Current Topics in Medicinal Chemistry - Volume 10, Issue 18, 2010

Multidrug-resistant Gram-negative bacteria, including the strains Escherichia, Klebsiella, Pseudomonas, and Acinetobacter, have become imminent threats to public health and welfare due to the lack of safe and broadly effective drugs in the markets, which is accompanied by the shortage of investigational compounds in clinical trials. These bacterial strains render known antibiotics either less effective or inactive through the reduction of intracellular permeability or increased extrusion, enzymatic inactivation (or degradation), or target modification. Comparatively, Gram-negative bacteria create the need for more advanced solutions to facilitate drug penetration and prevent ejection than Gram-positive pathogens require due to their outer membrane, which is covered with lipopolysaccharides and host for efflux pumps. Several enabling technologies have been developed and broadly applied in the antibiotics discovery area for decades. These include combinatorial chemistry and high throughput screening to facilitate the identification of promising hits and X-ray or NMR techniques, which increase the understanding of the structures of the targets and their interactions with ligands. The pool of genomic information for discovering new targets has also increased over time. Nevertheless, the transformation of potent hits and ligands to drug candidates with good efficacies and safety profiles continues to be a major challenge. To overcome resistance, new targets are continuously sought with the expectation of generating a new class of compounds. Efflux pumps and various types of enzymes have been explored. Compounds with novel structures interacting with known targets are also under investigation due to the lower probability of resistance to such structures. In addition, the modification of known antibiotics has been of interest in the discovery effort. There are ample examples in antibiotics' history indicating that a partial change of a core structure may lead to new antibiotics with different properties and antibacterial spectra, such as penicillin to cephalosporin or carbapenem, and erythromycin to azithromycin. However, history has also taught us that the window for bacteria to accept the structural variations is very narrow. Elegant design, as well as perhaps some good fortune, often essential for success. In this issue of “Current Topics in Medicinal Chemistry,” five papers have been assembled. They reflect the progress in understanding new promising targets and the development of either a new class of compounds or derivatives of known antibiotics to overcome resistance in Gram-negative pathogens. Here are the highlights. Efflux pumps and their inhibitors have attracted great attention, not only because of the success of β-lactamase inhibitors in recovering the efficacy of β-lactam antibiotics, but also because they are obstacles that most antibiotics must overcome. In the first review of this issue, Jean-Marie Pages, Sandrine Alibert-Franco, Abdallah Mahamoud, Jean-Michel Bolla, Anne Davin- Regli, Jacqueline Chevalier, and Eric Garnotel described the recent progress in the characterization of efflux pump structures. These authors presented potential efflux pump targets under a real dynamic environment and insightfully introduced the six strategies currently being pursued to circumvent efflux pumps. Furthermore, they also discussed five types of efflux pump inhibitors, highlighting the advances as well as the challenges associated with each type. The isoprenoid biosynthetic pathway has been extensively explored, and the enzymes involved in this pathway have been investigated as targets for the treatment of many human diseases. However, much less attention has been paid so far to them as potential targets for antibiotics. Andrew J. Wiemer, Chia-Hung Christine Hsiao, and David F. Wiemer covered the necessity of isoprenoid biosynthesis for bacterial growth and presented the differences between Human and Enterbacteria isoprenoid biosynthesis pathways. In the opening to their contribution, they provided an example showing that Enterobacteria carried out isoprenoid biosynthesis on a different pathway from eukaryotes. Inhibition of an enzyme, 1-deoxy-D-xylulose-5-phosphate reductoisomerase, used in this pathway led to the discovery of potent compounds active against Gram-negative bacteria. More pathways associated with quinone synthesis, bacterial electron transport chain and cell wall biosynthesis were discussed in detail, and enzymes were carefully selected as potential targets selective for bacterial species. Inhibitors that were developed for these enzymes have been presented, as well as the knowledge about inhibitor design, including charge and steric considerations.

Antibiotic resistance mechanisms reported in Gram-negative bacteria are a worldwide health problem. The continuous dissemination of multi-drug resistant (MDR) bacteria drastically reduces the efficacy of our antibiotic “arsenal” and consequently increases the frequency of therapeutic failure. In MDR bacteria the over-expression of efflux pumps expel structurally-unrelated antibiotics decreasing their intracellular concentration. It is necessary to clearly define the molecular and genetic bases of the efflux pump in order to combat this mechanism. The characterization of efflux pumps, from genetic to structural studies, allows the definition of a new, original antiresistance bullet, the efflux pump inhibitor (EPI). This new class of antibacterial molecules may act conjointly to the usual antibiotic in order to restore its activity. Several families of EPIs have been now reported and described. The use of these EPIs promotes a significant increase of susceptibility to one or more antibiotics in strains or clinical isolates which were initially resistant. These EPIs may target different efflux targets, (i) the expression of genes that induces MDR, the transporters that pump the antibiotic out of bacterium, (ii) the assembly of membrane transporter complex involved in drug efflux, (iii) the energy involved in this active transport, (iv) the inhibition of the flux of molecules inside the efflux channel by competition or blocking (via steric hindrances). With the recent thorough characterization of the efflux pump AcrB at its structural and physiological level including the identification of drug affinity sites and kinetic parameters for some antibiotics, it is now possible to rationally develop an improved new generation of EPIs.

Gram-negative Enterobacteria include a variety of human pathogens, perhaps most notably E. coli, Salmonella, Shigella, Yersinia, and Proteus. While there are treatment options for the diseases caused by these organisms, multi-drug resistance is often a problem and development of novel antibiotics has lagged over recent years. In humans, the isoprenoid biosynthetic pathway has become a subject of intense research for therapeutic modulation of human enzymes in diseases including hypercholesterolemia, osteoporosis, and cancer. In bacteria, isoprenoid metabolism is arguably just as important, giving rise to components that are essential for electron transport and cell wall biosynthesis. Blocking these biosynthetic processes, either with the antibiotic fosmidomycin or by gene knockout strategies, has demonstrated the necessity of isoprenoid biosynthesis for bacterial growth. In this review, current knowledge of the biochemical pathways involved in farnesyl diphosphate metabolism in Enterobacteria, efforts to develop inhibitors of the involved enzymes, and insights from inhibitors of human isoprenoid metabolism that may be relevant for future studies of antibiotics that target these key enzymes, are described.

Multi-drug resistant bacteria are appearing at an alarming rate and impose significant burdens on healthcare systems worldwide. Cationic peptides have shown great promise as broad spectrum antimicrobial agents with a demonstrated ability to kill resistant bacteria, however, issues such as protease susceptibility and toxicity issues have delayed their clinical development. This review summarizes recent progress in the advancement of cationic antimicrobial peptides for the treatment of bacterial infections. The major focus of the discussion relates to recent advances in the areas of screening and in silico modeling. A selection of novel strategies that diverge from classical linear α-peptide antimicrobials is also discussed. A diverse array of candidate structures will be key to the ultimate development of a stable platform for clinical development. The ability to accurately predict peptide activity in silico and in a high-throughput manner should benefit all classes of cationic antimicrobial peptides and provide a larger set of candidate structures for clinical evaluation.

β-Lactam antibiotics are the most prescribed antibacterial agents. They comprise more than half of all antibiotics. They are considered as the cornerstone of the antibiotic armamentarium. By inhibiting bacterial cell wall biosynthesis, they are highly effective against Gram-positive and Gram-negative bacteria. Antibiotic resistance among Gram-negative pathogens in hospitals represents a dangerous threat to public health. Since many bacteria have developed resistance to older agents, new β-lactam antibiotics have been continuously developed. In the late 1970s, a new class of exceptionally broad-spectrum non-traditional β-lactams, carbapenems, was developed. This review article focuses on the new developments related to the field of carbapenems for treatment of bacterial infections, especially those caused by Gram-negative bacteria. The structural features, principal characteristics, and clinical implications of carbapenems including thienamycin, imipenem/cilastatin, panipenem/betamipron, biapenem, tebipenem, tebipenem pivoxil, meropenem, ertapenem, doripenem, lenapenem, and tomopenem are discussed herein.

Aminoglycosides are important broad-spectrum antibiotics used in the therapy of many microbial infections. As the bacterial resistance to antibiotic therapy is appearing as an increasingly significant threat to public health, the development of aminoglycoside antibiotics with extended antibacterial spectrum and potency, devoid of nephro- and ototoxicity, and evading the resistance process returns to the focus of researchers. In this review, various developments brought to the aminoglycoside family of antibiotics effective against resistant bacteria have been described, focused on chemical modifications, drug-modifying enzyme inhibitors, and conformationally constrained analogs, as well as related antibacterial compounds, with the hope to provide information useful in rational design of novel antibiotics addressing bacterial resistance, and paving the way for new perspectives in antimicrobial therapy.

Drug discovery scientists are required to make important intellectual property decisions every day on what novel compounds to make, which processes to produce them, and which assays to evaluate them in, often with a modest knowledge of patent and legal issues that impact their ability to execute these proposals or obtain patent protection on them. When the practitioner seeks advice from internal counsel, it is often hard to get a definitive answer, because the issues are quite complex and the legal landscape is ever changing. The last several decades have been particularly turbulent in the pharmaceutical arena. With the advent of the Hatch-Waxman Act in 1984, virtually every commercially important patent is challenged by generic companies, hoping to gain early entry into the market. Therefore, it is more important than ever for inventors to craft the strongest patents possible. Recent court decisions have changed the determination of what is obvious and what is patentable, and have influenced the United States Patent and Trademark Office (USPTO) in issuing new guidelines. The purpose of this review is to lay out some basic principles of patent law and how it has evolved over time, to facilitate the dialog between practicing medicinal chemists and their legal colleagues. Specific examples of cases before the courts will be presented to help understand these complex issues. In the first manuscript by Xavier Pillai and myself, a brief history of patent law is presented, along with recent changes in its interpretation that are relevant in securing patents in the current landscape. In the case of KSR International Co. v. Teleflex, Inc, the United States Supreme Court developed a more flexible definition of the teaching-suggestion-motivation (TSM) test in determining obviousness. If an invention is obvious to try and there are a finite number of predictable solutions in the prior art, then the invention will be considered obvious, and therefore unpatentable, by current standards. In Bayer Schering Pharma AG v. Barr Laboratories, the court of appeals applied the KSR standard of obviousness in invalidating a formulation patent claim, in which only a finite number of predictable options were available to the formulator. Unlike the formulation patent example, patents covering new molecular entities have survived challenges more successfully. However in Altana Pharma AG v. Teva Pharmaceuticals USA, Inc., the court of appeals judged against the innovator company, when there was a clearer case of predictable prior art. Finally, the Ortho-McNeil Pharmaceutical, Inc. v. Mylan Laboratories, Inc. case involves a patent that was successfully defended, because the scientists had at their disposal a great number of unpredictable options and the results were clearly surprising. In light of these and other court decisions the USPTO has established new and possibly stricter guidelines for patent examinations going forward. Allen M. Sokal and Bart A. Gerstenblith describe the details of the Hatch-Waxman Act, which was enacted to spur new pharmaceutical development and to encourage greater public access to generic drugs. The Act contains important provisions favorable to either branded drug or generic drug manufacturers. The Hatch-Waxman Act also provides a means of vetting patent rights, while enhancing the public notice of such rights. With its enactment there has been a large increase in patent litigation as a means of resolving patent disputes. While the Hatch-Waxman Act has certainly benefitted generic manufacturers, the public, and the legal profession, the pharmaceutical industry has suffered in an increasingly hostile landscape. At some point congress may need to readdress whether the provisions of the Hatch-Waxman Act are properly balanced. Christopher M. Holman addresses the Bilski decision of the U. S. Supreme Court and delves into its “machine or transformation” test in determining process claim eligibility. Historically, patents were granted primarily on inventions arising out of the mechanical and chemical arts. With the growth of the diagnostics, biotechnology, and software industries, the U. S. patent system embarked upon an expansion in its definition of patent-eligible subject matter, which encouraged investments in these technologies. However in recent years, the threshold for patent-eligibility has been raised, particularly related to business method patents. This was done to ensure that patents fulfill their constitutional objective of encouraging innovation, rather than impeding it. For example, in recent years the courts and USPTO have tried to limit process claims to particular applications of a fundamental principle, rather than claims that preempt the principle itself. This shift in patent eligible subject matter is likely to have an impact on the pharmaceutical and biotechnology industries in the near future.

In this article, a brief history of patent law is presented, along with recent changes in its interpretation that are relevant in securing patents in the current landscape. Specific patent examples are presented to illustrate key issues. For example, the case of KSR International Co. v. Teleflex, Inc. is an important recent decision by the United States Supreme Court, which developed a more flexible definition of the teaching-suggestion-motivation (TSM) test in determining obviousness, which negates patentability. Although KSR case involved a mechanical invention, the ruling in this case has had implications in other areas of patent law, particularly as it applied to pharmaceutical and chemical inventions. It has had a significant impact on the outcome of patent prosecution at the United States Patent and Trademark Office (USPTO), as well as in defending patents in federal courts. If an invention is obvious to try and there are a finite number of predictable solutions in the prior art, then the invention will be considered obvious by current standards. Bayer Schering Pharma AG v. Barr Laboratories, Inc is presented as a case in which the court of appeals has applied the KSR standard of obviousness in invalidating a formulation patent claim, in which a finite number of options were available to the formulator. Unlike the formulation patent example, patents covering new molecules have survived challenges more successfully. In The Procter & Gamble Co. v. Teva Pharmaceuticals USA, Inc., the court of appeals for the Federal Circuit determined that the invention of risedronate was unobvious, although it was a mere positional isomer of a prior bisphosphonate. However in Altana Pharma AG v. Teva Pharmaceuticals USA, Inc., the court of appeals judged against the innovator company when there was a clearer case of predictable prior art. Finally, Ortho-McNeil Pharmaceutical, Inc. v. Mylan Laboratories, Inc. presents an example of a case at the Federal Circuit where topiramate was more easily defended, because the scientist had at his disposal a great number of unpredictable options and the results were clearly surprising. In light of these and other court decisions the USPTO has established new guidelines for patent examinations going forward that this article describes.

The patent-eligibility doctrine serves a gatekeeper role in excluding from patent protection natural phenomena, principles of nature, abstract ideas, and mental processes. Beginning around 1980, the U.S. patent system embarked upon a pronounced expansion in its definition of patent-eligible subject matter, particularly with respect to software and business method inventions, but also in the life sciences. In recent years, however, we have seen a backlash, with many critics from the public and private sectors arguing that the threshold for patent-eligibility needs to be raised in order to ensure that patents fulfill their constitutional objective of encouraging innovation rather than impeding it. The courts and PTO appear to have heard these critics, and have begun to actively rein in the scope of patent-eligible subject matter. This shift in the swing of the patent-eligibility pendulum will likely have a profound impact on the patentability of innovations arising out of the pharmaceutical and biotechnology industries, particularly those relating to diagnostics and personalized medicine. In this article, I discuss the current status of the patent-eligibility doctrine, how it is that we got here, and what the future might hold, particularly for the life science industries.

Congress carefully crafted the Hatch-Waxman Act to address two competing goals: to spur new pharmaceutical development and to encourage greater public access to generic drugs. To that end, the Act contains important provisions directed to fulfilling each goal, including provisions favorable to either branded drug or generic drug manufacturers. This article addresses those provisions in the context of issues pertaining to patent rights and in light of the congressional goals.

Many facets of drug discovery involve the use of patented materials and methods, subjecting the researcher to potential liability from infringement of the underlying patents. Enacted in 1984, the Hatch-Waxman Act established a “safe harbor” for activities that would otherwise constitute infringement of a patented invention, if those activities were “solely for uses reasonably related to the development and submission of information under a Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products”. This article examines the major court decisions interpreting the scope of the safe harbor and their application to various activities in drug development.