菌和枯草杆菌的抗菌活性,表明配合物对大肠杆菌有较好的抗菌活性。用紫外光谱和荧光光谱研究配合物与小牛胸腺DNA（ctDNA）的相互作用,初步表明配合物与DNA之间很可能是嵌入作用、静电作用的方式并存,并且配合物还可作为DNA的荧光染料。     

Novel dications with unfused aromatic systems: trithiophene and trifuran derivatives of furimidazoline

We report the synthesis, interaction with DNA, topoisomerase II inhibition, and cytotoxicity of two novel unfused aromatic dications derived from the antimicrobial agent furimidazoline. The central diphenylfuran core of furimidazoline has been replaced with a trithiophene (DB358) or a trifuran (DB669) unit and the terminal imidazoline groups were preserved. The strength and mode of binding of the drugs to nucleic acids were investigated by complementary spectroscopic techniques including spectrophotometric, surface plasmon resonance, circular and linear dichroism measurements. The trifuran derivative forms intercalation complexes with double-stranded DNA, whereas the mode of binding of the trithiophene derivative varies depending on the drug/DNA ratio, as independently confirmed by NMR spectroscopic studies performed with (A-T)7 and (G-C)7 oligomers. Two-dimensional NMR data provided a molecular model for the binding of DB358 within the minor groove of the AATT sequence of the decanucleotide d(GCGAATTCGC)(2). DNase I footprinting experiments confirmed the sequence-dependent binding of DB358 to DNA. The trithiophene derivative interacts preferentially with AT-rich sequences at low concentrations, but can accomodate GC sites at higher concentrations. DNA relaxation assays revealed that DB358 stimulated DNA cleavage by topoisomerase II, in contrast to DB669. The substitution of N-alkylamidines for the imidazoline terminal groups abolished the capacity of the drug to poison topoisomerase II. At the cellular level, flow cytometry analysis indicated that DB358, which is about six times more cytotoxic than the trifuran analogue, induced a significant accumulation of HL-60 human leukemia cells in the G2/M phase. The incorporation of thiophene heterocycles appears as a convenient procedure to limit the strict AT selectivity of dications containing an extended unfused aromatic system and to design cytotoxic DNA intercalating agents acting as poisons for human topoisomerase II.     

Selective Recognition of Substituted Chrysene-Diol Epoxide-2-DNA Adducts by Antiserum prepared Against DNA Adducts of Benzo[c]Phenanthrene-Diol Epoxide-2

Polyclonal antiserum prepared against DNA that was modified with racemic benzo[c]phenanthrene-3,4-diol-1,2-epoxide-2 (B[c]PhDE-2; benzylic hydroxyl and epoxide oxygen trans) was characterized for specificity of antigen recognition. Previous studies have demonstrated that the antisera stereoselectively recognized B[c]PhDE-2-DNA and failed to recognize DNA modified with racemic benzo[c]phenanthrene-3,4-diol-1,2-epoxide-1 (B[c]PhDE-1-DNA, benzylic hydroxyl and epoxide oxygen cis), benzo[a]pyrene-7,8-diol-9, 10-epoxide-2-DNA (B[a]PDE-2-DNA) and 7,12-dimethylbenz[a]anthracene-3,4-diol-1,2-epoxide-1-DNA (DMBADE-1-DNA). DNA samples modified by diol-epoxide-2 diastereomers of several hydrocarbons were tested in competitive ELISA assays utilizing B[c]PhDE-2-DNA (270 fmol adducts per well). DNA modified with racemic diol-epoxide-2 of various substituted chrysenes (including chrysene, benzo[g]chrysene (B[g]C), 6-methylchrysene (6-MeC), and 5-methychrysene (5-MeC), gave 50% inhibition of antisera binding at significantly higher concentrations (5 to 7-fold) than the parent B[c]PhDE-2-DNA or 5,6-diMeCDE-DNA. DNA modified with 5,7-dimethylchryseneDE-2 (5,7-diMeCDE-2) and dibenzo[a,l]pyreneDE-2 (DB[a,l] PDE-2) required 20 and > 100-fold greater levels of adducts to give 50% inhibition. Results with B[c]Pb, 5,6-diMeC, chrysene, 6-MeC and 5-MeC diol epoxide-2-DNA     

The role of hydrogen-bond in solubilizing drugs by ionic liquids: A molecular dynamics and density functional theory study

The solvation mechanisms of aspirin and etomidate in four combinations of [Emim]⁺ and [BuGun]⁺ paired with [OAc]⁻ and [NTf₂]⁻ were systematically studied by molecular dynamics simulations and DFT calculations. It was shown that the favorable solvation of aspirin and etomidate correlated well with hydrogen-bond (H-bond) basicity of anions and the H-bond acidity of cations, respectively. Wherein, the H-bond between aspirin and [OAc]⁻ anion with high H-bond basicity possessed covalent feature, so ILs containing [OAc]⁻ anion has the best effective in solubilizing aspirin. However, H-bond interactions between etomidate and cations exhibited an electrostatic dominant, and moderate cation–anion interaction could weaken it. Accordingly, for etomidate, the best ILs solvent comprised a weakly interacting anion and a cation with strong H-bond acidity, that is, [BuGun][NTf₂]. This solvation difference was because aspirin with carboxyl group displayed strongly H-bond donating characteristic, whereas etomidate with no active hydrogen protons mainly formed H-bond with cations. Additionally, we found that π–π stacking interactions were of secondary importance for the solubilization of etomidate, but little for aspirin. These simulations will be helpful for experimental design new ILs to solubilize some drugs with aspirin-like or etomidate-like structures.     

蛋白质体系分子动力学模拟的前沿进展-从介科学角度重新审视

蛋白质是生命的物质基础,是生命活动的主要承担者,对蛋白质时空多尺度结构及其控制机制的深入理解是探索生命起源、病理认知及新药开发的基础. 受实验表征手段及时空分辨率的限制,计算机模拟已成为研究蛋白质体系结构及功能的重要手段之一. 由于蛋白质体系模拟所涉及的时间和空间跨度均相当大,因此,准确且快速地描述其时空多尺度结构,从而分析体系的控制机制及相关生理过程,成为分子动力学模拟面临的巨大挑战. 本工作对近半个世纪以来的分子模拟方法,特别是分子动力学方法和相关的增强采样技术在蛋白质体系研究中的应用进行了总结,综述了近年来分子动力学的理论模型和算法的发展,并介绍了这些方法在结构化蛋白质的天然结构与构象变化、固有无序蛋白质的动态结构及其结合底物的动力学过程及分子机理、分子伴侣及病毒等蛋白质复合物体系中的研究成果;汇总了高性能计算的飞速发展所带动的分子动力学模拟软件的变革,拓展了蛋白质模拟的时空尺度,重点阐述了大规模高性能分子动力学模拟在蛋白质研究中的应用;最后,基于介科学理论的飞速发展及其在多种复杂体系的成功运用,对未来蛋白质体系的模拟方法和理论研究的趋势进行了思考和展望.     

稀土三元配合物的合成、表征及其生物活性研究

以氯化镧、席夫碱、邻菲啰啉为原料,制备了新型稀土镧三元配合物,通过元素分析、紫外光谱、红外光谱、透射电子显微镜等手段对其进行了表征,确定了三元配合物的化学组成为La(L)phen(NO3)3C2H5OH.CH3OH。抗菌实验结果表明,配合物对大肠杆菌和金黄色葡萄球菌的抑菌圈直径分别为26 mm和20 mm,最小抑菌浓度分别为60 mg/L和130 mg/L,具有较强的抑制作用,且对大肠杆菌的抑制效果较强。