AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore

PL02-05 

All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Patterns of Somatic Mutation in Human Cancer Genomes

Dramatic accumulation of proline due to increased synthesis and decreased degradation under a variety of stress conditions such as salt, drought and metal has been documented in many plants. Similarly, a decrease in the level of accumulated proline in the rehydrated plants is due to both down regulation of proline biosynthetic pathway enzymes and upregulation of proline degrading enzymes. But, the role of proline during plant development and the molecular basis of the effect of proline accumulation during stress and upon relief of stress are still largely obscure. Here, we summarize the genes governing the proline biosynthetic pathway, its degradation and regulation. Sequentially, we provide an account on transgenics raised so far to engineer the overproduction of osmolyte proline. Also, the identification of specific cellular pathways involved in proline biosynthesis and metabolic changes occurring in transgenic plants developed for proline enhancements are discussed. Further, emphasis is also made on an untouched area of signal transduction of proline biosynthetic pathway.

Regulation of proline biosynthesis, degradation, uptake and transport in higher plants: Its implications in plant growth and abiotic stress tolerance

Enzyme stabilization—recent experimental progress

Proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress

pH-dependent structures and properties of casein micelles

Compatibility of osmolytes with Gibbs energy of stabilization of proteins.

MAP/Microtubule affinity-regulating kinase 4 (MARK4) belongs to the family of serine/threonine kinases that phosphorylate the microtubule-associated proteins (MAP) causing their detachment from the microtubules thereby increasing microtubule dynamics and facilitating cell division, cell cycle control, cell polarity determination, cell shape alterations, etc. The MARK4 gene encodes two alternatively spliced isoforms, L and S that differ in their C-terminal region. These isoforms are differentially regulated in human tissues including central nervous system. MARK4L is a 752-residue-long polypeptide that is divided into three distinct domains: (1) protein kinase domain (59–314), (2) ubiquitin-associated domain (322–369), and (3) kinase-associated domain (703–752) plus 54 residues (649–703) involved in the proper folding and function of the enzyme. In addition, residues 65–73 are considered to be the ATP-binding domain and Lys88 is considered as ATP-binding site. Asp181 has been proposed to be the active site of MARK4 that is activated by phosphorylation of Thr214 side chain. The isoform MARK4S is highly expressed in the normal brain and is presumably involved in neuronal differentiation. On the other hand, the isoform MARK4L is upregulated in hepatocarcinoma cells and gliomas suggesting its involvement in cell cycle. Several biological functions are also associated with MARK4 including microtubule bundle formation, nervous system development, and positive regulation of programmed cell death. Therefore, MARK4 is considered as the most suitable target for structure-based rational drug design. Our sequence, structure- and function-based analysis should be helpful for better understanding of mechanisms of regulation of microtubule dynamics and MARK4 associated diseases.

Microtubule Affinity-Regulating Kinase 4: Structure, Function, and Regulation

This study is a systematic attempt to understand the roles of non-compatible osmolytes, i.e. solutes that have inhibitory effects on enzymes, in the stabilization of proteins against denaturing stress. Thermal denaturation of RNase A, holo-alpha-lactalbumin, apo-alpha-lactalbumin, lysozyme and metmyoglobin in the absence and presence of various concentrations of free basic amino acids was studied by observing changes in the absorption coefficients of these proteins. It has been observed that arginine and histidine destabilize all proteins in terms of the midpoint of the transition curve and Gibbs energy change on denaturation. Study of the heat-induced denaturation of the proteins in the presence of various concentrations of arginine at different pH values demonstrated that arginine binds to the denatured molecules. In contrast with the effect of arginine and histidine on protein stability, it was observed that the effect of lysine on proteins stability is unpredictable, i.e. it may have a stabilizing effect, no effect or a destabilizing effect on proteins during denaturing stress. The results of this study are considered from an evolutionary perspective.

Role of non-compatible osmolytes in the stabilization of proteins during heat stress

Background: New Delhi metallo-β-lactamase-1 (NDM-1)-producing Gram-negative bacteria are today's major worldwide health concern. The enzyme NDM-1 provides bacterial resistance by its hydrolytic activity against the β-lactam ring of antibiotics. Inhibition of NDM-1 may prevent the hydrolysis of β-lactam ring of the antibiotics, and therefore, plays an important role against antibacterial resistance. Materials and Methods: Here we made an attempt to design suitable inhibitors against NDM-1 from different natural antibacterial compounds using molecular docking approach. Results: We observed that natural compounds such as Nimbolide and Isomargololone are showing an appreciable IC50 value as well as significant binding energy value for NDM-1. We further observed these compounds showing better affinity to NDM-1 on comparison with 14 β-lactam antibiotics. Conclusion: Finally, our study provides a platform for the development of a potent inhibitor of NDM-1, which may be considered as a potential drug candidate against bacterial resistance.

Search of potential inhibitor against New Delhi metallo-beta-lactamase 1 from a series of antibacterial natural compounds

Testing the paradigm that the denaturing effect of urea on protein stability is offset by methylamines at the physiological concentration ratio of 2:1 (urea:methylamines).

Farah Anjum

Papers

Compatibility of osmolytes with Gibbs energy of stabilization of proteins.

Microtubule Affinity-Regulating Kinase 4: Structure, Function, and Regulation

Role of non-compatible osmolytes in the stabilization of proteins during heat stress

Search of potential inhibitor against New Delhi metallo-beta-lactamase 1 from a series of antibacterial natural compounds

Testing the paradigm that the denaturing effect of urea on protein stability is offset by methylamines at the physiological concentration ratio of 2:1 (urea:methylamines).