Innovative Drug Targets Research Articles

A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations.

The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.

Lipoprotein association studies: taking stock and moving forward

Over the last year, huge progress has been made using SNP arrays to identify genes associated with lipid traits. The single genome-wide association studies (GWASs) may have reached a limit in identifying novel genes, but there has been tremendous progress from collaborative consortia examining pooled data from GWASs, often employing SNP imputation. For example, the Global Lipid Consortium reported that 56 of the 95 lipid-associated loci were novel to the pooled analysis from over 100 000 individuals. Complementary to this, a gene-centric approach, such as the 50K IBC HumanCVD chip, which provides deep coverage of approximately 2100 genes, has had success in ascertaining independently acting variants and helped us to move a step closer to identify functional variants. Yet irrespective of the platform used, for each trait, the percentage variance explained by these genes remains in the order of approximately 10-12% and it is still unclear to what extent rare mutations, identified by resequencing or exome sequencing approaches, or gene × gene and gene × environment studies, might boost this. GWAS-identified novel lipid-related loci highlight new pathways in lipid metabolism and may provide innovative drug targets. Furthermore, the use of lipid gene scores, over and above a single lipid measure, may have clinical utility.

Stem Cells of the Breast and Cancer Therapy

Breast cancer remains a significant public health problem despite advances in the understanding of the molecular and cellular events that underlie the disease. Crucial pathways regulating the cell cycle, proliferation and survival of breast cancer cells have been investigated and aberrant components of these pathways have been exploited as new drug targets. However, the mortality from breast cancer is only slowly declining. Recently, a model has been proposed that might explain the heterogeneous biological features of breast cancer cell populations and their differential response to therapeutic agents, which has interesting implications for further progress in therapy. This model links the emergence of breast cancer cells to stem cells and progenitors, an observation originally made in other cancer entities. It hypothesizes that the tumors originate from a small population of undifferentiated cells. These cells can undergo self-renewal and are able to generate a large number of partially differentiated cells, which constitute the bulk of the tumor. These cancer stem cells resemble adult stem and progenitor cells found in the normal breast, but are deregulated in their patterns of proliferation and differentiation. They could originate from normal stem cells or from more differentiated progenitors and lose their normal growth restraints through a series of oncogenic mutations that deregulate a small number of central signaling pathways. If breast cancer really is a stem and progenitor cell disease, this will have important implications for the understanding of the emergence of cancer cells. A combination of the cell-type of origin, stem cells, early or late progenitors and the particular oncogenic mutations acquired could provide a new classification of the different types of breast cancer. These parameters might determine the mechanisms of cancer progression and the responsiveness of patients to drug treatment. Stem cell-specific features could possibly be exploited as innovative drug targets.

BK Channel Modulators: A Comprehensive Overview

The large Ca(2+)-activated K(+) channel (BK channel) reflects per excellence the dilemma of the molecular target driven drug discovery process. Significant experimental evidence suggests that the BK channels play a pivotal and specific role in many pathophysiological conditions supporting the notion that the channel represents an innovative and promising drug target. However, after more than ten years of intense research effort both in academia and industry, scientists have yet to witness the approval of a single BK channel modulator for clinical use. On the contrary, three BK openers that were progressed to clinical development have recently been discontinued (NS8, BMS204352 and TA1702) and, at the present time, only one drug candidate targeting BK channels (andolast) remains in the early phases of clinical development. Since biological studies keep strengthening the concept of BK channels as a potentially attractive target, the design and synthesis of potent and selective BK modulators continue based on novel chemical ideas. A comprehensive overview of BK channel modulators is therefore timely and important to the current medicinal chemist for review, summary, and classification of the multitude of chemical entities claimed to be BK-modulating agents. Such chemical entities are, herein, classified by both origin and chemical structure in 1) Endogenous BK channel modulators and structural analogues 2) Naturally-occurring BK channel inhibitors and blockers 3) Synthetic BK channel inhibitors and blockers 4) Marketed and/or investigational drugs with BK-modulating side properties and structural analogues 5) Naturally-occurring BK channel openers and structural analogues 6) Synthetic BK channel openers. This review is intended to provide readers with current opinion on the BK channel as a drug target, the chemical structures of BK channel modulators, the structural and chemical features involved in the BK channel modulating activity and, where and when possible, with highlights of structure-activity relationships.

The Role of DNA-Microarray in Translational Cancer Research

The overall prognosis for the majority of cancer patients remains poor. Current conventional strategies in clinical cancer research are unable to adequately answer a large number of important unsolved questions. Although some patients achieve substantial benefits from classical cytotoxic chemotherapy, others will not. The mechanisms behind this phenomenon are still not identified in detail. Furthermore, the activity of promising novel molecular targeting anticancer agents like tyrosinkinase inhibitors is currently not predictable within the individual patient. The biological background for this clinical and prognostic heterogeneity in behavior is more or less the large individual variation in the biological nature of tumors within the same classified histological subgroup. The overall usefulness of conventional histopathological classifications to adequately predict patient prognosis or response to chemotherapy is limited. The most promising way to solve this issue is to found clinical research strategies on basic biological evidence. New genomic technologies have been developed within recent years. These techniques are able to analyze thousands of genes and their expression profiles simultaneously. An increasing number of investigations has reported applications of these novel technologies within clinical trials settings. The aim of this approach is to identify new subsets of cancer patients, to improve prediction of their clinical outcome or response to treatment and select new targets for innovative therapeutic drugs based on the findings from gene expression profiles. Results of these gene expression profile studies could potentially lead to more individually tailored systemic cancer therapy. In the recent years, a remarkable number of studies based on these techniques have already been reported. Although the published results are clearly impressive and highly promising, a lot of work remains to be done. Moreover, there is a strong need for an increase in reliability and reproducibility of such gene expression profiling techniques and thus introduction of reproducible quality control in the performance of these assays. Although a large number of issues remain to be clarified prior to a more general application of genomic profiling techniques in clinical cancer research, this strategy will eventually turn out as a promising approach to improve successful management of cancer patients. Keywords: chemotherapy, tumor biology, breast cancer, predictor, lung cancer, gastrointestinal cancer, retinoblastoma-binding protein.

Deductive Genomics: a Functional Approach to Identify Innovative Drug Targets in the Post-Genome Era

Deductive Genomics: a Functional Approach to Identify Innovative Drug Targets in the Post-Genome Era

Commentary on the article presented by Murdoch et al.

British Journal of Pharmacology (2003) 138, 731–731. doi:10.1038/sj.bjp.0705122