ABSTRACT
Recent studies on cyclin-dependent kinase (CDK) inhibitors have revealed that small molecule drugs have become very attractive for the treatment of cancer and neurodegenerative disorders. Most CDK inhibitors have been developed to target the ATP binding pocket. However, CDK kinases possess a very similar catalytic domain and three-dimensional structure. These features make it difficult to achieve required selectivity. Therefore, inhibitors which bind outside the ATP binding site present a great interest in the biomedical field, both from the fundamental point of view and for the wide range of their potential applications. This review tries to explain whether the ATP competitive inhibitors are still an option for future research, and highlights alternative approaches to discover more selective and potent small molecule inhibitors.
Subject(s)
Cyclin-Dependent Kinases , Neoplasm Proteins , Neoplasms , Neurodegenerative Diseases , Protein Kinase Inhibitors , Binding Sites , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/chemistry , Cyclin-Dependent Kinases/metabolism , Humans , Neoplasm Proteins/antagonists & inhibitors , Neoplasm Proteins/chemistry , Neoplasm Proteins/metabolism , Neoplasms/drug therapy , Neoplasms/enzymology , Neurodegenerative Diseases/drug therapy , Neurodegenerative Diseases/enzymology , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/therapeutic use , Structure-Activity RelationshipABSTRACT
Methylation of the promoter of the BRCA1 gene in DNA derived from peripheral blood cells is a possible risk factor for breast cancer. It is not clear if this association is restricted to certain types of breast cancer or is a general phenomenon. We evaluated BRCA1 methylation status in peripheral blood cells from 942 breast cancer patients and from 500 controls. We also assessed methylation status in 262 paraffin-embedded breast cancer tissues. Methylation status was assessed using methylation-sensitive high-resolution melting and was categorized as positive or negative. BRCA1 methylation in peripheral blood cells was strongly associated with the risk of triple-negative breast cancer (TNBC) (odds ratio [OR] 4.70; 95% confidence interval [CI]: 3.13-7.07; p < 0.001), but not of estrogen-receptor positive breast cancer (OR 0.80; 95% CI: 0.46-1.42; p = 0.46). Methylation was also overrepresented among patients with high-grade cancers (OR 4.53; 95% CI: 2.91-7.05; p < 0.001) and medullary cancers (OR 3.08; 95% CI: 1.38-6.88; p = 0.006). Moreover, we detected a significant concordance of BRCA1 promoter methylation in peripheral blood and paired tumor tissue (p < 0.001). We found that BRCA1 promoter methylation in peripheral blood cells is associated with approximately five times greater risk of TNBC. We propose that BRCA1 methylation in blood-derived DNA could be a novel biomarker of increased breast cancer susceptibility, in particular for triple-negative tumors.
Subject(s)
BRCA1 Protein/genetics , Biomarkers, Tumor/genetics , Genetic Predisposition to Disease , Promoter Regions, Genetic/genetics , Triple Negative Breast Neoplasms/genetics , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/blood , Breast/pathology , Case-Control Studies , DNA Methylation , Female , Follow-Up Studies , Humans , Middle Aged , Triple Negative Breast Neoplasms/blood , Triple Negative Breast Neoplasms/pathologyABSTRACT
Translation on the ribosome is controlled by external factors. During polypeptide lengthening, elongation factors EF-Tu and EF-G consecutively interact with the bacterial ribosome. EF-Tu binds and delivers an aminoacyl-tRNA to the ribosomal A site and EF-G helps translocate the tRNAs between their binding sites after the peptide bond is formed. These processes occur at the expense of GTP. EF-Tu:tRNA and EF-G are of similar shape, share a common binding site, and undergo large conformational changes on interaction with the ribosome. To characterize the internal motion of these two elongation factors, we used 25 ns long all-atom molecular dynamics simulations. We observed enhanced mobility of EF-G domains III, IV, and V and of tRNA in the EF-Tu:tRNA complex. EF-Tu:GDP complex acquired a configuration different from that found in the crystal structure of EF-Tu with a GTP analogue, showing conformational changes in the switch I and II regions. The calculated electrostatic properties of elongation factors showed no global similarity even though matching electrostatic surface patches were found around the domain I that contacts the ribosome, and in the GDP/GTP binding region.
Subject(s)
Guanosine Triphosphate/chemistry , Molecular Dynamics Simulation , Peptide Elongation Factor G/chemistry , Peptide Elongation Factor Tu/chemistry , RNA, Transfer, Amino Acyl/chemistry , Ribosomes/chemistry , Binding Sites , Guanosine Diphosphate/chemistry , Guanosine Diphosphate/metabolism , Guanosine Triphosphate/metabolism , Models, Molecular , Motion , Peptide Elongation Factor G/biosynthesis , Peptide Elongation Factor G/metabolism , Peptide Elongation Factor Tu/biosynthesis , Peptide Elongation Factor Tu/metabolism , Protein Binding , Protein Biosynthesis/physiology , Protein Conformation , RNA, Transfer, Amino Acyl/metabolism , Ribosomes/metabolism , Thermus/enzymology , Thermus/metabolismABSTRACT
Dynamics, structures, energetics, and vibrational spectra of the ternary complexes of hydrogen chloride with either methanol and water or methanol and ammonia were investigated by on-the-fly molecular dynamics and ab initio and density functional theory (DFT) with aug-cc-pvDZ basis sets. Addition of CH3OH to the HCl-NH3 system catalyzes the proton transfer from HCl to NH3. However, the dynamics of the system show that the proton is not localized on NH3; rather, it is shared between N and Cl.
