Showing papers in "ChemMedChem in 2008"

Prodrug strategies in anticancer chemotherapy.

Abstract: The majority of clinically approved anticancer drugs are characterized by a narrow therapeutic window that results mainly from a high systemic toxicity of the drugs in combination with an evident lack of tumor selectivity. Besides the development of suitable galenic formulations such as liposomes or micelles, several promising prodrug approaches have been followed in the last decades with the aim of improving chemotherapy. In this review we elucidate the two main concepts that underlie the design of most anticancer prodrugs: drug targeting and controlled release of the drug at the tumor site. Consequently, active and passive targeting using tumor-specific ligands or macromolecular carriers are discussed as well as release strategies that are based on tumor-specific characteristics such as low pH or the expression of tumor-associated enzymes. Furthermore, other strategies such as ADEPT (antibody-directed enzyme prodrug therapy) and the design of self-eliminating structures are introduced. Chemical realization of prodrug approaches is illustrated by drug candidates that have or may have clinical importance.

G-Quadruplexes: Targets in Anticancer Drug Design

Abstract: G-quadruplexes are special secondary structures adopted in some guanine-rich DNA sequences. As guanine-rich sequences are present in important regions of the eukaryotic genome, such as telomeres and the regulatory regions of many genes, such structures may play important roles in the regulation of biological events in the body. G-quadruplexes have become valid targets for new anticancer drugs in the past few decades. Many leading compounds that target these structures have been reported, and a few of them have entered preclinical or clinical trials. Nonetheless, the selectivity of this kind of antitumor compound has yet to be improved in order to suppress the side effects caused by nonselective binding. As drug design targets, the topology and structural characteristics of quadruplexes, their possible biological roles, and the modes and sites of small-ligand binding to these structures should be understood clearly. Herein we provide a summary of published research that has set out to address the above problem to provide useful information on the design of small ligands that target G-quadruplexes. This review also covers research methodologies that have been developed to study the binding of ligands to G-quadruplexes.

Lessons learnt from assembling screening libraries for drug discovery for neglected diseases.

Abstract: To enable the establishment of a drug discovery operation for neglected diseases, out of 2.3 million commercially available compounds 222 552 compounds were selected for an in silico library, 57 438 for a diverse general screening library, and 1 697 compounds for a focused kinase set. Compiling these libraries required a robust strategy for compound selection. Rules for unwanted groups were defined and selection criteria to enrich for lead-like compounds which facilitate straightforward structure–activity relationship exploration were established. Further, a literature and patent review was undertaken to extract key recognition elements of kinase inhibitors (“core fragments”) to assemble a focused library for hit discovery for kinases. Computational and experimental characterisation of the general screening library revealed that the selected compounds 1) span a broad range of lead-like space, 2) show a high degree of structural integrity and purity, and 3) demonstrate appropriate solubility for the purposes of biochemical screening. The implications of this study for compound selection, especially in an academic environment with limited resources, are considered.

Superparamagnetic Iron Oxide Nanoparticle-Aptamer Bioconjugates for Combined Prostate Cancer Imaging and Therapy

Abstract: ThemajorshortcomingofCombidexisitsinabilitytodetectPCadiseaseoutsideofthelymphnodes.Herein, we report the development of a novel, multifunc-tional, thermally cross-linked SPION (TCL-SPION) that can bothdetect PCa cells, and deliver targeted chemotherapeuticagents directly to the PCa cells. We previously reported theuseoftheA10RNAaptamer (Apt), which bindstheextracellu-lar domain of the prostate-specific membrane antigen (PSMA),to engineer targeted nanoparticles for PCa therapy and imag-ing.

Molecular recognition of small-cell lung cancer cells using aptamers.

Abstract: Early diagnosis is the way to improve the rate of lung cancer survival, but is almost impossible today due to the lack of molecular probes that recognize lung cancer cells sensitively and selectively We developed a new aptamer approach for the recognition of specific small-cell lung cancer (SCLC) cell-surface molecular markers Our approach relies on cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX) to evolve aptamers for whole live cells that express a variety of surface markers representing molecular differences among cancer cells When applied to different lung cancer cells including those from patient samples, these aptamers bind to SCLC cells with high affinity and specificity in various assay formats When conjugated with magnetic and fluorescent nanoparticles, the aptamer nanoconjugates could effectively extract SCLC cells from mixed cell media for isolation, enrichment, and sensitive detection These studies demonstrate the potential of the aptamer approach for early lung cancer detection

Cellular uptake, cytotoxicity, and metabolic profiling of human cancer cells treated with ruthenium(II) polypyridyl complexes [Ru(bpy)2(N--N)]Cl2 with N--N=bpy, phen, dpq, dppz, and dppn.

Abstract: A series of five ruthenium(II) polypyridyl complexes [Ru(bpy)2(N--N)]Cl2 was tested against human HT-29 and MCF-7 cancer cell lines. Cellular uptake efficiency and cytotoxicity were found to increase with the size of the aromatic surface area of the N--N ligand. The most active compound carrying the dppn ligand exhibits a low micromolar IC(50) value against both cell lines comparable to that of cisplatin under similar conditions. Continuous measurement of oxygen consumption, extracellular acidification rate, and impedance of the cell layer with a chip-based sensor system upon exposure to the complexes showed only small changes for the first two parameters throughout the series. A significant and irreversible decrease in impedance was, however, found for the dppn compound. This suggests that its biological activity is related to modifications in cell morphology or cell-cell and cell-matrix contacts.

On the art of compiling and using 'drug-like' chemical fragment spaces.

Abstract: Ever since the first rational approaches to the discovery of promising lead candidate structures were applied, it has been a challenge for both medicinal and computational chemists to assess, generate, and combine promising structural motifs to form new and potent chemical entities for biological screening against potential drug targets. Many scientists have committed themselves to the analysis and identification of valuable chemical building blocks and have also developed strategies on how to best recombine them. In this context, the retrosynthetic fragmentation and recombination of chemical motifs derived from known inhibitors is a common and well-known procedure. Meanwhile, fragment-based approaches have become established and valuable processes in pharmaceutical lead discovery and validation. Several application studies have yielded promising lead candidates. Chemical space is huge. Corporate as well as public databases are in the millions and are still increasing in size in order to cover a larger part of the chemical universe. For several good reasons, there is the common trend to standardize experimental and computational protocols in pharmaceutical research. This trend demands systematic and consistent approaches, although they can hardly match the creativity and intuition of medicinal chemists. Consequently, they can and should not substitute, but rather assist, the expert in this task. The most prominent automated example for fragment generation is the retrosynthetic combinatorial analysis procedure (RECAP). It was the first of its kind to apply 11 distinct rules that were supposed to model chemical motifs that could easily be formed by combinatorial chemistry. In this context, the “fragment space” concept was introduced. In contrast to a fragment library, such a space consists not only of a set of fragments, but also of a set of rules that specifies how to recombine fragments by fusing the respective chemical motifs. RECAP is widely used and often referred to, yet even though authors frequently state to have used modified improved versions of the original, actual publications that communicate the extensions that were carried out are rare. An extension of the fragment space concept was recently published, but with a focus on obtaining scaffolds and not on retaining supposedly ’drug-like’ substituents or functional groups. Apart from that, the question remains what a ’drug-like’ fragment space actually is, and whether or not ’drug-likeness’ depends on the origin of the fragments: that is, if they necessarily have to be derived from drugs. In this context, it is highly interesting and important to measure the extent and accuracy with which current models and methods are able to represent the available chemical space. In an attempt to improve existing approaches for the automatic decomposition of molecules into fragments, we compiled a new and more elaborate set of rules for the breaking of retrosynthetically interesting chemical substructures (BRICS) and used this for obtaining fragments from biologically active compounds and vendor catalogue sources. Based on this, we compiled corresponding fragment spaces by specifying a complementary set of rules for the recombination of the corresponding chemical motifs. Furthermore, we put considerable effort into compiling a set of high-quality, high-performance, and, in contrast to all other approaches, publicly available fragments that are meant to serve as a possible basis for various molecular design objectives and techniques. We incorporated more elaborate medicinal chemistry concepts and, for example, modeled explicit isosteric replacements for cyclic and acyclic cases and further distinguished activated from inactivated heterocyclic ring systems and their corresponding substituents. Overall, this work led us to more comprehensive sets of fragments, and the corresponding fragment spaces show a significant increase in performance over existing methods. Moreover, by incorporating fragments from vendor catalogue sources, the performance can be increased even further. The shredding procedure we used for BRICS applies all possible retrosynthetic cuts simultaneously, which avoids the generation of overlapping (redundant) fragments. This is in accordance with RECAP and simplifies the calculation later on. Scheme 1 shows a simple fragmentation example and highlights the key steps. In addition to splitting retrosynthetically relevant bonds, we directly included substructure filters into the shredding procedure to avoid the generation of unwanted chemical motifs as well as small terminal fragments such as single hydrogen and halogen atoms, hydroxy, nitro, carboxylate, methoxy, methyl, ethyl, and isopropyl groups. These motifs are therefore discarded or left uncleaved, respectively. The BRICS model consists of 16 chemical environments indicated by link atoms of different types. The corresponding fragment prototypes are depicted in Scheme 2 and show only the direct chemical environment of the cleavage sites for reasons of simplicity. Therefore, the diversity of the fragments is within the R groups that can also contain further links. Note that the carbonyl and alkyl fragments are shown twice (L1/L6, L4/L8). This is because we wanted to keep track of their origin for medicinal chemistry and modeling reasons, that is, whether they appeared as cyclic or acyclic substituents or linkers. The corresponding fragment space results from the definition of the [a] J. Degen, Dr. A. Zaliani, Prof. Dr. M. Rarey Center for Bioinformatics, University of Hamburg Bundesstrasse 43, 20146 Hamburg (Germany) Fax: (+49)40-42838-7352 E-mail : rarey@zbh.uni-hamburg.de [b] Dr. C. Wegscheid-Gerlach Medicinal Chemistry VII Computational Chemistry Bayer Schering Pharma AG, M:llerstrasse 178, 13342 Berlin (Germany) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.200800178 and from the authors’ website .

Ferrocene Conjugates of Chloroquine and other Antimalarials: the Development of Ferroquine, a New Antimalarial

Abstract: A convenient approach to antimalarial drug discovery is the use of the organic scaffold of a known antimalarial drug and an organometallic moiety to alter its unwanted properties and/or to optimize its initial effects. This minireview focuses mainly on the discovery of ferroquine, which has emerged from a collaborative French discovery project, and efforts to understand its mechanism of action and resistance.WILEY-VCH

Click chemistry and medicinal chemistry: a case of "cyclo-addiction".

Abstract: It is fair to say that in the current climate, the concept of click chemistry (CC) perhaps requires no introduction. Most organic chemists are familiar with the term, but for many, the original meaning and philosophy have been misplaced. When the topic of click chemistry is discussed, some immediately think of the Cu-catalysed Huisgen cycloaddition as a synthetic ideal, others might consider polymer synthesis, whilst others may think of enzyme-catalysed templated reactions. Therefore, it seems pertinent to begin by reiterating the original definitions as originally laid down by the orchestrators of the concept, namely Sharpless, Finn, and Kolb. It is worth remembering that the impetus behind defining the philosophy was the bleak reality that the estimated number of ’reasonable’ drug candidates—those with fewer than 30 non-hydrogen atoms; with mass <500 Da composed of only H, C, N, O, P, S, F, Cl and Br; and that are likely to be stable at ambient temperature in the presence of water and oxygen—is on the order of 10 molecules. Faced with this fact, it might seem clear that synthetic propositions aimed at drug discovery should be aimed at molecules that are easy to make. The rules defining a click chemistry approach are as follows: A reaction must be modular, wide in scope, give very high yields, generate only inoffensive byproducts that are easily separated, and be stereospecific. The process must include simple reaction conditions, readily available starting materials and reagents, the use of no solvent, or a solvent that is benign or easily removed, and simple product isolation.

HER-2-targeted nanoparticle-affibody bioconjugates for cancer therapy.

Abstract: Affibodies are a class of polypeptide ligands that are potential candidates for cell- or tissue-specific targeting of drug-encapsulated controlled release polymeric nanoparticles (NPs). Here we report the development of drug delivery vehicles comprised of polymeric NPs that are surface modified with Affibody ligands that bind to the extracellular domain of the trans-membrane human epidermal growth factor receptor 2 (HER-2) for targeted delivery to cells which over express the HER-2 antigen. NPs lacking the anti-HER-2 Affibody did not show significant uptake by these cells. Using paclitaxel encapsulated NP-Affibody (1 wt% drug loading), we demonstrated increased cytotoxicity of these bioconjugates in SK-BR-3 and SKOV-3 cell lines. These targeted, drug encapsulated NPAffibody bioconjugates may be efficacious in treating HER-2 expressing carcinoma.

Curcumin-Derived Pyrazoles and Isoxazoles: Swiss Army Knives or Blunt Tools for Alzheimer's Disease?

Abstract: Curcumin binds to the amyloid beta peptide (Abeta) and inhibits or modulates amyloid precursor protein (APP) metabolism. Therefore, curcumin-derived isoxazoles and pyrazoles were synthesized to minimize the metal chelation properties of curcumin. The decreased rotational freedom and absence of stereoisomers was predicted to enhance affinity toward Abeta(42) aggregates. Accordingly, replacement of the 1,3-dicarbonyl moiety with isosteric heterocycles turned curcumin analogue isoxazoles and pyrazoles into potent ligands of fibrillar Abeta(42) aggregates. Additionally, several compounds are potent inhibitors of tau protein aggregation and depolymerized tau protein aggregates at low micromolar concentrations.

Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function.

Abstract: We developed a new empirical scoring function, HYDE, for the evaluation of protein-ligand complexes. HYDE estimates binding free energy based on two terms for dehydration and hydrogen bonding only. The essential feature of this scoring function is the integrated use of log P-derived atomic increments for the prediction of free dehydration energy and hydrogen bonding energy. Taking the dehydration of atoms within the interface into account shows that some atoms contribute favorably to the overall score, while others contribute unfavorably. For instance, hydrogen bond functions are penalized if they are dehydrated unless they can overcompensate this loss by forming a hydrogen bond with excellent geometry. The main stabilizing contribution represents the removal of apolar groups from the water: the hydrophobic effect. Initial studies using the DUD dataset show that with HYDE, there is a significant decrease in false positives, a reasonable categorization of compounds as either non-binders, weak, medium or strong binders, and in particular, there is a generally applicable and thermodynamically sensible cutoff score below which there is a high likelihood that the compound is indeed a binder.

Reduction of Alzheimer’s Disease Amyloid Plaque Load in Transgenic Mice by D3, a D-Enantiomeric Peptide Identified by Mirror Image Phage Display

Abstract: Alzheimer’s disease (AD) is a multifactorial disorder, which is characterized by progressive memory deficits, cognitive impairments and personality changes. More than 20 million people are affected worldwide. The histopathological hallmarks of AD are aggregated protein deposits (i.e. , senile plaques and neurofibrillary tangles) in the brain. Senile plaques consist mainly of extracellular amyloid-b peptide (Ab) deposits. While there is still debated over whether Ab is the causative agent in AD, the inhibition of Ab production and aggregation is often targeted for therapy development. Recently, we used mirror image phage display to identify a novel d-amino acid peptide binding specifically to Ab ACHTUNGTRENNUNG(1–42) with a binding affinity in the submicromolar dissociation constant range and called it “d-pep” or “D1”. 3] d-peptides are known to be extremely protease resistant and less immunogenic than their respective l-enantiomers, thus being more suitable for in vivo use. d-Peptides have previously been used as inhibitors of amyloid formation to prevent the associated Ab cytotoxicity. Recently, another strategy to obtain d-peptides specifically interacting with amyloid stretches, inhibiting amyloid formation and cell toxicity, was presented. In the present work, we identified a novel d-enantiomeric amino acid peptide “D3” which might provide a novel basis for therapeutic and preventive approaches to AD. D3 might also be useful as a tool to study the role of Ab plaques in AD progression. We performed phage display selections of a peptide library encoding more than 1 10 randomly different 12amino acid sequences with d-enantiomeric Ab ACHTUNGTRENNUNG(1–42) (d-Ab) as the target. d-Ab was dissolved to obtain a low final concentration of 2 nm. Under those conditions, we expected monomeric Ab or small Ab oligomers to be the dominant target species during the phage display screening. After 6 rounds of biopanning, we determined the peptide sequences of the enriched phage displayed peptides by DNA sequence analysis of the respective genome region. The dominant peptide sequence obtained from the selection was RPRTRLHTHRNR, referred to as D3. This sequence was found in 9 out of 23 randomly chosen phage clones. Additionally, 9 of the selected peptides were related to the dominating peptide by at least 9 amino acids (table S1, Supporting Information). We investigated the influence of D3 on Ab aggregation. The content of amyloid fibrils was determined by Thioflavin T (ThT) fluorescence upon incubation of various Ab/D3 mixtures. ThT is a benzothiazole dye that exhibits enhanced fluorescence upon binding to amyloid fibrils, and is commonly used to detect amyloid fibrils. ThT fluorescence of Ab mixtures with D3 was significantly lower than those without D3 (Figure 1 a). These results suggest that D3 significantly decreased the formation of ThT-positive Ab aggregates. These results were confirmed using a fluorescence correlation spectroscopy (FCS) based assay. FCS allows the detection of Ab aggregates in highly dilute samples, with concentrations in the nanomolar range. Fluorescence fluctuations generated by single molecules passing the confocal volume of the focused laser beam are measured, and can be evaluated by autocorrelation to obtain the diffusion time of the studied molecules. When Ab aggregates, containing at least one molecule of Oregon Green (OG) labeled Ab, are present within a given solution, they can be directly detected as spikes in the fluorescence fluctuation recordings. Due to their size, they have an increased duration of stay in the confocal volume and increased fluorescence intensities because most or all of them contain more than one fluorescence label. FCS measurements were carried out with 5 nm OG-labeled Ab in the absence or presence of D3 in various concentrations. Figure 1 b shows how the number of peaks decreases with increasing amounts of added D3. A 50 % inhibition of aggregate formation by D3 is obtained at ~1 mm. This result suggests that D3 prevents aggregation of Ab in the nanomolar concentration range. To assay the ability of D3 to dissolve pre-existing ThT positive Ab aggregates, Ab was preincubated without D3 for seven days to allow aggregation. Then, D3 at various concentrations was added and ThT fluorescence was followed (Figure 1 c). The results clearly show a dose-dependent aggregate disassembly activity of D3 for preformed ThT positive Ab aggregates without stirring, ultrasonic treatment, or any other mechanical support. We studied the effect of D3 on Ab-induced cytotoxicity in rat pheochromocytoma (PC12) cells. Ab (10 mm) was incubated without or with varying concentrations of D3 for 6 days at 37 8C. Cells were then treated with various Ab/D3 mixtures and their viability was measured by MTT reduction (Figure 1 d). In the presence of 2 mm of Ab cell viability dropped to 40 %, this effect was reversed in a dose-dependant manner by the addition of D3, and cell viability could be completely rescued in [a] Dr. K. Wiesehan, Dr. S. A. Funke, Prof. Dr. D. Willbold INB-2/Molekulare Biophysik II Forschungszentrum J lich, 52425 J lich (Germany) Fax: (+ 49) 2461612233 E-mail : d.willbold@fz-juelich.de [b] Dr. L. Nagel-Steger, Prof. Dr. D. Willbold Institut f r Physikalische Biologie, BMFZ, Heinrich-Heine-Universit t 40225 D sseldorf (Germany) [c] Dr. T. van Groen, Dr. I. Kadish Dept. Cell Biology, University of Alabama at Birmingham, AL 35294 (USA) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.200800273.

Zinc-Binding Groups Modulate Selective Inhibition of MMPs

Abstract: The need for selective matrix metalloproteinase (MMP) inhibition is of interest because of the range of pathologies mediated by different MMP isoforms. The development of more selective MMP inhibitors (MMPi) may help to overcome some of the undesired side effects that have hindered the clinical success of these compounds. In an effort to devise new approaches to selective inhibitors, herein we describe several novel MMPi and show that their selectivity is dependent on the nature of the zinc-binding group (ZBG). This is in contrast to most current MMPi, which obtain isoform selectivity solely from the peptidomimetic backbone portion of the compound. In the present study, six different hydroxypyrone and hydroxypyridinone ZBGs were appended to a common biphenyl backbone and the inhibition efficiency of each inhibitor was determined in vitro (IC(50) values) against MMP-1, -2, -3, -7, -8, -9, -12, and -13. The results show that the selectivity profile of each inhibitor is different as a result of the various ZBGs. Computational modeling studies were used to explain some trends in the observed selectivity profiles. To assess the importance of the ZBG in a biological model, two of the semiselective, potent MMPi (and one control) were evaluated using an isolated perfused rat heart system. Hearts were subjected to ischemia reperfusion injury, and recovery of contractile function was examined. In this model, only one of the two MMPi showed significant and sustained heart recovery, demonstrating that the choice of ZBG can have a significant effect in a relevant pathophysiological endpoint.

Small-molecule inhibitors of PDK1.

Abstract: Signal transduction of many growth factors and oncogenes is mediated by 3-phosphoinositide-dependent protein kinase-1 (PDK1), a master regulator of a number of downstream signal protein kinase cascades. Hence, PDK1 represents a convergence point for receptor tyrosine kinase and cytokine-mediated pathways for the regulation of vital cell processes such as cell survival and proliferation. Pathological upregulation of PDK1 signalling due to constitutive growth factor receptor activation and/or PTEN (phosphatase and tensin homologue) mutations significantly triggers downstream signalling, e.g. PKB/Akt, which subsequently promote proliferative events such as tumour invasiveness, angiogenesis, and progression. Consistent with this, a mouse model expressing low levels of PDK1 is protected from tumourigenesis resulting from loss of PTEN. Because more than 50 % of all human cancers possess significant overstimulation of the PDK1 signalling pathway, inhibition of this protein kinase by small molecules is predicted to result in effective inhibition of cancer cell proliferation and thus be therapeutically beneficial. Various classes of small-molecule PDK1 inhibitors have been published in patents and papers. Herein we present for the first time a comprehensive collection of small molecules reported to interact with PDK1, and we refer to their biological characterisation in terms of activity and selectivity for PDK1.

Phenanthroline derivatives with improved selectivity as DNA-targeting anticancer or antimicrobial drugs.

Abstract: Phenanthroline derivatives are of interest due to their potential activity against cancer, and viral, bacterial, and fungal infections. In a search for highly specific antitumor and antibacterial compounds, we report the activities of 1,10-phenanthroline-5,6-dione (phendione or L(1)), dipyrido[3,2-a:2',3'-c]phenazine (dppz or L(2)), and their corresponding platinum complexes ([PtL(1)Cl2] and [PtL(2)Cl2]), and provide the solid-state 3D structure for [PtL(1)Cl2]. It is generally known that a toxic metal ion coordinated to an active organic moiety leads to a synergistic effect; however, we report herein that the platinum complexes [PtL(1)Cl2] and [PtL(2)Cl2] have weaker activities relative to those of the free ligands, especially against bacteria. Testing these agents against a variety of human cancer cell lines revealed that L(1) and [PtL(1)Cl2] were at least as active as cisplatin against several of the cell lines (including a cisplatin-resistant cell line). The absence of antibacterial activity of [PtL(1)Cl2] removes the detrimental effect of phenanthrolines toward intestinal flora, suggesting a highly promising new strategy for the development of anticancer drugs with reduced side effects.

Towards a Self‐Adjuvanting Multivalent B and T cell Epitope Containing Synthetic Glycolipopeptide Cancer Vaccine

Abstract: Malignant tumor cells are characterized by the overexpression of altered glycoproteins or glycolipids resulting from the deregulation of glycosylation processes. The identification of these tumor-associated carbohydrate antigens (TACA) has largely contributed to the development of cancer diagnostic and immunotherapy. Particularly, TACA present strong antibody determinants (B cell epitopes) which are primarily targeted by tumor-specific antibodies (Abs). Although TACA are rightly considered as tremendous potential targets for cancer vaccines, their poor immunogenicity still hampers their use as therapeutic vaccines. To address this challenge, both careful rational design and robust chemical procedures should be considered to construct TACA-based vaccine prototypes capable of promoting a strong and selective Ab response against tumor cells. In the last decade, intensive research has focused on the development of molecularly defined TACA-based vaccine prototypes. These studies have clearly defined that not only the display of TACA, but also their nature and molecular formulation are crucial to improve immunity against tumors. First, a multivalent presentation of TACA, either on carrier protein (for example keyhole limpet hemocyanin) or on synthetic delivery systems containing CD4+ T helper (Th) cell epitope (for example multiple antigen glycopeptide) is required to elicit strong B cell responses and raise high affinity tumor-specific Abs. In addition, it was established that priming and sustaining of both Ab and CD8+ cytotoxic T cell (CTL) responses, the latter also crucial in cancer immunity, requires CD4+ Th cell help. This suggests that an ideal cancer vaccine formulation must incorporate B cell, CD4+ , and CD8+ T cell epitopes to ensure both humoral and cellular eradication of tumors. Finally, these synthetic multivalent vaccines should be delivered together with potent and safe external immunoadjuvants to ensure an early and strong immunity. To avoid the potential toxicity related to most of external adjuvants, especially often in immunocompromised cancer patients, recent reports have highlighted that palmitoyl-tailed B and T cell epitope peptides delivered in adjuvant-free saline are clinically safe, eliciting strong, long-lasting, and multivalent protective immunity. However, except for a few studies reporting the synthesis of up to three-component multivalent or “polytope” vaccines, 8] no molecular constructions have been designed so far on the basis of these overall structural features. This is presumably because of inherent difficulties, despite recent progresses in the synthesis, assembly, and formulation of oligosaccharide and glycoconjugate biomolecules. In this communication, we report for the first time on the design, synthesis, safety, immunogenicity, and protective efficacy of a prototype, molecularly defined, fully synthetic, self-adjuvanting multivalent glycolipopeptide (GLP) cancer vaccine. As illustrated on Figure 1, our GLP vaccine prototype associated four essential components displayed on a molecular delivery system: 1) a cluster of TACA B-cell epitope; 2) a CD4+ Th

Molecular Approaches towards the Inhibition of the Signal Transducer and Activator of Transcription 3 (Stat3) Protein

Abstract: The signal transducers and activators of transcription (STATs) are a class of transcription factor proteins that regulate cell growth and survival by modulating the expression of specific target genes.[1] A total of seven different STAT isoforms, encoded in distinct genes, have been identified in mammalian cells. Stat3, a member of the STAT family, has been identified in an increasing number of tumor cell lines. Stat3 drives malignant progression through the misregulation of key proteins, including cell survival proteins such as Bcl-xL and Mcl-1, cell cycle regulators such as cyclin D1/D2 and c-myc, and inducers of angiogenesis such as vascular endothelial growth factor (VEGF).[2] In contrast to normal cells, where Stat3 activation is rapid and transient, neoplastic cells are found to display constitutive Stat3 activation that, once inhibited, correlates with suppression of both cell transformation and growth, and induction of apoptosis.[3-8] While STAT signaling is just one of many pathways compromised in oncogenesis, interruption of this pathway is sufficient to block cell transformation; this suggests that these cells have an irreversible dependence on constitutively active Stat3 for survival. Numerous reports highlight the relevance of persistent Stat3 activation in human cancers; abnormal levels of Stat3 activation have been observed in breast,[9,10] ovarian,[9] prostate,[11] haematological,[12] and head and neck cancer cell lines.[13] These investigations suggest that agents designed to disrupt Stat3 signaling hold considerable promise for the prevention and treatment of human cancers.

SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites.

Abstract: Predictions of potential metabolites based on chemical structure are becoming increasingly important in drug discovery to guide medicinal chemistry efforts that address metabolic issues and to support experimental metabolite screening and identification. Herein we present a novel rule-based method, SyGMa (Systematic Generation of potential Metabolites), to predict the potential metabolites of a given parent structure. A set of reaction rules covering a broad range of phase 1 and phase 2 metabolism has been derived from metabolic reactions reported in the Metabolite Database to occur in humans. An empirical probability score is assigned to each rule representing the fraction of correctly predicted metabolites in the training database. This score is used to refine the rules and to rank predicted metabolites. The current rule set of SyGMa covers approximately 70 % of biotransformation reactions observed in humans. Evaluation of the rule-based predictions demonstrated a significant enrichment of true metabolites in the top of the ranking list: while in total, 68 % of all observed metabolites in an independent test set were reproduced by SyGMa, a large part, 30 % of the observed metabolites, were identified among the top three predictions. From a subset of cytochrome P450 specific metabolites, 84 % were reproduced overall, with 66 % in the top three predicted phase 1 metabolites. A similarity analysis of the reactions present in the database was performed to obtain an overview of the metabolic reactions predicted by SyGMa and to support ongoing efforts to extend the rules. Specific examples demonstrate the use of SyGMa in experimental metabolite identification and the application of SyGMa to suggest chemical modifications that improve the metabolic stability of compounds.

Targeted RNA Interference of Cyclin A2 Mediated by Functionalized Single-Walled Carbon Nanotubes Induces Proliferation Arrest and Apoptosis in Chronic Myelogenous Leukemia K562 Cells

Abstract: Cyclin A(2) plays critical role in DNA replication, transcription, and cell cycle regulation. Its overexpression has been detected and related to many types of cancers including leukemia, suggesting that suppression of cyclin A(2) would be an attractive strategy to prevent tumor progression. Herein, we apply functionalized single wall carbon nanotubes (f-SWNTs) to carry small interfering RNA (siRNA) into K562 cells and determine whether inhibition of cyclin A(2) would be a potential therapeutic target for chronic myelogenous leukemia. The results show functionalized SWNTs can facilitate the coupling of siRNA specifically targeting human cyclin A(2) to form cyclin A(2) siRNA-f-SWNTs complexes. These functionalized SWNTs readily enter K562 cells, resulting in suppression of cyclin A(2) expression. We demonstrate that depletion of cyclin A(2) in this manner inhibits cell proliferation and promotes apoptosis, and cyclin A(2) can serve as a novel therapeutic target. siRNA against cyclin A(2) delivered by functionalized single wall carbon nanotubes may be a useful therapeutic strategy for chronic myelogenous leukemia cells. This would provide new insights on additional therapeutic options for chronic myelogenous leukemia beyond chemotherapy in light of increasing multidrug resistance.

A combinatorial approach to 2,4,6-trisubstituted triazines with potent antimalarial activity: combining conventional synthesis and microwave-assistance.

Abstract: Malaria nowadays remains one of the world’s greatest public health problems. It is responsible for two million deaths per year, mostly African children under five years old, particularly affecting peoples in developing countries. Among the four malaria species that infect humans, the parasite P. falciparum is universally considered the most aggressive. Particularly impressive is its ability in mutating forms in response to administered antiplasmodial treatment, rapidly giving rise to adaptation and resistance. Hence, it is extremely urgent to find an effective combination of antimalarial drugs, not only to improve the efficacy of the therapy, but also to prevent further development of resistance. The discovery of the great potential of artemisinin has significantly encouraged the search in this area of medicinal chemistry. However, artemisinin and its active derivatives are ideal for rapid parasite clearance and clinical recovery, but they need to be combined with longer-acting drugs to prevent recrudescence. Continuous efforts in the search for new drugs together with modeling and analytical investigations on the plasmodia mechanism of invasion have highlighted two possible important targets. The dihydrofolate reductase (DHFR) of P. falciparum is one of the few well-defined targets in antimalarial therapy. This enzyme catalyzes the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate. DHFR is considered the target of cycloguanil 1 and of other antifolates in use for anti-

Biomedical potentials of crown ethers: prospective antitumor agents.

Abstract: Crown ethers are of enormous interest and importance in chemistry, biochemistry, materials science, catalysis, separation, transport and encapsulated processes, as well as in the design and synthesis of various synthetic systems with specific properties, diverse capabilities, and programmable functions. Classical crown ethers are macrocyclic polyethers that contain 3-20 oxygen atoms separated from each other by two or more carbon atoms. They are exceptionally versatile in selectively binding a range of metal ions and a variety of organic neutral and ionic species. Crown ethers are currently being studied and used in a variety of applications beyond their traditional place in chemistry. This review presents additional applications and the ever-increasing biomedical potentials of these intriguing compounds, with particular emphasis on the prospects of their relevance as anticancer agents. We believe that further research in this direction should be encouraged, as crown compounds could either induce toxicities that are different from those of conventional antitumor drugs, or complement drugs in current use, thereby providing a valuable adjunct to therapy.

Towards small-molecule CXCR3 ligands with clinical potential.

Abstract: The CXCR3 chemokine receptor was first discovered in 1996 and has been shown to play an important role in several diseases, most of which are related to inflammation. This review describes in detail the development of small CXCR3 ligands and their therapeutic potential. Classes of CXCR3 antagonists with strikingly variable core structures have emerged. Some of these compounds have confirmed the beneficial role of CXCR3 antagonism in animal models of disease. One of the compounds, AMG487, progressed to Phase II clinical trials but has been withdrawn because of lack of efficacy. New antagonist classes are being developed to reveal the full therapeutic potential of CXCR3.

Group efficiency: a guideline for hits-to-leads chemistry.

Abstract: Herein we describe the concept of group efficiency (GE), which is an extension of ligand efficiency (LE), that we find particularly useful during the hit-tolead and optimisation stages of drug discovery projects. LE has already become popular amongst medicinal chemists. It is used to normalise the binding affinity of a compound with respect to its molecular weight and is a simple way to rank and compare the affinities of compounds with different sizes. The term LE was first suggested by Hopkins et al. as a measure of the free energy of binding (DGb) divided by the molecular size and is related to a publication from Kuntz et al. :

Identification of Putative Binding Sites of P-glycoprotein Based on its Homology Model

Abstract: A homology model of P-glycoprotein based on the crystal structure of the multidrug transporter Sav1866 is developed, incorporated into a membrane environment, and optimized The resulting model is analyzed in relation to the functional state and potential binding sites The comparison of modeled distances to distances reported in experimental studies between particular residues suggests that the model corresponds most closely to the first ATP hydrolysis step of the protein transport cycle Comparison to the protein 3D structure confirms this suggestion Using SiteID and Site Finder programs three membrane related binding regions are identified: a region at the interface between the membrane and cytosol and two regions located in the transmembrane domains The regions contain binding pockets of different size, orientation, and amino acids A binding pocket located inside the membrane cavity is also identified The pockets are analyzed in relation to amino acids shown experimentally to influence the protein function The results suggest that the protein has multiple binding sites and may bind and/or release substrates in multiple pathways

Targeting the folate receptor (FR): imaging and cytotoxicity of ReI conjugates in FR-overexpressing cancer cells.

Abstract: The synthesis, characterization, in vitro imaging, and cytotoxic properties of a new folate conjugate of rhenium(I) are reported. The conjugate [FA-PEG-BQAV-Re(CO)3]+ (gamma-4) was screened against an adriamycin- and cisplatin-resistant human ovarian cancer cell line (A2780/AD) that overexpresses the folate receptor (FR). Compound gamma-4 was internalized by a folate-receptor-mediated endocytotic pathway, which results in internal accumulation of gamma-4. This was contrasted with a FR-negative Chinese hamster ovary cell line in which no internalization of gamma-4 was observed. gamma-4 was found to be cytotoxic with IC(50) values of 189 and 78 microM at 6 and 24 h, respectively, toward the FR-positive cell line. This is in contrast to the IC(50) value of 502 microM at 6 h and 84 microM at 24 h for cisplatin in the same cell line, with a significantly greater toxicity at the earlier time point. The cytotoxicity of gamma-4 as explained by interactions that occur between the rhenium(I) complex moiety and DNA is described.

Sila-haloperidol, a silicon analogue of the dopamine (D2) receptor antagonist haloperidol: synthesis, pharmacological properties, and metabolic fate.

Abstract: Haloperidol (1 a), a dopamine (D(2)) receptor antagonist, is in clinical use as an antipsychotic agent. Carbon/silicon exchange (sila-substitution) at the 4-position of the piperidine ring of 1 a (R(3)COH --> R(3)SiOH) leads to sila-haloperidol (1 b). Sila-haloperidol was synthesized in a new multistep synthesis, starting from tetramethoxysilane and taking advantage of the properties of the 2,4,6-trimethoxyphenyl unit as a unique protecting group for silicon. The pharmacological profiles of the C/Si analogues 1 a and 1 b were studied in competitive receptor binding assays at D(1)-D(5), sigma(1), and sigma(2) receptors. Sila-haloperidol (1 b) exhibits significantly different receptor subtype selectivities from haloperidol (1 a) at both receptor families. The C/Si analogues 1 a and 1 b were also studied for 1) their physicochemical properties (log D, pK(a), solubility in HBSS buffer (pH 7.4)), 2) their permeability in a human Caco-2 model, 3) their pharmacokinetic profiles in human and rat liver microsomes, and 4) their inhibition of the five major cytochrome P450 isoforms. In addition, the major in vitro metabolites of sila-haloperidol (1 b) in human liver microsomes were identified using mass-spectrometric techniques. Due to the special chemical properties of silicon, the metabolic fates of the C/Si analogues 1 a and 1 b are totally different.

Structure-based discovery and experimental verification of novel AI-2 quorum sensing inhibitors against Vibrio harveyi.

Abstract: Quorum sensing has been implicated in the control of pathologically relevant bacterial behavior such as secretion of virulence factors, biofilm formation, sporulation, and swarming motility. The AI-2 quorum sensing pathway is found in both gram-positive and gram-negative bacteria. Therefore, antagonizing AI-2 quorum sensing is a possible approach to modifying bacterial behaviour. However, efforts in developing inhibitors of AI-2-mediated quorum sensing are especially lacking. High-throughput virtual screening using the V. harveyi LuxP crystal structure identified two compounds that were found to antagonize AI-2-mediated quorum sensing in V. harveyi without cytotoxicity. The sulfone functionality of these inhibitors was identified as critical to their ability to mimic the natural ligand in their interactions with Arg 215 and Arg 310 of the active site.

Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets.

Abstract: Similarity searching is often used to preselect compounds for docking, thereby decreasing the size of screening databases. However, integrated structure- and ligand-based screening schemes are rare at present. Docking and similarity search calculations using 2D fingerprints were carried out in a comparative manner on nine target enzymes, for which significant numbers of diverse inhibitors could be obtained. In the absence of knowledge-based docking constraints and target-directed parameter optimisation, fingerprint searching displayed a clear preference over docking calculations. Alternative combinations of docking and similarity search results were investigated and found to further increase compound recall of individual methods in a number of instances. When the results of similarity searching and docking were combined, parallel selection of candidate compounds from individual rankings was generally superior to rank fusion. We suggest that complementary results from docking and similarity searching can be captured by integrated compound selection schemes.

Synthesis and biological activity of a novel inhibitor of dihydroceramide desaturase.

Abstract: A novel mechanism-based dihydroceramide desaturase inhibitor (XM462) in which the substrate C5 methylene group is replaced by a sulfur atom is reported. Dihydroceramide desaturase inhibition occurred both in vitro and in cultured cells with IC(50) values of 8.2 and 0.78 microM, respectively, at a substrate concentration of 10 microM. In vitro experiments showed that XM462 produced a mixed-type inhibition (K(i)=2 microM, alpha=0.83). LC-MS analyses showed that accumulation of endogenous dihydroceramides occurred in cells upon treatment with XM462 in serum-free medium, whereas ceramides built up in controls. In addition, XM462 was found to be metabolised to its 1-glucosyl and 1-phosphocholine derivatives, and to the products of N-deacylation and reacylation with palmitoyl and stearoyl groups. In Jurkat A3 cells cultured in serum-free medium, viability, as the percentage of trypan blue unstained cells in total cells, was reduced upon XM462 treatment (5 microM, 24 h), but not in controls. The interest of this compound is discussed.