Current Medicinal Chemistry - Volume 19, Issue 36, 2012

Bcl-2 (B-cell lymphoma 2) family proteins have been studied intensively due to their association with cancer and other human diseases. These proteins were originally associated with the regulation of outer mitochondrial membrane integrity and apoptosis. However, there is experimental evidence that suggests that several members of this family play instrumental roles in other cellular pathways including autophagy, endoplasmic reticulum signaling, mitochondrial morphology and synaptic activity among others. Bcl-2 family proteins have been explored using diverse experimental and theoretical methods to obtain structural information that can provide valuable insight for drug development. This review is focused on computational studies related to Bcl-2 family proteins. Different strategies are described and evaluated, such as Molecular Dynamics simulations, docking, and rational drug design with the aim of demonstrating the importance of structural details of either ligands or proteins. The relevance of the knowledge obtained using these tools to drug design is discussed.

BACE-1 is a membrane associated aspartyl protease and is one of the enzymes responsible for the hydrolysis of the amyloid precursor protein. Due to its central role in the generation of the amyloid-β peptide, it is considered as a primary drug target for Alzheimer's disease. BACE-1 has been the focus of many drug discovery programs aimed at identifying inhibitors that effectively block this enzyme and trigger the sought therapeutic effects. Thanks to the availability of a large number of crystal structures of the catalytic domain of this enzyme, computational methods, ranging from molecular dynamics simulations, quantum mechanical calculations and ligand docking, have played a fundamental role in almost every hit discovery and hit optimization campaign performed on this target. The present article reviews the latest computational modeling and drug discovery efforts that have been carried out on this target.

In the course of neurodegenerative disorders there are several mechanisms that may counteract the pathological process, mitigating the clinical manifestations of the disease. Usually referred as cognitive reserve hypothesis, this theoretical framework posits that individuals with enriched cognitive status (i.e. with higher educational and occupational levels and higher individual social achievement) may cope better with the occurrence of cognitive decline by a more efficient recruitment of neural networks sustaining higher-level functions. Cognitive reserve was initially studied in Alzheimer's disease, but this concept has been soon after extended also to other neurodegenerative disorders, such as Frontotemporal Dementia, Parkinson's disease, and Huntington's disease, suggesting a general applicability of cortical plasticity phenomena in contrasting neurodegeneration. The neural underpinnings of these dynamic compensatory mechanisms open the possibility for strategic interventions based on environmental approaches. In this continuously growing field, the aim of the present review is to explore new acquisitions, derived from basic research and clinical grounds, on cognitive reserve mechanisms and the potential application as novel therapeutic targets in neurodegenerative diseases.

Retinoids regulate several physiological and pathological processes through the interaction with nuclear receptors. Retinoidassociated signaling which plays an essential role in neurodevelopment appears to remain active in the adult central nervous system (CNS), thus assuming a high significance in the context of neurodegeneration, and indeed retinoid analogs are thought to be promising therapeutic agents for the treatment of neurodegenerative disorders. The ability of retinoids to exert antioxidant effects, inhibit amyloid-β (Aβ) deposits and likely Aβ-induced mitochondrial dysfunction, tau hyperphosphorylation, Aβ-induced IL6 production and neuroinflammation, increase survival in hippocampal neurons, and reverse cognitive deficits in animal models of Alzheimer's disease (AD) is discussed. Although retinoids with their multi-target activity are revealing to be promising for management of AD which is a multifaceted biochemical phenomenon, timing as well as appropriate dosage and safety remain, however, a challenge. The end-stage lesions, namely senile plaques and neurofibrillary tangles, are, at present, considered an adaptive response to oxidative stress underlying AD, thus paradoxically late administration of retinoids could even suppress a protective mechanism by inhibiting Aβ deposits.

Isocitrate lyase plays a key role for survival of Mycobacterium tuberculosis in the latent form during a chronic stage of infection. This enzyme is important for M. tuberculosis during steady stage growth when it converts isocitrate to succinate and glyoxylate. Then, the glyoxylate is condensed with acetyl-CoA to form malate by malate synthase. The carbon conserving glyoxylate pathway has not been observed in mammals; therefore, it has been determined as a potential drug target for discovery of a new antituberculosis agent. Novel active molecules should shorten the duration of therapy, prevent resistance development and eliminate latent disease. The review summarizes recent progresses in isocitrate lyase inhibitors, overviews structural analogues of several metabolic intermediates (3- nitropropionate, 3-bromopyruvate, itaconate, itaconic anhydride), peptide inhibitors, and recently developed inhibitors with various chemical structures. The largest inhibitory activity against isocitrate lyase (IC50 of 0.10 ± 0.01 μM) and concomitantly a significant antimycobacterial activity has been presented by fluoroquinolone derivative 1-cyclopropyl-7-[3,5-dimethyl-4-(3-nitropropanoyl)piperazin- 1-yl]-6-fluoro-8-methoxy-4-oxo-1,4-dihydroquinoline-3-carboxylic acid, which has incorporated 3-nitropropionyl group as one of the structural analogue of succinate, a metabolic intermediate.

Capravirine (S-1153, AG1549), a 1,2,4,5-tetrasubstituted imidazole derivative, was firstly reported by the Shionogi company to inhibit HIV-1 strains which were resistant to other NNRTIs. However, safety and efficacy studies showed that capravirine had no specific advantages over currently used NNRTIs. Consequently, clinical trials were discontinued after phase IIb. Notwithstanding, with aim to obtain novel inhibitors against drug-resistant HIV-1 strains, an in-depth analysis of the particular binding mode of capravirine, together with the wide use of analogue-based chemical evolution strategies, such as bioisosteric replacement, molecular hybridization, prodrug approach, ligand efficiency, etc., gave a huge impetus to the optimization of capravirine. Especially, lersivirine (UK-453,061) was selected for further clinical evaluation due to its very impressive potency against a broad panel of key HIV-1 mutants, safety, pharmacokinetics and other pharmaceutical factors. In this review, we present a comprehensive survey of the literature on the development of capravirine- based NNRTIs. Other interesting NNRTIs with the same or similar binding mode like capravirine have been reported to highlight the structural diversity, pharmacophoric similarity of NNRTIs, which provided important hints for drug design.

The majority of snake venom phospholipases A2 (svPLA2s) are toxic and induce a wide spectrum of biological effects. They are cysteine-rich proteins that contain 119-134 amino acids and share similar structures and functions. About 50% of the residues are incorporated into α-helices, whereas only 10% are in β-sheets. Fourteen conserved cysteines form a network of seven disulfide bridges that stabilize the tertiary structure. They show a high degree of sequence and structural similarity, and are believed to have a common calcium- dependent catalytic mechanism. Additionally, svPLA2s display an array of biological actions that are either dependent or independent of catalysis. The PLA2s of mammalian origin also exert potent bactericidal activity by binding to anionic surfaces and enzymatic degradation of phospholipids in the target membranes, preferentially of Gram-positive species. The bactericidal activity against Gramnegatives by svPLA2 requires a synergistic action with bactericidal/permeability-increasing protein (BPI), but is equally dependent on enzymatic- based membrane degradation. Several hypotheses account for the bactericidal properties of svPLA2s, which include “fatal depolarization” of the bacterial membrane, creation of physical holes in the membrane, scrambling of normal distribution of lipids between the bilayer leaflets, and damage of critical intracellular targets after internalization of the peptide. The present review discusses several svPLA2s and derived peptides that exhibit strong bactericidal activity. The reports demonstrate that svPLA2-derived peptides have the potential to counteract microbial infections. In fact, the C-terminal cationic/hydrophobic segment (residues 115-129) of svPLA2s is bactericidal. Thus identification of the bactericidal sites in svPLA2s has potential for developing novel antimicrobials.

Apoliporotein A5 (APOA5), a member of the apolipoprotein family, plays a key regulatory role in triglyceride (TG) metabolism. Even though the exact biochemical background of its mechanism is not yet fully understood, diseases associated with this particular gene highlighted its key role in the metabolism of triglycerides in humans. Naturally occurring functional variants of the gene and their natural major haplotypes are known to associate with moderately elevated triglyceride levels, and are also known to confer risk or protection for major polygenic diseases, like coronary heart disease, stroke, or metabolic syndrome. On the other hand, case reports and even robust resequencing studies verified APOA5 mutations as underlying genetic defects behind extreme hypertriglyceridemic phenotype. Soon after the recognition of the first cases, there were indications which suggest the existence of less frequent genetic variants which, in combination with the common allelic variants of the gene, can define haplotypes that are associated with substantial triglyceride level increase. In addition, it became evident, that there are rare mutations of the APOA5 gene which can be associated with specific complex phenotypes and different types of hyperlipoproteinemia, which includes extremely high triglyceride levels with multiple organ pathology. These rare mutations may cause inheritable hypertriglyceridemia, but they presented at a low frequency and could not be captured by standard genotyping array screenings. The identification of new mutations still relies on the direct sequencing of APOA5 gene of patients with hypertriglyceridemia with an unusual pattern, individually or in huge resequencing studies.

Medical radiation from x-rays and nuclear medicine is the largest man-made source of radiation exposure in Western countries, accounting for a mean effective dose of 3.0 mSv per capita per year, comparable to the radiologic risk of 150 chest x-rays, and in many cases gonads fall in the imaging field, with > 20 millions examinations per year in US being abdominal and pelvic CT, and >0.5 million barium enema. Of the over 7 million workers exposed to medical radiation, special attention has been paid to those working in the interventional cardiology and radiology labs, with high and increasing professional exposures, two-to three times higher than diagnostic radiologists. Thus, adverse effects of radiation exposure are well worth of the scientific community's interest. Aims of this review are: 1) to assess gonad dose to patients undergoing diagnostic testing or interventional fluoroscopy therapy and in professionally exposed interventional fluoroscopists; and 2) to evaluate the evidence linking radiation exposure in the low-to-moderate range (besides the radiotherapy high dose range) to adverse reproductive effects. In patients, the gonad radiation exposure can reach 5 mSv for a lower limb angiography, 20 mSv for a CT pelvis and hips, and 36 (in females) to 90 mSv (for males) for a lower gastrointestinal series. For interventional cardiologists, the gonad dose (below lead apron) is in the same order of magnitude of the shielded thyroid dose, with a median of 50 to 100 microSievert per cine-angiography procedure. The dose can be ten-fold higher for a complex interventional procedure. This leads to a cumulative exposure in the 0.5-1 Sv range over a professional lifetime of 30 years. At present, the epidemiological approach provided inconclusive results, inadequate for a robust evidence-based advice to exposed subjects, since large groups followed-up for decades would be required to detect a small increase in risk. A molecular epidemiology approach and/or the use of integrated biomarkers of reproductive health (e.h., reproductive hormone balance, sperm quality, sperm DNA damage) might be more fruitful in future research focused in the low-to-moderate dose range (< 1000 mSv) of greatest interest for diagnostic and professional exposures.

Kinetic and sequential kinetic enzymatic routes for the synthesis of enantiomeric β- and γ-amino acids through enzymatic ring cleavage of the corresponding lactams in organic solvents or solvent-free systems or a supercritical CO2 medium, and for the enantioselective hydrolysis of the corresponding amino esters in organic solvents are reviewed. In the frame of a practical guide, a simple and rapid GC enantioseparation technique for amino acids, including exact descriptions of selected enzymatic reactions, is additionally presented.

For many years a battle has been going on between bacteria and humans, with bacteria trying to survive against the antibiotics used by humans. Bacteria are found to be dominant in this battle since they can develop resistance. In fact, in the last decade multi-, extended- and pan-drug resistant bacteria have been isolated. On the other hand, the number of new antibiotics approved by the FDA has dramatically decreased during the last 20 years. Therefore, there is a desperate need for developing new types of antibacterial agents, where antimicrobial peptides may play an important role. This review provides an update of the recently identified antimicrobial peptides. Three valid approaches for developing a future antibacterial agent, as are the mechanisms of action as well as the in vitro and in vivo assays have been described in depth. In comparison to the antibacterial agents available at present, the targets for most of the antimicrobial peptides are not well known. However several proposals having been introduced for many antimicrobial peptides of different mechanisms of action, there still lies some uncertainty about their utility. Hundreds of antimicrobial peptides have been tested in vitro against all types of bacteria, but in this review we will highlight only those which have been tested against the most important Grampositive and Gram-negative bacteria. The last step to get a potential antibiotic includes studies with an in vivo model. Therefore only antimicrobial peptides with good activity are tested that have been described in this review.

G-Protein Coupled Receptor (GPCR) superfamily, which comprises approximately 900 members, is the largest family of protein targets with proven therapeutic value. Although at least 500 GPCRs have been identified as therapeutically relevant, only thirteen GPCRs have been structurally characterized in apo-form or in complex with ligands. GPCRs share relatively low sequence similarity making hard the process of homology modelling, nevertheless some successful hits have been determined. Recently, the G-proteincoupled estrogen receptor 1 (GPER, formerly known as GPR30) has attracted increasing interest due to its ability in mediating estrogen signaling in different normal and cancer tissues. In this regard, the identification of selective GPER ligands has provided valuable tools in order to differentiate the specific functions elicited by this novel estrogen receptor respect to those exerted by the classical estrogen receptors (ERs). In this review, we focus on GPER examining “in silico” docking simulations and evaluating the different binding modes of diverse natural and synthetic ligands.

The main challenge encountered while treating using Paclitaxel (PTX) is its poor solubility in aqueous solutions. The cremophor used in the formulation can cause various side effects such as hypersensitivity, myelosuppression and neurotoxicity and also leads to non-specific distribution in tumor and normal tissues. Since the structure of Paclitaxel does not possess a functional group, it is not easy to manipulate to enhance the solubility. Such limitations can be overcome by delivering Paclitaxel with the aid of drug delivery systems such as polymeric micelles, nanoparticles, hydrogels and liposomes. The review discusses various approaches of Paclitaxel delivery via polymeric nanoparticles. It focuses on the passive and active targeting of Paclitaxel.

MicroRNAs (miRNA) are a recently recognised class of small, non-coding RNAs involved in the post-transcriptional regulation of gene expression and with crucial implication for mammalian development. In particular, they play key roles in neuronal development, from early neurogenesis to neuronal differentiation and synaptic development, and also in in vitro systems. The detection of embryotoxic hazards in the preclinical phase is still a challenge, often due to species-species variations. In this study we analysed whether miRNA expression profiles in a human pluripotent cell model can be a helpful tool for a more mechanistic approach to pharmacology and toxicology. Differentiating human pluripotent cells were repeatedly treated with non-cytotoxic doses of methylmercury chloride (MeHgCl), a well known brain developmental toxicant. The expression of proteins, mRNA and miRNAs were used to monitor successful neural differentiation. Significant changes in the expression of 12 miRNAs were detected. By using available bioinformatics tools, we obtained validated and predicted targets for the identified miRNAs, on which we performed functional clustering analysis. Through this approach, we identified several terms and functional clusters associated with neural development, together with indicators of general toxic effect, such as apoptosis or stress response-related genes. Interestingly, our results also suggest a previously undiscovered association between MeHgCl and the ubiquitin-proteasome protein degradation pathway. Although further investigations are needed, our results suggest that miRNA expression analysis is a powerful tool in pathway-oriented toxicity and could improve earlyphase hazard assessments.

Traditional approaches in evaluating the hazard of drug candidates on the developing offspring are often time-consuming and cost-intensive. Moreover, variations in the toxicological response of different animal species to the tested substance cause severe problems when extrapolating safety dosages for humans. Therefore, more predictive and relevant toxicological systems based on human cell models are required. In the presented study the environmental toxicant methylmercury chloride (MeHgCl), known to cause structural developmental abnormalities in the brain, was used as reference compound to develop a concept contributing to a mechanistic understanding of the toxicity of an investigated substance. Despite the fact, that there are significant data available from animal studies and from poisonings in Japan and Iraq, uncertainties on the mechanism of MeHgCl during human development are still remaining and qualify the substance for further analysis. Transcriptomics analysis in combination with a human cell based in vitro model has been used in order to elucidate the toxicity of MeHgCl at molecular level. Differentiating neural precursor cells that have been exposed continuously to non- and low-cytotoxic concentrations of MeHgCl were investigated. Quantitative change in the mRNA expression profiles of selected genes demonstrated the sensitivity of the cell model and its qualification for a transcriptomics study screening changes in the expression profile of the complete human genome of MeHgCl-treated human neural cells. Potential biomarkers were identified and these candidate marker genes as well as their involvement in a possible toxic mechanism of MeHgCl during the human neurulation process are hereby introduced. The study confirmed the hypothesis that a cellular model based on a human stem cell line can be applied for elucidating unknown mode of actions of developmental toxicants.

Cationic phosphorus-containing dendrimers (CPDs) are a class of highly-branched polymers with potential medical relevance. However, little is known about CPD modes of interactions with cell and its components, including DNA. In the present work we investigated cytotoxicity and genotoxicity of CPDs generation 3 and 4 (CPD G3 and CPD G4) in human mononuclear blood cells, A549 human cancer cells and human gingival fibroblasts (HGFs). CPD G3 and CPD G4 at concentrations up to 10 μM induced a concentrationdependent decrease in cell viability as assessed by flow cytometry. Both compounds did not induce breaks in isolated DNA as evaluated by the plasmid relaxation assay but they induced DNA cross-links in the cells, as examined by comet assay. CPD G3 and 4 induced slight perturbations in the cell cycle leading to a decrease in the G2/M cell population accompanied by an increase in the S cell population. Upon treatment with CPDs, the cells showed changes in their morphology, including loss of cell attachment, disruption of cell membrane and nucleus condensation. Our results indicate that CPD G3 and G4 are cytotoxic and genotoxic for the assorted human cells. Therefore, CPDs may form stable complexes with DNA and interfere with cellular processes.