New topoisomerases inhibitors: Synthesis of rutaecarpine derivatives and their inhibitory activity against topoisomerases

A series of rutaecarpine derivatives were prepared by employing previously reported methods and their inhibitory activities against topoisomerase I and II were evaluated. Among them, strongly cytotoxic 10-bromorutaecarpine and 3-chlororutaecarpine showed strong inhibitory activities against topo I and II.     

Acetyl-boswellic acids are novel catalytic inhibitors of human topoisomerases I and IIalpha

Acetyl-boswellic acids (acetyl-BA) are pentacyclic triterpenes derived from the gum resin of frankincense. We have previously shown that these compounds are effective cytotoxic agents, acting through a mechanism that appears to involve the inhibition of topoisomerase activity. We have now investigated the mechanism of action of acetyl-BA and show that these compounds are more potent inhibitors of human topoisomerases I and IIalpha than camptothecin, and amsacrine or etoposide, respectively. Our data demonstrate that acetyl-BA and, to a lesser extent, some other pentacyclic triterpenes, such as betulinic acid, ursolic acid, and oleanolic acid, inhibit topoisomerases I and IIalpha through a mechanism that does not involve stabilization of the cleavable complex or the intercalation of DNA. Surface plasmon resonance analysis revealed that topoisomerases I and IIalpha bind directly to an immobilized derivative of acetyl-BA. This acetyl-BA derivative interacts with human topoisomerases through high-affinity binding sites yielding K(D) values of 70.6 nM for topoisomerase I and 7.6 nM for topoisomerase IIalpha. Based on our data, we propose that acetyl-BA inhibit topoisomerases I and IIalpha through competition with DNA for binding to the enzyme. Thus, acetyl-BA are a unique class of dual catalytic inhibitors of human topoisomerases I and IIalpha.     

Protease inhibitors: synthesis of a series of bacterial collagenase inhibitors of the sulfonyl amino acyl hydroxamate type

A series of sulfonyl amino acyl hydroxamates incorporating alkyl/arylsulfonyl-N-2-nitrobenzyl-L-alanine was prepared. Related compounds were obtained by reaction of N-2-nitrobenzyl-L-Ala with aryl isocyanates, arylsulfonyl isocyanates, or benzoyl isothiocyanate, followed by the conversion of the COOH into the CONHOH moiety. The new compounds were assayed as inhibitors of the Clostridium histolyticum collagenase (ChC), a bacterial protease involved in the degradation of extracellular matrix. Many of the obtained hydroxamates proved to be effective bacterial collagenase inhibitors, the main contributor to activity being the substitution pattern at the sulfonamido moiety. The best ChC inhibitors were those containing pentafluorophenylsulfonyl and 3- and 4-protected-aminophenylsulfonyl P(1)(') groups among others, with affinities in the low nanomolar range. This study also proves that the 2-nitrobenzyl- moiety, similarly to the 4-nitrobenyl one previously investigated (Scozzafava, A.; Supuran, C. T. J. Med. Chem. 2000, 43, 1858-1865) is an efficient P(2)(') anchoring moiety for obtaining potent bacterial collagenase inhibitors.     

Substituted 2-imino-5-arylidenethiazolidin-4-one inhibitors of bacterial type III secretion

Diverse species of pathogenic Gram-negative bacteria use secretion systems to export a variety of protein toxins and virulence factors that help establish and maintain infection. Disruption of such secretion systems is a potentially effective therapeutic strategy. We developed a high-throughput screen and identified a tris-aryl substituted 2-imino-5-arylidenethiazolidin-4-one, compound 1, as an inhibitor of the type III secretion system. Expansion of this chemotype enabled us to define the essential pharmacophore for type III secretion inhibition by this structural class. A synthetic diversity set helped us identify N-3 as the most permissive locus and led to the design of a panel of novel N-3-dipeptide-modified congeners with improved activity and physiochemical properties. We now report on the synthesis of these compounds, including a novel solid phase approach to the rapid generation of the dipeptide-thiazolidinone hybrids, and their in vitro characterization as inhibitors of type III secretion in Salmonella enterica serovar Typhimurium.     

Inhibitors of bacterial topoisomerases: mechanisms of action and resistance and clinical aspects

The quinolone class of inhibitors of bacterial type II topoisomerases has gained major clinical importance during the last years due to improvements in both pharmacokinetic and pharmacodynamic properties. These include favorable bioavailability allowing oral administration, good tolerability, high tissue concentrations as well as superior bactericidal activity against a broad spectrum of clinically relevant pathogens, like enterobacteria, Pseudomonas aeruginoso, Staphylococcus aureus, and Streptococcus pneumoniae. In addition, no enzymatic mechanism of drug inactivation exists in bacteria and no indications for transfer of clinically relevant resistance exist. Nevertheless, resistance is being increasingly reported, even for naturally highly susceptible species like Escherichia coli. The underlying mechanisms of resistance include alterations in both bacterial targets, DNA gyrase and topoisomerase IV, often combined with mutations affecting drug accumulation, e.g., by increased drug efflux, reduced drug influx, or both. Investigations aiming at understanding the molecular mechanisms of quinolone action and resistance in more detail should provide a basis for a rational design of more potent derivatives. In addition, a prudent use of these highly valuable "magic bullets" is necessary to preserve their potential for the future.     

Pre-clinical pharmacokinetics and anti-chlamydial activity of salicylidene acylhydrazide inhibitors of bacterial type III secretion

Salicylidene acylhydrazides belong to a class of compounds shown to inhibit bacterial type III secretion (T3S) in pathogenic Gram-negative bacteria. This class of compounds also inhibits growth and replication of Chlamydiae, strict intracellular bacteria that possess a T3S system. In this study a library of 58 salicylidene acylhydrazides was screened to identify inhibitors of Chlamydia growth. Compounds inhibiting growth of both Chlamydia trachomatis and Chlamydophila pneumoniae were tested for cell toxicity and seven compounds were selected for preliminary pharmacokinetic analysis in mice using cassette dosing. Two compounds, ME0177 and ME0192, were further investigated by individual pharmacokinetic analysis. Compound ME0177 had a relatively high peak plasma concentration (C(max)) and area under curve and therefore may be considered for systemic treatment of Chlamydia infections. The other compound, ME0192, had poor pharmacokinetic properties but the highest anti-chlamydial activity in vitro and therefore was tested for topical treatment in a mouse vaginal infection model. ME0192 administered vaginally significantly reduced the infectious burden of C. trachomatis and the number of infected mice.     

新型非喹诺酮类细菌IIA型拓扑异构酶抑制剂抗菌药物研究进展

自1962年第一代喹诺酮类药物萘啶酮酸发明以来,成百上千种可分为四代的喹诺酮衍生物已经被成功合成,并且细菌IIA型拓扑异构酶(DNA旋转酶和拓扑异构酶IV)已经被确认为该类抗菌药物的作用靶点。先前研究表明：细菌DNA复制过程对菌体生长与存活至关重要,而这一过程需要DNA旋转酶和拓扑异构酶IV的共同作用。在过去50多年中,喹诺酮类药物的广泛使用也说明这一药物作用靶点在临床治疗上的重要性;但是由于对喹诺酮类药物不恰当的使用乃至滥用,导致细菌耐药性的逐步上升,为确保这一行之有效的抗菌药物作用靶点继续发挥其良好的治疗效果,研发作用于该靶点的非喹诺酮类抗菌药物来克服现有的喹诺酮耐药迫在眉睫。     

The ATP-binding site of type II topoisomerases as a target for antibacterial drugs

DNA topoisomerases are essential enzymes in all cell types and have been found to be valuable drug targets both for antibacterial and anti-cancer chemotherapy. Type II topoisomerases possess a binding site for ATP, which can be exploited as a target for chemo-therapeutic agents. High-resolution structures of protein fragments containing this site complexed with antibiotics or an ATP analogue have provided vital information for the understanding of the action of existing drugs and for the potential development of novel anti-bacterial agents. In this article we have reviewed the structure and function of the ATPase domain of DNA gyrase (bacterial topoisomerase II), particularly highlighting novel information that has been revealed by structural studies. We discuss the efficacy and mode of action of existing drugs and consider the prospects for the development of novel agents.     

Recent advances in bacterial topoisomerase inhibitors

Bacterial topoisomerase inhibitors continue to be actively developed as clinical antibacterial agents, largely owing to the success of the currently marketed inhibitors, the quinolones, and the increasing resistance to these agents. New quinolone analogs such as isothiazoloquinolones and quinazolinediones show some potential in overcoming this problem. Quinolones linked to other antibacterial agents such as rifamycins and oxazolidinones are designed to overcome both quinolone-specific resistance and resistance to the coupled agents. Novel inhibitors targeting non-quinolone-binding regions of topoisomerase continue to expand beyond the known coumarin class. The benzimidazoles and pyrazoles have shown promise but have been surpassed into the clinic by novel quinolines. Improved screening techniques and high-throughput methods offer new hope of further expanding the chemical space of topoisomerase inhibitors.     

Coumarins as inhibitors of bacterial DNA gyrase

Chlorobiocic acid and 3-(carbobenzoxyamino)-4,7-dihydroxy-8-methylcoumarin were identified as two new inhibitors of Micrococcus luteus DNA gyrase. Both compounds possess weak antibacterial activity against whole M. luteus cells which indicates that they probably lack efficient transport functions to penetrate the cell envelope.     

Novel N-linked aminopiperidine inhibitors of bacterial topoisomerase type II: broad-spectrum antibacterial agents with reduced hERG activity

Novel non-fluoroquinolone inhibitors of bacterial type II topoisomerases (DNA gyrase and topoisomerase IV) are of interest for the development of new antibacterial agents that are not impacted by target-mediated cross-resistance with fluoroquinolones. Aminopiperidines that have a bicyclic aromatic moiety linked through a carbon to an ethyl bridge, such as 1, generally show potent broad-spectrum antibacterial activity, including quinolone-resistant isolates, but suffer from potent hERG inhibition (IC(50)= 3 μM for 1). We now disclose the finding that new analogues of 1 with an N-linked cyclic amide moiety attached to the ethyl bridge, such as 24m, retain the broad-spectrum antibacterial activity of 1 but show significantly less hERG inhibition (IC(50)= 31 μM for 24m) and higher free fraction than 1. One optimized analogue, compound 24l, showed moderate clearance in the dog and promising efficacy against Staphylococcus aureus in a mouse thigh infection model.     

Tetrapentylammonium block of chloramine-T and veratridine modified rat brain type IIA sodium channels

Tetrapentylammonium (TPeA) block of rat brain type IIA sodium channel alpha subunit was studied using whole cell patch clamp. Results indicate that TPeA blocks the inactivating brain sodium channel in a potential and use-dependent manner similar to that of the cardiac sodium channel. Removal of inactivation using chloramine-T (CT) unmasks a time-dependent block by TPeA consistent with slow blocking kinetics. On the other hand, no time dependence is observed when inactivation is abolished by modification with veratridine. TPeA does not bind in a potential-dependent fashion to veratridine-modified channels and does not significantly affect gating of veratridine-modified channels suggesting that high affinity binding of TPeA to the brain sodium channel is lost after veratridine modification.     

细菌转位酶MraY及其抑制剂的研究进展（英文）

磷酸-N-乙酰胞壁酸酯-胸腺喷丁转位酶(Mra Y,转位酶I)是细菌中普遍存在且对细菌生长有重要作用的一种酶,是发展新的抗菌药物的重要靶点。此外,几类此酶的抑制剂已经被发现。近来,Mra Y的晶体结构也被Chung等阐明。结合晶体结构及其抑制剂的构效关系研究将有助于活性药效团的确定和对作用机制的深入了解。本文概述了Mra Y的整体结构及其抑制剂,并对这些抑制剂的构效关系和Mra Y作为抗菌药物靶点的前景进行了讨论。     

Identification of inhibitors of bacterial enoyl-acyl carrier protein reductase

The FabI-related enoyl-ACP reductase enzymes of bacteria meet many of the criteria for antibacterial targets. These enzymes are essential for the growth of several pathogenic species, have no significant mammalian homologs, catalyze a rate-limiting step in a vital macromolecular biosynthetic pathway, and are already the targets of antibacterials used in the clinic (isoniazid) and in consumer products (triclosan). The suitability of FabI as an antibiotic target is diminished somewhat by the discovery that many pathogens carry an alternate unrelated enoyl-ACP reductase (FabK) or both reductases. However, a key human pathogen, Staphylococcus aureus and its increasingly common drug-resistant derivative MRSA are sensitive to FabI inhibitors. Screening for inhibitors of this target has resulted in the identification of five chemical classes of potent inhibitors. In addition, analogs of triclosan with increased potency and with pro-drug features have been engineered. At least one of these classes of inhibitors has been optimized and tested in animals for pharmacokinetic properties and efficacy. Further development of one or more of these classes and further screening are expected to generate new FabI inhibitors for application in the clinic against drug-resistant S. aureus.     

DNA topoisomerases in cancer therapy

DNA topoisomerases I and II are nuclear enzymes which modify DNA topology by their ability to break and reseal one or both strands in concert. Each of these enzymes has important functions in DNA replication, and very likely in other genetic processes as well. In addition, each can serve as a cancer chemotherapy target. The plant alkaloid camptothecin traps DNA topoisomerase I in a form which is covalently linked to DNA. Presumably this action is the basis for its anti-tumor effect, although this has not been conclusively demonstrated. The evidence for DNA topoisomerase II as a target for intercalating agents and epipodophyllotoxins is more formidable. Each of these classes of agents traps the enzyme on DNA in a structure referred to as a 'cleavable complex'. Illicit recombination events, as well as induction of an 'SOS-like' response analogous to that found in bacteria, have been suggested as possible mechanisms for cell death following cleavable complex formation. Development of new agents directed at topoisomerase II will depend heavily on understanding the nature of the interaction between the drug, enzyme and DNA. Hypotheses are presented in this paper on this interaction. Intracellular content of topoisomerase II is linked to the ability of the cell to enter a G0-like state, and the inability of malignant cells to undergo such a change may provide part of the basis for therapeutic selectivity. The ability to modulate topoisomerase II levels may provide an opportunity for therapeutic intervention.     

Mechanisms of resistance to topoisomerases poisons

• 1.1. Drug resistance remains a major obstacle to cancer treatment. Resistance to chemotherapy can be intrinsic, characterised by the nonresponsiveness of the tumour to the initial treatment. Alternatively, cancers that initially respond to chemotherapy can relapse after various times because of acquired resistance.
• 2.2. Resistance to drugs used as single agents is generally accompanied by the development of resistance to other drugs that can be structurally and functionally different.
• 3.3. Among the drugs commonly used in cancer treatment there are compounds that have been shown to inhibit DNA topoisomerases (Topos). These critical enzymes regulate the topological conformation of the DNA and participate in essential cellular processes.
• 4.4. This paper reviews the Topos' cellular functions, their catalytic activities and the mechanisms of resistance to inhibitors of Topos, with particular attention to the atypical multidrug resistance phenotype.

     

Binding inhibitors of the bacterial sliding clamp by design

The bacterial replisome is a target for the development of new antibiotics to combat drug resistant strains. The β(2) sliding clamp is an essential component of the replicative machinery, providing a platform for recruitment and function of other replisomal components and ensuring polymerase processivity during DNA replication and repair. A single binding region of the clamp is utilized by its binding partners, which all contain conserved binding motifs. The C-terminal Leu and Phe residues of these motifs are integral to the binding interaction. We acquired three-dimensional structural information on the binding site in β(2) by a study of the binding of modified peptides. Development of a three-dimensional pharmacophore based on the C-terminal dipeptide of the motif enabled identification of compounds that on further development inhibited α-β(2) interaction at low micromolar concentrations. We report the crystal structure of the complex containing one of these inhibitors, a biphenyl oxime, bound to β(2), as a starting point for further inhibitor design.     

seco-Cyclothialidines: new concise synthesis, inhibitory activity toward bacterial and human DNA topoisomerases, and antibacterial properties

seco-Cyclothialidines are a promising class of bacterial DNA gyrase B subunit inhibitors. A new seco-cyclothialidine derivative containing a dioxazine moiety, BAY 50-7952, was synthesized through a new concise pathway. One key step of the synthesis is the straightforward formation of the 2-aminothiazole derivative of S-tritylcysteine. In biological tests, BAY 50-7952 and other known seco-cyclothialidines exhibited high and selective activity toward bacterial DNA gyrase and toward Gram-positive bacteria. The dioxazine moiety and other similar groups were found to be important for the ability of the seco-cyclothialidines to penetrate bacterial membranes. The opposite enantiomer ((S)-form) of BAY 50-7952 was also synthesized, and neither significant target activity nor in vitro antibacterial activity were found, suggesting a highly selective fit of the (R)-form. Despite promising in vitro activity, only poor activity was found in the murine infection model.