Current Medicinal Chemistry - Volume 17, Issue 1, 2010

Ras GTPases are membrane-anchored molecular switches that mediate signaling pathways controlling a variety of cellular processes, including cell division and development. Despite their prominent role in many forms of cancer, little is known about the structure of the membrane bound protein or the mechanism and thermodynamics of membrane insertion. The modulation of membrane binding by the catalytic domain is another area of on-going scrutiny. Recent computational and experimental efforts that have begun to shed some light on these issues are the subject of this review. The bulk of the available structural and thermodynamic information on membrane-bound Ras has been obtained by studying peptides derived from the membrane-anchoring regions of N-ras and H-ras proteins. However, those results have been complemented by data, though limited, on the membrane binding of the full-length Ras as well as by predictions about putative communication routes between the GTP-hydrolyzing catalytic domain and the membrane-interacting C-terminus. A tentative mechanistic picture of Ras signaling that is emerging from these studies will be discussed in connection with allostery and implication for the design of selective anti-cancer drugs.

Single-walled carbon nanotubes (SWNTs), a member of the carbon family, are the one-dimensional analogues of zero-dimensional fullerene molecules with unique structural and electronic properties. Since the discovery of SWNTs, they have been extensively studied for biomedical applications. In biological media SWNTs have unique near-infrared intrinsic fluorescence, inherent Raman spectroscopy and photoacoustic signal associated with the graphene in SWNTs which makes them ideal for noninvasive and high sensitivity detection. SWNTs have been broadly investigated as imaging agents for the evaluation of tumor targeting and localization of SWNTs in vitro and in vivo. Rational functionalization can also endow SWNTs with desired properties for biomedical applications. Functionalized SWNTs with significantly reduced toxicity have been employed as carriers to deliver various anticancer drugs, proteins and nucleic acids to the diseased tissues specifically and maximize the bioavailability of the drugs by improving solubility and increasing circulation time. This manuscript will highlight the recent employment of SWNTs in the field of nanomedicine and bioimaging, and also outline the challenges and future opportunities for biomedical applications of SWNTs.

Molecular recognition and ligand binding involving proteins underlie the most important life processes within the cell, such as substrate transport, catalysis, signal transmission, receptor trafficking, gene regulation, switching on and off of biochemical pathways. Despite recent successes in predicting the structures of many protein-substrate complexes, the dynamic aspects of binding have been largely neglected by computational/theoretical investigations. Recently, several groups have started tackling these problems with the use of experimental and simulation methods and developed models describing the variation of protein dynamics upon complex formation, shedding light on how substrate or inhibitor binding can alter protein flexibility and function. The study of ligand-induced dynamic variations has also been exploited to review the concept of allosteric changes, in the absence of major conformational changes. In this context, the study of the influence of protein motions on signal transduction and on catalytic activities has been used to develop pharmacophore models based on ensembles of protein conformations. These models, taking flexibility explicitly into account, are able to distinguish active inhibitors versus nonactive drug-like compounds, to define new molecular motifs and to preferentially identify specific ligands for a certain protein target. The application of these methods holds great promise in advancing structure-based drug discovery and medicinal chemistry in general, opening up the possibility to explore broader chemical spaces than is normally done in an efficient way. In this review, examples illustrating the extent to which simulations can be used to understand these phenomena will be presented along with examples of methodological developments to increase physical understanding of the processes and improve the possibility to rationally design new molecules.

Bacterial infections represent a major health problem, especially in third world countries. In endemic regions, large populations of people are greatly affected, but the medical care is very limited. In this review, the neglected diseases buruli ulcer and trachoma are elucidated. Buruli ulcer is caused by Mycobacterium ulcerans which produces an outstanding immunosuppressive toxin mycolactone that induces an ulcerative, necrotic skin disease. Until today, only the combination of rifampin/streptomycin is used to treat buruli ulcer. However, this therapy is ineffective and expensive. Here, we report new findings that suggest pharmaceutical formulations such as rifapentine, in combination with clarithromycin or moxifloxacin that have shown promising results in mice footpad trials. Moreover, alternative treatment options such as heat therapy, nitric oxide cremes and French clay show bactericidal effects. The genotyping of M. ulcerans also promises new ways of finding drug targets and vaccines. Trachoma, induced by the bacterium Chlamydia trachomatis, is the primary infectious cause of blindness worldwide. Recurrent infections lead to chronic inflammation of the upper tarsal conjunctiva. As a consequence, scarring and distortion of the eye lids occur, eventually resulting in blindness. First-line medications for trachoma treatment are bacteriostatic agents such as topically applied tetracylines and systematically administered azithromycin. Surgery, environmental improvements and personal hygiene are further crucial factors in controlling trachoma. Moreover, efforts are being undertaken towards the development of vaccine systems, with the major outer membrane protein and the polymorphic membrane protein acting as attractive candidates.

Nitric oxide is becoming an increasingly important signalling molecule implicated in a growing number of physiological and pathophysiological processes. Moreover, with the recent advances in nitric oxide biochemistry, many well known drugs have been shown to act totally or partially by modulating NO metabolism with varying therapeutic results. The classic organic nitrates have been shown to exhibit beneficial therapeutic but suffer from some well known pitfalls (tolerability induction, abrupt cephalea and hypotension). Similarly, sydnonimines, another well known class of NO donor drugs, have a characteristically low therapeutic index (i.e., cyanide toxicity). At present, pharmacological researchers are designing and synthesising various chemical compounds capable of modulating NO metabolism for therapeutic purposes that also possess an optimal therapeutic index. Specifically, various new classes of NO donors are under intense pharmacological investigation (such as S-nitrosothiols, diazeniumdiolates, furoxans, zeolites and so on), each characterised by a particular pharmacokinetic and pharmacodynamic profile. To know the pharmacological development of these new NO donor drugs could help to ameliorate the use of these molecules in various therapeutic protocols. In fact, the pharmacologically modulated nitric oxide release showed to have an important therapeutic impact in the treatment of diseases such as arteriopathies, various acute and chronic inflammatory conditions, and several degenerative diseases. At present, the most important obstacle in the field of new NO donor drugs seems to be carefully targeting NO release to a particular tissue at an optimal concentration, so as to achieve a beneficial action and to limit possible toxic effects.

To date more than 4000 compounds are recognized to belong to the class of flavonoids. These natural phenolic drugs are poorly soluble in water and are rapidly degraded and metabolized in the human body, but nevertheless are very promising for their potential contribution to the prevention and therapy of major chronic diseases, including cardiovascular and neurodegenerative diseases and cancer. In recent years a number of flavanols (e.g. catechins), flavonols (e.g. quercetin, myricetin) and isoflavones (e.g. genistein, daidzein) have been confirmed to possess strong antioxidant, antiinflammatory, anti-proliferative and anti-aging activities. Incorporation into lipidic or polymer-based nanoparticles appears to markedly help the oral delivery of flavonoids, as these particles can protect the drug from degradation in the gastrointestinal tract and, by virtue of their unique absorption mechanism through the lymphatic system, also from first-pass metabolism in the liver. In addition, both oral and parenteral administration of flavonoids exploits a pharmacologic delivery route that guarantees sustained release of the active principle at the desired site of action. A comprehensive review of studies currently available on the in vitro and in vivo experimental administration of flavonoids by means of nanovectors may be of use as a foundation for the development of advanced delivery systems for these powerful compounds, in view of their adoption in primary and secondary disease prevention.