Antibacterial drug discovery in the 21st century

Old dogs that learn new tricks: Modified antimicrobial agents that escape pre-existing resistance mechanisms

Increasing numbers of resistant bacteria and decreasing numbers of efficient antimicrobial agents demand for the development of new highly potent antimicrobial agents. The two main directions for the development of new antimicrobial agents are either the development of completely novel antimicrobial agents, or the modification of already existing antimicrobial molecules. The second direction proved to be a more successful and cost-efficient way of generating new antimicrobial agents. For this, chemical modifications have been included which render the antimicrobial agents insensitive to prevalent bacterial resistance mechanisms. However, detailed knowledge of the resistance mechanisms is indispensable. Molecular analysis of resistance mechanisms provides the required data to identify critical target structures. Furthermore, modification of antimicrobial agents makes it possible to escape known resistance mechanisms. In this report, two examples for such successful developments, one from human medicine (telithromycin) and the other from veterinary medicine (florfenicol), are presented.

Antibacterial drug discovery and structure-based design

Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.

Why tackling MRSA needs a comprehensive approach

Methicillin-resistant Staphylococcus aureus (MRSA) causes a fifth of hospital-acquired infections and many other bacteria now show increased resistance to antibacterials. In some parts of the world, community-associated MRSA infections cause a growing number of infections (Fridkin et al, 2005). Attempts to control the spread of MRSA rely on several factors: detecting and isolating infected or colonized patients (cordon sanitaire), rational antibiotic prescribing, hand hygiene and cleanliness. Nurses are key to implementing all of these measures. This article examines the epidemiology of MRSA, as exemplifying an antibiotic-resistant bacterium, and reviews the evidence for the various interventions. A single measure alone is unlikely to eradicate MRSA from either hospitals or the community; indeed, eradicating MRSA is probably impossible. However, a comprehensive approach, including, in particular, good hand hygiene, could reduce the morbidity and mortality arising from MRSA and other hospital-acquired infections.

Practical applications and feasibility of efflux pump inhibitors in the clinic--a vision for applied use

The world of antibiotic drug discovery and development is driven by the necessity to overcome antibiotic resistance in common Gram-positive and Gram-negative pathogens. However, the lack of Gram-negative activity among both recently approved antibiotics and compounds in the developmental pipeline is a general trend despite the fact that the plethora of covered drug targets are well-conserved across the bacterial kingdom. Such intrinsic resistance in Gram-negative bacteria is largely attributed to the activity of multidrug resistance (MDR) efflux pumps. Moreover, these pumps also play a significant role in acquired clinical resistance. Together, these considerations make efflux pumps attractive targets for inhibition in that the resultant efflux pump inhibitor (EPI)/antibiotic combination drug should exhibit increased potency, enhanced spectrum of activity and reduced propensity for acquired resistance. To date, at least one class of broad-spectrum EPI has been extensively characterized. While these efforts indicated a significant potential for developing small molecule inhibitors against efflux pumps, they did not result in a clinically useful compound. Stemming from the continued clinical pressure for novel approaches to combat drug resistant bacterial infections, second-generation programs have been initiated and show early promise to significantly improve the clinical usefulness of currently available and future antibiotics against otherwise recalcitrant Gram-negative infections. It is also apparent that some changes in regulatory decision-making regarding resistance would be very helpful in order to facilitate approval of agents aiming to reverse resistance and prevent its further development.

Antibacterial peptides and proteins with multiple cellular targets

Native antimicrobial peptides and proteins represent bridges between innate and adaptive immunity in mammals. On the one hand they possess direct bacterial killing properties, partly by disintegrating bacterial membranes, and some also by inhibiting functions of intracellular biopolymers. On the other, native antimicrobial peptides and proteins upregulate the host defense as chemoattractants or by various additional immunostimulatory effects. Structure-activity relationship studies indicate that residues responsible for the activities on bacterial membranes or for the secondary functions do not perfectly overlap. In reality, in spite of the relatively short size (18-20 amino acid residues) of some of these molecules, the functional domains can frequently be separated, with the cell-penetrating fragments located at the C-termini and the protein binding domains found upstream. As a cumulative effect, multifunctional and target-specific (agonist or antagonist) antimicrobial peptides and proteins interfere with more than one bacterial function at low concentrations, eliminating toxicity concerns of the earlier generations of antibacterial peptides observed in the clinical setting.

Use of constraint-based modeling for the prediction and validation of antimicrobial targets

The overall process of antimicrobial drug discovery and development seems simple, to cure infectious disease by identifying suitable antibiotic drugs. However, this goal has been difficult to fulfill in recent years. Despite the promise of the high-throughput innovations sparked by the genomics revolution, discovery, and development of new antibiotics has lagged in recent years exacerbating the already serious problem of evolution of antibiotic resistance. Therefore, both new antimicrobials are desperately needed as are improvements to speed up or improve nearly all steps in the process of discovering novel antibiotics and bringing these to clinical use. Another product of the genomic revolution is the modeling of metabolism using computational methodologies. Genomic-scale networks of metabolic reactions based on stoichiometry, thermodynamics and other physico-chemical constraints that emulate microbial metabolism have been developed into valuable research tools in metabolic engineering and other fields. This constraint-based modeling is predictive in identifying critical reactions, metabolites, and genes in metabolism. This is extremely useful in determining and rationalizing cellular metabolic requirements. In turn, these methods can be used to predict potential metabolic targets for antimicrobial research especially if used to increase the confidence in prioritization of metabolic targets. The many different capacities of constraint-based modeling also enable prediction of cellular response to specific inhibitors such as antibiotics and this may, ultimately find a role in drug discovery and development. Herein, we describe the principles of metabolic modeling and how they might initially be applied to antimicrobial research.

Designer antibacterial peptides kill fluoroquinolone-resistant clinical isolates

A significant number of Escherichia coli and Klebsiella pneumoniae bacterial strains in urinary tract infections are resistant to fluoroquinolones. Peptide antibiotics are viable alternatives although these are usually either toxic or insufficiently active. By applying multiple alignment and sequence optimization steps, we designed multifunctional proline-rich antibacterial peptides that maintained their DnaK-binding ability in bacteria and low toxicity in eukaryotes, but entered bacterial cells much more avidly than earlier peptide derivatives. The resulting chimeric and statistical analogues exhibited 8-32 microg/mL minimal inhibitory concentration efficacies in Muller-Hinton broth against a series of clinical pathogens. Significantly, the best peptide, compound 5, A3-APO, retained full antibacterial activity in the presence of mouse serum. Across a set of eight fluoroquinolone-resistant clinical isolates, peptide 5 was 4 times more potent than ciprofloxacin. On the basis of the in vitro efficacy, toxicity, and pharmacokinetics data, we estimate that peptide 5 will be suitable for treating infections in the 3-5 mg/kg dose range.