Neural network techniques for informatics of cancer drug discovery

Network models in drug discovery and regenerative medicine

Network motifs and modelling paradigms are attracting increasing attention as modelling tools in drug design and development, and in regenerative medicine. There is a gradual but inexorable convergence between these hitherto disparate disciplines. This review summarizes some very recent work in these areas, leading to an understanding of the complementary roles networks play and factors driving this convergence: network paradigms can be excellent ways of modelling and understanding drug molecules and their action, an understanding of the robustness and vulnerabilities of biological targets may improve the efficacy of drug design and discovery, drug design has an increasingly large role to play in directing stem cell properties, stem cell regulatory networks can be modelled in useful ways using network models at a reasonable level of scale, and the network tools of drug design are also very useful for the design of biomaterials used in regenerative medicine.

Ethidium and proflavine binding to a 2',5'-linked RNA duplex

Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.

Transcriptomic analysis of the NCI-60 cancer cell lines

Pharmacogenomics aims at molecular subsetting of patients for more effective therapy. Transcriptomic profiling of the 60 human cancer cell lines (the NCI-60) used by the US National Cancer Institute serves that aim because the cells have been treated with > 100,000 chemical compounds over the last 13 years. Patterns of potency can be mapped into molecular structures of the compounds or into molecular characteristics of the cells. We discuss conceptual and experimental aspects of the profiling, as well as a number of bioinformatic computer programs that we have developed for biological interpretation of the profiles.

Triplex selective 2-(2-naphthyl)quinoline compounds: origins of affinity and new design principles

A novel competition dialysis assay was used to investigate the structural selectivity of a series of substituted 2-(2-naphthyl)quinoline compounds designed to target triplex DNA. The interaction of 14 compounds with 13 different nucleic acid sequences and structures was studied. A striking selectivity for the triplex structure poly dA:[poly dT](2) was found for the majority of compounds studied. Quantitative analysis of the competition dialysis binding data using newly developed metrics revealed that these compounds are among the most selective triplex-binding agents synthesized to date. A quantitative structure-affinity relationship (QSAR) was derived using triplex binding data for all 14 compounds used in these studies. The QSAR revealed that the primary favorable determinant of triplex binding free energy is the solvent accessible surface area. Triplex binding affinity is negatively correlated with compound electron affinity and the number of hydrogen bond donors. The QSAR provides guidelines for the design of improved triplex-binding agents.

Advances in biomedical informatics for the management of cancer

Increased access to health care, and advances in education and technology have resulted in a larger proportion of the population having longer life expectancy. The strong correlation between age and cancer has resulted in a major healthcare problem for this century, and until recently cancer has defied any long-lasting cure. However, progress, especially in the field of biomedical informatics, promises a successful prediction and possibly a permanent cure for cancer within the next two decades. Biomedical informatics-with its roots in computer science, biomedical engineering, biostatistics, and mathematics-helps to bring the patient closer to the physician, facilitates access to specialist information and knowledge bases across the world, and makes it possible to identify genetic expression profiles for malignant or cancerous cells. This paper reviews the new research findings in biomedical informatics, working toward the ultimate goal of successfully predicting cancer, solving complex problems in prevention and treatment of cancer, and perhaps completely curing the scourge of cancer.

Hydration changes for DNA intercalation reactions

The hydration changes that accompany the DNA binding of five intercalators (ethidium, propidium, proflavine, daunomycin, and 7-aminoactinomycin D) were measured by the osmotic stress method with use of the osmolytes betaine, sucrose, and triethylene glycol. Water uptake was found to accompany complex formation for all intercalators except ethidium. The difference in the number of bound water molecules between the complex and the free reactants (Deltan(w)) was different for each intercalator. The values found for Deltan(w) were the following: propidium, +6; daunomycin, +18; proflavine, +30; and 7-aminoactinomycin D, +32. For ethidium binding to DNA a value of Deltan(w) = +0.25(+/-0.3) was found, indicating that within experimental error no water was released or taken up upon complex formation. Intercalation association constants measured in D2O were found to increase relative to values measured in H2O for all compounds except ethidium. A positive correlation between the ratio of binding constants (K(D2O)/K(H2O)) and Deltan(w) was found. These combined studies identify water as an important thermodynamic participant in the formation of certain intercalation complexes.