The Ras superfamily of small monomeric GTPases includes some of the most prominent cancer targets for which no selective therapeutic agent has yet been successfully developed. The turn of the millennium saw a resurgence of efforts to target these enzymes using new and improved biophysical techniques to overcome the perceived difficulties of insurmountably high affinity for guanosine nucleotides and flat, flexible topology lacking suitable pockets for small molecule inhibitors. Further, recent investigations have begun to probe the dynamic conformational status of GTP-bound Ras, opening up new mechanisms of inhibition. While much of the literature has focused on the oncogenic Ras proteins, particularly K-Ras, these represent only a small minority of therapeutically interesting targets within the superfamily; for example, the Rab GTPases are the largest subfamily of about 70 members, and present an as yet untapped class of potential targets. The present review documents the key methodologies employed to date in structure-guided attempts to drug the Ras GTPases, and forecasts their transferability to other similarly challenging proteins in the superfamily.
Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27aMut, crystallized within 24 h and diffracted to 2.82 Å resolution, with a unit cell possessing room for a large number of protein copies. Initial efforts to solve the structure using molecular replacement by Phaser were not successful. Analysis of the data set revealed that the crystals suffered from both extreme anisotropy and strong tNCS. As a result, large numbers of reflections had estimated standard deviations that were much larger than their measured intensities and their expected intensities, revealing problems with the use of such data at the time in Phaser. By eliminating extremely weak reflections with the largest combined effects of anisotropy and tNCS, these problems could be avoided, allowing a molecular-replacement solution to be found. The lessons that were learned in solving this structure have guided improvements in the numerical analysis used in Phaser, particularly in identifying diffraction measurements that convey very little information content. The calculation of information content could also be applied as an alternative to ellipsoidal truncation. The post-mortem analysis also revealed an oversight in accounting for measurement errors in the fast rotation function. While the crystal of mutant Rab27a is not amenable to drug screening, the structure can guide new modifications to obtain more suitable crystal forms.
A novel Rab27A construct enables elucidation of covalent ligand binding, paving the way for structure-guided approaches against this challenging target.
Cyclooxygenase-2 (COX-2) enzyme is believed to play a role in tumor angiogenesis, differentiation, and apoptosis. The inducible isoform of nitric oxide synthase (iNOS) also has the potential ability to damage DNA and conceivably contribute to tumor formation by a rise in nitric oxide production. Seventeen patients diagnosed with colorectal adenocarcinoma, who underwent surgical resection of the tumor, were enrolled in the study. Two macroscopic tissue samples, one from the tumor and the other from the tumor free surgical margin were collected from every patient as formalin fixed paraffin embedded blocks. Samples were analyzed for iNOS and COX-2 expression by immunohistochemistry and Western blotting. Results were digitized and semi-quantitatively analyzed. Immunohistochemistry revealed a similar pattern of expression for both iNOS and COX-2, as both were detected in tumor and epithelial cells. The mean iNOS and COX-2 levels determined by Western blotting method were significantly higher in tumor than in the tumor-free tissues (Wilcoxon signed-rank test, p < 0.001 both for iNOS and COX-2). Patients with lymph node involvement had higher levels of both enzymes in tumors (Mann-Whitney U test, p < 0.05). There was correlation between iNOS and COX-2 expression of tumor determined by immunohistochemistry and also by Western blotting (Spearman's rho test, R = 0.53, p = 0.03 and R = 0.57, p = 0.02, respectively). In conclusion, our results point out a relationship between iNOS and COX-2 expression in human colorectal adenocarcinomas and may also suggest a possible link between advanced stages of the disease and higher expression of iNOS and COX-2.
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