Designing Type II Topoisomerase Inhibitors: a Molecular Modeling Approach
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Send Orders for Reprints to [email protected] 40 Current Topics in Medicinal Chemistry, 2014, 14, 40-50 Designing Type II Topoisomerase Inhibitors: A Molecular Modeling Approach Juan J. Perez*, Cecylia S. Lupala and Patricia Gomez-Gutierrez Department of Chemical Engineering. Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, 647; 08028 Barcelona, Spain Abstract: Nosocomial infections are produced by pathogens with the ability to persist in hospital environments and with the propensity to develop resistance to diverse antimicrobials. In order to tackle resistance, it has been pointed as good strategy to select resilient drug targets that are evolutionally constrained to design drugs less susceptible to develop resis- tance. Molecular modeling can help to fulfill this goal by providing a rationalization of the observed resistance at the mo- lecular level and, suggesting modifications on existing drugs or in the design of new ones to overcome the problem. The present report focus on type II topoisomerases, a clinical validated target for antibacterials and describe diverse modes of intervention including, inhibition of their ATPase function, stabilization of the cleavage complex or prevention of DNA strand hydrolysis. Moreover, the origin of resistance is also rationalized on the base of ligand-target interactions. Finally, efforts are described to circumvent the effect of non-susceptible strains by the design of new drugs based on existing ones, like the case of diones that act through the same mechanism as quinolones or the newly released quinole-carbonitrile de- rivatives that inhibit type II topoisomerases through a new mechanism. Keywords: Topoisomerases inhibitors, antibiotics design, nosocomial infections, quinolones. INTRODUCTION cephalosporins prevent the formation of the bacterial wall, while others like polymixins disrupt the structure of the Nosocomial infections affect about 5-10% of hospitalized membrane by intercalation [5]. Finally, other compounds patients and are among the major causes of death and in- inhibit protein synthesis by binding to the ribosome, like creased morbidity in this population. Furthermore, these in- macrolides that prevent the transfer of the peptidyl-tRNA fections hamper the success of advanced surgical procedures, complex from the A to the P site [6], lincosamides that cause including organ and prosthetic transplants. In addition to a premature separation of peptidyl-tRNA complex from the their morbidity and mortality burdens, nosocomial infections ribosomes [7] or tetracyclines preventing the attachment of are associated to higher healthcare costs due to the increased new amino acids to the nascent polypeptide chain [8]. length of stay in hospitals for infected patients. These infec- tions are caused by pathogens -commonly bacteria- with the Antibacterial resistance is defined as the point at which ability to persist in hospital environments and with propen- the administration of the drug can no longer safely treat the sity to develop resistance to diverse antimicrobials. Accord- infection due to an induced change in the drug target or an ingly, there is a great deal of interest to establish new proto- inability of the drug to reach the target. Moreover, microor- cols that include stricter measures in infection control and ganisms may also exhibit resistance towards more than one antibiotic use, as well as to find new antibiotics [1]. As it drug, in this case, depending on the number of the antibacte- will be discussed later, molecular modeling can help in un- rial classes towards they show resistance, strains are referred derstanding the causes of antibacterial resistance at the mo- to exhibit multidrug, extended drug, and pandrug resistance lecular level and to direct efforts to design new compounds. [9]. Antibacterial resistance is nothing new, microorganisms have survived for thousands of years due to their ability to Antibacterials are drugs that arrest bacterial growth or adapt against these compounds. Drug resistance is the result kill them. This goal can be achieved acting at different levels of the evolutionary pressure on bacteria and is typically ac- on the microorganism. Some drugs target key enzymes. For quired by gene mutation or lateral gene transfer within or example, rifamycins and lipiarmycins inhibit prokaryotic between species. Genetic diversity within populations com- RNA-polymerase function [2]; quinolones kill bacteria by bined with rapid microbial generation time gives microbes a increasing levels of DNA strand breaks generated by type II remarkable adaptability in response to selective pressure topoisomerases [3]; or sulphamides kill bacteria by inhibit- from antimicrobials. ing dihydropteroate synthetase, an enzyme involved in folate synthesis [4]. Other group of drugs, like penicillins and The observed antibiotic resistance experienced nowadays is a consequence of a complex interaction among natural selection, environment, and patterns of drug use and misuse *Address correspondence to this author at the Department of Chemical [10]. Thus, considering that most of the antibacterials are Engineering. Universitat Politecnica de Catalunya, ETSEIB. Av. Diagonal, natural or semi-synthetic compounds and, the robust antibac- 647; 08028 Barcelona, Spain; Tel: +34934016679; Fax: +34934017150; Email: [email protected] terial machinery of these microorganisms together with their 1873-5294/14 $58.00+.00 © 2014 Bentham Science Publishers Designing Type II Topoisomerase Inhibitors Current Topics in Medicinal Chemistry, 2014, Vol. 14, No. 1 41 rapid generation time, it is understandable the ability of these ligands, putatively binders of the same target, permits to microorganisms to escape new antibacterials after treatment identify the stereospecific features of the ligand-receptor for a short period of time. For example, it took only four interaction, that are described through a pharmacophore that years after penicillin was commercialized in the early 1940s, can be used to design new compounds [19]. Finally, a broad to identify penicillin-resistant strains of S. aureus [11]. In a class of studies can be classified as quantitative structure- recent study taking advantage of the advances in sequencing, activity studies, where the activity of a series of compounds the time evolution of the genome of a S. aureus multidrug is related with structural or physicochemical parameters of a resistance strain was tracked from the blood samples of a set of ligands [20, 21]. patient undergoing chemotherapy with vancomycin and The present contribution is aimed at reviewing available other antibiotics. Interestingly, it was found that from the structure-activity studies on the inhibition of type II topoiso- sequence of the first vancomycin susceptible isolate to the imerases, to exemplify how structural information helps to last vancomycin non-susceptible isolate, 35 point mutations understand how specific mutations are responsible for resis- could be identified in three months of treatment [12]. tance and how new ligands can be designed to avoid these In regard to the mechanisms bacteria use to raise resis- limitations [17]. tance to antibacterial drugs, the most direct mechanism pro- ceeds via modification of the binding site features in the tar- BACTERIAL TYPE IIA TOPOISOMERASES get macromolecule. In fact, slight modifications of the bind- DNA is organized in large loops both in eukaryotic and ing site can reduce dramatically the effectiveness of a drug, prokaryotic cells, which essentially renders it a closed circu- being numerous the reports describing point mutations in a lar system. This structure is mechanically constrained, and therapeutic target that provoke resistance to a group of anti- imposes that DNA adopts diverse topological isoforms, in- bacterials [13]. In addition, there are other resistance mecha- cluding supercoiled configurations (positively or negatively) nisms that use as strategy the reduction of antibacterial up- as compared to the relaxed reference form, knots or even take. One of them consists of enzymatic antibacterial degra- catenanes. Interestingly, DNA topology plays an active role dation. Indeed, many bacteria contain specific versions of - in regulating basic biological processes, including control of lactamases, capable to hydrolyze antibiotics like penicillins, gene transcription, DNA replication and segregation, ge- cephalosporins, monobactams or carbapenems [14]. Bacte- nome maintenance and cellular differentiation [22]. Accord- rial resistance may also rise by adaptation of these enzymes ingly, control of DNA topology is essential for cellular func- to a specific antibacterial after a period of treatment, turning tion. This control is exercised in all organisms by a family of the strain non-susceptible to the drug. Other mechanisms enzymes called topoisomerases, found throughout all cellular concern drug transport systems in and out the cell. Thus, domains of life [23]. Topoisomerases alter DNA topology by bacteria may raise resistance through drug influx reduction repeated cycles of DNA strand breaking and religation at the by alteration of porin expression [15]. Moreover, resistance incredible frequency of 250-6000 cycles per minute, depend- may also be raised through efflux enhancement. Efflux is a ing of enzyme type. Although the double-stranded DNA mechanism to pump out unwanted toxic substances out of breaks generated by topoisomerases are essential for cell the cell. Active efflux is an active transport mechanism