Current Topics in Medicinal Chemistry - Volume 8, Issue 15, 2008

DNA is our “blueprint” and it can be envisioned as a pristine code that contains the instructions for life. However, DNA has inherent problems to be maintained as a pristine code. DNA has to be replicated with almost perfect accuracy, and as an organic molecule it can react with chemical substances of the cellular milieu. The DNA polymerases that replicate our DNA are far from perfect. Our nuclear replicative DNA polymerases, DNA polymerases δ and ε, make a mistake in approximately 5x105 of their incorporation events, although this accuracy is enormous, it is compromised along the replication of the billions of base pairs that comprise our genome. DNA polymerase γ, our replicative mitochondrial DNA polymerase, makes a mistake in approximately 1x104 attempts; however we are born with a set of mitochondrial DNA molecules that have to be maintained nearly intact during our life. Although the fidelity of DNA polymerases can seem reasonable, DNA is prone to react with chemical substances that can alter its coding potential. For instance, guanosine can react with reactive oxidative species to be converted to 8-oxo guanosine, and when a normally faithful replicative DNA polymerase, like T7 DNA polymerases encounters 8-oxo guanosine as a template, it will misincorporate dATP in approximately one of three events. In order to maintain DNA as the pristine code, humans have evolved a series of metabolic pathways that maintain its integrity, both in the nuclei and in the mitochondria. This issue of Current Topics in Medicinal Chemistry addresses the interplay between “Nucleic Acids Metabolism and Human Disease”. The first review provides a brief summary of human template dependent DNA polymerases, with emphasis in their structure and their association with human diseases. In the second review, Hector Viadiu revisits the structural significance of the transcription factor p53 as a tumor suppressor. All the effort to understand the structure of p53 rests in the goal to restore wild type p53 activity by rational efforts, as p53 plays a pivotal role in cancer development. Mitochondria are the organelle responsible to synthesize ATP, the molecule used as the energy source by the cell. The team leaded by Xochilt Perez-Martínez reviews the state of the art knowledge in protein synthesis and assembly at the mitochondria, and the link of specific mutations of the mitochondria macromolecular assemblies involved in translation and protein folding with mitochondrial disorders. The team leaded by Rafael Montiel reviews the link between mitochondrial DNA mutations and cancer. This review contains a comprehensive list of somatic mitochondrial mutations that have been observed in cancer tissues. In the fifth review, Felix Recillas-Targa discusses the links between epigenetic regulation and novel therapeutic approaches in cancer. The last two reviews highlight the role of DNA as a therapeutic agent. Luis M. Alvarez-Salas reviews the role of therapeutic nuclei acids, such as nucleosides, nucleotides, ribozymes, antisense aptamers, and small interfering RNA, with an emphasis in those therapeutic nucleic acids that are in clinical trials in cancer and viral diseases. Anna Arola and Raul Vilar discuss the use of small molecules that promote the stabilization of quadruplex DNA. The stabilization of quadruplex DNA opens the possibility to be use as a potential target for rational drug design against cancer. Finally, I thank Dr. Allen Reitz for the opportunity to serve as a Guest Editor of this issue and to the authors whom kindly wrote their insightful contributions.

The genetic material in humans contains approximately 6 billion base pairs in the nuclear genome and 16,569 base pairs in the mitochondrial genome [1-3]. In some cases the difference between a healthy and a sick individual consists in only one nucleotide. Thus, it is evident that the pristine replication of the genome is a key event in the avoidance of mutations and therefore diseases. Although it is generally believed that DNA is an inert molecule, it contains reactive groups that are exposed to a multitude of chemical agents like Reactive Oxidative Species (ROS), xenobiotic compounds, and UV light which can react with DNA to form adducts that compromise its coding potential. For instance, it is estimated that a mammalian genome suffers close to 100,000 abasic sites per day [4, 5]. In general, replicative DNA polymerases are responsible for maintaining the integrity of the genome during it replication, family X polymerases are important in DNA repair mechanisms, and Translesion Synthesis DNA polymerases ensure the faithful replication across from DNA lesions. This revision attempts to briefly summarize the role of human template dependent DNA polymerases involved in replication, DNA repair, and lesion bypass.

p53 is a transcription factor central to cellular DNA metabolism that controls cellular responses to DNA damage. p53 activity, finely regulated, integrates the information from several pathways to preserve the cell's genetic information. Great attention has been given to the structural determination of p53 domains and its cancerous mutants because 50% of cancer cases present mutations in p53 that hinder its activity resulting in uncontrolled cell reproduction. We enumerate the multiple studies carried to elucidate the structure of p53 domains and we highlight their main findings. The ultimate goal of the reviewed structural efforts is to understand p53 function at atomic level with the aim to overcome cancer by reversing p53 mutant activity to its normal function.

Human mitochondrial DNA (mtDNA) codes for 13 polypeptides which constitute the central core of the oxidative phosphorylation (OXPHOS) complexes. The machinery for mitochondrial protein synthesis has a dual origin: a full set of tRNAs, as well as the 12S and 16S rRNAs are encoded in the mitochondrial genome, while most factors necessary for translation are encoded by nuclear genes. The mitochondrial translation apparatus is highly specialized in expressing membrane proteins, and couples the synthesis of proteins to the insertion into the mitochondrial inner membrane. In recent years it has become clear that defects of mitochondrial translation and protein assembly cause several mitochondrial disorders. Since direct studies on protein synthesis in human mitochondria are still a relatively difficult task, we owe our current knowledge of this field to the large amount of genetic and biochemical studies performed in the yeast Saccharomyces cerevisiae. These studies have allowed the identification of several genes involved in mitochondrial protein synthesis and assembly, and have provided insights into the conserved mechanisms of mitochondrial gene expression. In the present review we will discuss the most recent advances in the understanding of the mechanisms and factors that govern mammalian mitochondrial translation/protein insertion, as well as known pathologies associated with them.

As mitochondria participate in fundamental process of the cellular metabolism, recent research has addressed the role of mitochondria, and of mitochondrial DNA (mtDNA), in apoptosis, aging, and complex diseases. The association between mtDNA and cancer has been discussed since the beginning of the last century, and more recently, it has gained attention due to the observation of many somatic mutations in several types of cancers. In this review we describe those germinal mutations that have been associated to cancer, and present a compilation of somatic mutations that have been observed in different cancer tissues, describing relevant characteristics among them in a phylogenetic context. We also summarize the drawbacks and criticisms made towards the studies that report an association between mtDNA mutations and cancer, and discuss the experimental models used to analyse this relationship. Although many reported somatic mutations may actually be the outcome of laboratory artefacts, a considerable number could be authentic and may have a relationship with cancer development. In our compilation, we have observed 271 cancer mutations occurring in conserved positions of mtDNA, 70 of them appearing in more than one tumour. These mutations may be candidates to be used as cancer biomarkers, and deserve further investigation, perhaps through the use of experimental models and by an analysis of tumours of distinct grade to determine if the mutations arose early during tumourigenesis. Experiments with cybrids have been successfully used; however, models are needed in which specific mtDNA variants may be introduced into the same mitochondrial and cellular background.

The interdependency between genetic and epigenetic regulatory processes renders cancer therapeutics and translational clinic possible, even though they remain difficult tasks considering all the evidence supporting a central role of progenitor-stem cells as a causative source of cellular transformation. In contrast to genetic alterations, epigenetic processes are potentially reversible allowing a better action of complementary therapeutic compounds. Here I would first describe the plethora of interconnected epigenetic processes and targets to then discuss several therapeutic strategies on the basis of different compounds. I conclude that the advent of new and specific epigenetic target drugs will certainly contribute to better treatments and to the development of predictive protocols in a next future.

Therapeutic nucleic acids (TNAs) and its precursors are applied to treat several pathologies and infections. TNA-based therapy has different rationales and mechanisms and can be classified into three main groups: 1) Therapeutic nucleotides and nucleosides; 2) Therapeutic oligonucleotides; and 3) Therapeutic polynucleotides. This review will focus in those TNAs that have reached clinical trials with anticancer and antiviral protocols, the two most common applications of TNAs. Although therapeutic nucleotides and nucleosides that interfere with nucleic acid metabolism and DNA polymerization have been successfully used as anticancer and antiviral drugs, they often produce toxic secondary effects related to dosage and continuous use. The use of oligonucleotides such as ribozyme and antisense oligodeoxynucleotides (AS-ODNs) showed promise as therapeutic moieties but faced several issues such as nuclease sensitivity, off-target effects and efficient delivery. Nevertheless, immunostimulatory oligodeoxynucleotides and AS-ODNs represent the most successful group of therapeutic oligonucleotides in the clinic. A newer group of therapeutic oligonucleotides, the aptamers, is rapidly advancing towards early detection and treatment alternatives the have reached the commercial interest. Despite the very high in vitro efficiency of small interfering RNAs (siRNAs) they present issues with intracellular target accessibility, specificity and delivery. DNA vaccines showed great promise, but they resulted in very poor responses in the clinic and further development is uncertain. Despite their many issues, the exquisite specificity and versatility of therapeutic oligonucleotides attracts a great deal of research and resources that will certainly convert them in the TNA of choice for treating cancer and viral diseases in the near future.

Guanine-rich sequences of DNA can form quadruply-stranded structures. It has been shown that folding singlestranded telomeric DNA into a quadruplex structure inhibits telomerase (an enzyme overexpressed in 85-90% of cancer cells). On the other hand, it has been hypothesised that the formation of quadruplex DNA structures in the promoter region of some oncogenes plays an important role in regulating the transcription of the corresponding gene. Consequently, there is great current interest in developing small molecules that can bind selectively to quadruplex DNA and in doing so could act as anticancer drugs. This review aims to discuss the different types of ligands that have been recently developed as quadruplex DNA stabilisers. The review is organised by the type of compound and mainly covers the literature between 2004 and 2007.

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