Current Topics in Medicinal Chemistry - Volume 14, Issue 1, 2014

Biotin protein ligase (BPL) represents a promising target for the discovery of new antibacterial chemotherapeutics. Here we review the central role of BPL for the survival and virulence of clinically important Staphylococcus aureus in support of this claim. X-ray crystallography structures of BPLs in complex with ligands and small molecule inhibitors provide new insights into the mechanism of protein biotinylation, and a template for structure guided approaches to the design of inhibitors for antibacterial discovery. Most BPLs employ an ordered ligand binding mechanism for the synthesis of the reaction intermediate biotinyl-5´-AMP from substrates biotin and ATP. Recent studies reporting chemical analogs of biotin and biotinyl-5´-AMP as BPL inhibitors that represent new classes of anti-S. aureus agents are reviewed. We highlight strategies to selectively inhibit bacterial BPL over the mammalian equivalent using a 1,2,3-triazole isostere to replace the labile phosphoanhydride naturally present in biotinyl-5´-AMP. A novel in situ approach to improve the detection of triazole-based inhibitors is also presented that could potentially be widely applied to other protein targets.

Bacterial resistance to antibiotics, particularly to multiple drug resistant antibiotics, is becoming cause for significant concern. The only really viable course of action is to discover new antibiotics with novel mode of actions. This review focuses on antibiotic resistance mechanisms of Enterococcus and Campylobacter, and new antibacterial agents against Enterococcus and Campylobacter through de novo or semi- synthesis in the period from 2003 until mid- 2013.

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 resistance. Molecular modeling can help to fulfill this goal by providing a rationalization of the observed resistance at the molecular 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 derivatives that inhibit type II topoisomerases through a new mechanism.

Mycobacterium tuberculosis is the causative agent of tuberculosis, a lethal infection disease that attacks the lungs. Now it becomes the major global health risk because of very long latent period, the persistent increase of new cases, and the emergence of multidrug-resistant and extensively drug-resistant strains. Therefore, there is an urgent need for the development of new, safe and more efficient tuberculosis drugs. The shikimate pathway has been considered as the attractive drug target due to its essentiality in algae, higher plants, bacteria, and fungi, but absence from mammals. In this review, we focus on the recent development of a wide variety of inhibitors of type II Mycobacterium tuberculosis dehydroquinate dehydratase, the third enzyme of this pathway. The structural and mechanistic features of the enzyme for the design and discovery of the inhibitors have been described. The key factors on the structure, binding, and affinity of the inhibitors have been also highlighted. This may direct the further development of type II Mycobacterium tuberculosis dehydroquinate dehydratase inhibitors as potent tuberculosis drugs.

Staphylococcus aureus lives in commensalism with the majority of the population, being recognized as an important pathogen in patients with chronic liver diseases and can cause a deadly infection. The use of antibiotics as rifampin for the chemotherapy of infections caused by S. aureus has resulted in the selection of mutants with resistance. In an attempt to combat resistant strains new research is continuously conducted, as example searching new biological targets or new inhibitors such as tiophenes derivatives that can inhibit the RNA polymerase enzyme. This work investigated the set of tiophenes, selected from of literature and with RNA polymerase enzyme inhibitory activity of S. aureus. After seeking further information on existing scientific literature, the compounds under study were applied the methodologies of PLS, docking and calculation of Molecular Interaction Fields (MIFs) using Pentacle and VolSurf programmes. In addition, a comparison was made with two tiophenes synthesized in our laboratory and which have been tested against the bacteria. Docking studies showed that active compounds had more interactions with the amino acids on active site when compared with rifampicin. The best model obtained in PLS, considering two LVs (latent variables), after leave-one-outvalidation, exhibited the statistical parameters qcv 2 = 0.68 and r2 = 0.85. External prediction model presented a rext 2 = 0.67. The obtained model through PLS analyses was able to predict the behavior of compounds synthesized by us. So we extract structural features important for the activity of these compounds. In this paper, first we discussed the topics: S. aureus, tiophenes, RNA polymerase, docking and QSAR methodologies. Then we have selected a series of 56 tiophenes from literature, which have their biological activity tested against the RNA polymerase enzyme of S. aureus. The compounds were subsequently carried out for Partial Least Squares (PLS) Analysis.

The bacterial biofilms and the emergence of multiple drug resistance have become a major threat for current medical treatment of nosocomial infections. It has been estimated that about 65-80% of microbial infections in the developed countries are associated with biofilms. Given the prominence of biofilms in infectious diseases, increasing efforts toward the development of small molecules that will modulate bacterial biofilm development and maintenance is on the rise. Till date, marine natural products have shown a tremendous potential as pharma leads and also given new skeletons which would be used as biofilm/QS inhibitors. Medically relevant biofilm forming bacteria such as Pseudomonas aeruginosa which is most frequently isolated bacteria in nosocomial infection is believed to be a model organism for biofilm studies. Hence, in this review, we have highlighted the development of small molecules that inhibit and/or disperse bacterial biofilms of P. aeruginosa in particular. Additionally, the rational design approaches as well as synthetic methodologies along with biological studies has been accounted in this article.

Tuberculosis is a major global health problem. In the middle of the last century several laboratories identified, developed and synthesized several substances which were active against Mycobacterium tuberculosis, the causative agent of the disease. In the 1980s the standard oral treatment regimen was introduced with isoniazid, rifampicin, pyrazinamide, and ethambutol. In combination with the DOTS strategy it was possible treat TB within 6–8 months. But with the emergence of drug resistant strains, the formerly successful regiment became ineffective for MDR and XDR TB patients. Even more alarming, the rapidly increasing HIV epidemic also increases the number of HIV-related TB. Facing these facts, it became evident that novel strategies and antibiotics were needed to treat the new forms of TB. But over the last 60 years no novel TB drug was developed or even in the drug pipeline. But during the last ten years several novel substances have been developed to combat the deadly disease. For the first time in decades the TB drug pipeline is filled again with several promising compounds and many of them have reached Phase II and Phase III clinical trials. Several laboratories and companies all over the world currently are developing and evaluating these substances. This review presents novel substances, which were for the first time exclusively developed for TB such as bedaquilines, nitroimidazoles and the diamine SQ109. We also summarize the present knowledge about enzymes and biosynthesis pathways which offer potential targets for drug discovery against M. tuberculosis.

The modulation of DNA topology by DNA gyrase and topoisomerase IV, both of which are type IIA topoisomerases and found in most bacteria, is a function vital to DNA replication, repair and decatenation. Despite the potential for resistance development, DNA gyrase and/or topoisomerase IV have been proven to be and remain highly attractive targets in antibacterial drug discovery due to their potential for dual targeting. The search for new GyrA and/or ParC inhibitors that can overcome the increasing spread of multidrug-resistant bacteria has been successfully focused in the last decades on the modification of the known fluoroquinolone scaffold as primarily guided by ligand-based design via classical structure-activity relationship studies and the optimisation of physicochemical properties. This focus has resulted in several novel fluoroquinolones that have been introduced into clinical practice since 2000, and several of these new compounds are currently in different phases of clinical trials. Due to increasing resistance to fluoroquinolones, a significant part of DNA gyrase research has shifted to the discovery of new GyrB and/or ParE inhibitors, which are commonly identified through fragment-based design as well as virtual screening techniques and structure-based hit optimisation programs. This research often results in lead compounds with potent inhibitory activity and promising antibacterial activity profiles. Nevertheless, it is important to understand how different physicochemical properties (e.g., logD and total polar surface area) and different structural motifs influence the compounds’ permeability to ensure the efficient discovery of potent, small-molecule antibacterials particularly against Gram-negative strains.

Clostridium difficile is an anaerobic, Gram-positive pathogen that causes C. difficile infection, which results in significant morbidity and mortality. The incidence of C. difficile infection in developed countries has become increasingly high due to the emergence of newer epidemic strains, a growing elderly population, extensive use of broad spectrum antibiotics, and limited therapies for this diarrheal disease. Because treatment options currently available for C. difficile infection have some drawbacks, including cost, promotion of resistance, and selectivity problems, new agents are urgently needed to address these challenges. This review article focuses on two parts: the first part summarizes current clinical treatment strategies and agents under clinical development for C. difficile infection; the second part reviews newly reported anti-difficile agents that have been evaluated or reevaluated in the last five years and are in the early stages of drug discovery and development. Antibiotics are divided into natural product inspired and synthetic small molecule compounds that may have the potential to be more efficacious than currently approved treatments. This includes potency, selectivity, reduced cytotoxicity, and novel modes of action to prevent resistance.

Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis and is a common infectious disease with high mortality and morbidity. The increasing prevalence of drug-resistant strains of TB presents a major public health problem. Due to the lack of effective drugs to treat these drug-resistant strains, the discovery or development of novel anti-TB drugs is important. Computer-aided drug design has become an established strategy for the identification of novel active chemicals through a combination of several drug design tools. In this review, we summarise the current chemotherapy for TB, describe attractive target proteins for the development of antibiotics against TB, and detail several computational drug design strategies that may contribute to the further identification of active chemicals for the treatment of not only TB but also other diseases.