Current Chemical Biology - Volume 2, Issue 3, 2008

Simulation of the correct side chain conformations of amino acid residues is an intriguing issue not only for computational biology, but also for practical outcomes in biotechnology and medicine. This is also a main challenge for molecular simulations, since even in the homology modelling strategy (which uses templates to predict the unknown structure of a protein), the conformation of a side chain generally cannot be easily deduced from the structure of the template. It is important also for applications such as molecular design and docking. Moreover, the correct simulation of the effects of amino acid mutations occurring in many genetic diseases may help in understanding the molecular mechanisms that underlie those pathologies. This review aims to summarize the different strategies developed to predict side chain conformations in proteins. In the current review, differences in approaches are discussed and problems are analyzed, as well as parameters and criteria to compare and evaluate performances of the programs.

This comprehensive review describes contemporary computational (in silico) quantitative structure-activity relationship (QSAR) approaches that have been used to elucidate the molecular features that influence the Absorption, Distribution, Metabolism and Elimination (ADME) of drugs. Recent studies have applied 2D and 3D QSAR, pharmacophore approaches and nonlinear techniques (for example: recursive partitioning, neural networks and support vector machines) to model ADME processes. Furthermore, this review highlights some of the challenges and opportunities for future research; the need to develop ‘global’ models and to extend the QSAR for the protein transporters that influence ADME.

Protein mobility, chromatin movement and the formation of molecular assemblies in the cell nucleus have, until fairly recently, been viewed in a pseudo-static light, even though the dynamics of other cellular regions have been partly, or wholly understood for a number of years. The new science that has recently emerged on nuclear kinetics reveals a nucleus that has mobile proteins, dynamic intra-nuclear compartments and chromatin that is far from being static. This new knowledge has given scientists a deeper understanding of transcription, translation and the cell cycle. With these fundamentals of nuclear operation, has come a greater understanding of genetics and genetic diseases - so much so that, by way of example, diseases of chromatin have as a category, made significant advances. Whilst certain questions relating to protein mobility, chromatin movement and the formation of molecular assemblies have been answered, many key questions still remain. Those remaining questions have now started to be answered by technological developments. This review marshals the latest scientific evidence on the molecular kinetics of the nucleus that has arisen from a number of recent, elegant experiments.

Organophosphates (OPs) are a class of synthetic compounds used both as pesticides and nerve agents. They are chemically phosphoesters and biologically potent irreversible inhibitors of serine esterases, particularly acetylcholinesterase (ACh), the key enzyme of the nervous system. Enzymes able to degrade these compounds are at the moment the focus of several research studies in the environmental decontamination/detoxification field. OP hydrolysing enzymes have been found in Bacteria, Archaea and Eukarya. The best known and characterised enzyme is phosphotriesterase from the soil bacterium Pseudomonas diminuta (PTE). It shows a high catalytic activity, close to the molecular diffusion limit, against some triester organophosphates. Its natural substrate and its main physiological function are still unknown. In the last few years, two phosphotriesterase activities have been found in the hyperthermoacidophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, which have been ascribed to two PTE-related genes (ssopox and sacpox). The corresponding proteins, SsoPox and SacPox, have recently been inserted in the Phosphotriesterase-Like-Lactonase (PLL) group. Their lactonase activity is around 100-fold higher than that of phosphotriesterase and it depends on the same active site. These enzymes are thermophilic and extremely thermostable. Stability in high temperatures and in other stressful conditions is an important feature for every biotechnological application in the industrial field. Finally, the lactonase activity would suggest a potential physiological role for SsoPox and SacPox in the quenching of signals involved in the pathways for cell-to-cell communication.

The function of a protein correlates closely with its structure; even partial structural disorder/misfolding may lead to various diseases such as Parkinson's disease. Therefore, analysis of the local structure of a protein (e.g., detecting conformation changes during folding/unfolding, and obtaining the information on local polarity, viscosity, etc.) is of great importance for proteomics studies, and in this respect fluorescence spectroscopy plays a crucial role because of its great temporal and spatial sampling capability. In particular, fluorescent probes combined with a site-specific labeling technique have been widely used in structural analysis of proteins due to their powerful ability in the elucidation of various properties and functions of proteins. The developments of excellent spectroscopic probes as well as site-specific labeling methods are the prerequisites for conducting such a kind of study. Herein we review the progress and use of N-terminal specific labeling and fluorescence probes in local structure analysis of proteins, including some results of our recent studies on α-lactalbumin, β-lactoglobulin, and a dimeric protein of DsbC.

Trace elements as Cu (copper), Fe (iron), and Zn (zinc) can be toxic when their distribution is not carefully regulated, and also their inappropriate binding may compromise cellular function and homeostatic mechanisms. Metal transcription factor-1 (MTF-1), a multiple Zn finger protein, activates metal response element-driven (reporter) gene expression, in a similar way as it happens in metallothionein-1 and -2 (MT-1 and MT-2), zinc transporter-1 (ZnT-1), superoxide dismutase (SOD) and γ-glutamylcysteine synthetase (γ-GCS), a rate-determining enzyme of glutathione synthesis. Virtually, MTF-1 directly coordinates the regulation of genes involved in Zn homeostasis and the protection against metal toxicity. This transcription factor is able to sense changes in metal concentrations and coordinate the expression of genes involved in acquisition, distribution, sequestration, and use of metals. This review is focused on the role of MTF-1 in regulating trace metal metabolism and gene expression of some proteins such as, for example, MT-1, MT-2 and ZnT-1. The aim of the study has been to investigate the role of MTF-1 on the Cu, Fe and Zn uptake and accumulation, and the gene expression of some proteins involved in homeostasis of trace metals in MTF-1 mutant cells as compared to their wild-type cells also were considered.

Modern ultra-sensitive instrumental skill and expertise on surface modification of single biological molecules have sharpened the capabilities of scientists to address important current problems and explore new frontiers in many scientific disciplines including chemistry, molecular biology, molecular medicine and nano-structured materials. Development in single molecule studies (SMS) and manipulation (SMM) in the past two decades has unearthed very important information hidden in chemical biology and nanosciences that was not possible earlier by ensemble measurements. For example, studying motion of biological motors like ATP synthase, DNA polymerase, RNA polymerase, etc could only be possible through single molecule manipulation. Single molecule fluorescence spectroscopy and studies could, for the first time directly show the surface dependent catalytic activities of a catalyst and angular distribution of emission of single chromophore unit. Estimation of step size of linear motors like myosin, kinesin, dynein, etc. was possible due to the development of single molecule fluorescence imaging with one nanometer accuracy and other techniques. Single molecule fluorescence resonance energy transfer could measure the distance between two moieties present in a single biomolecule and study the kinetics. Twisting DNA topoisomerase was directly observed by single molecule imaging technique. The dynamic properties of biomolecules through SMS have been expanding to DNA sequencing, sizing, conformational study, protein-DNA interaction, molecular motors, protein folding, conformational study, diffusion of single biomolecule in membrane, biomolecular reaction dynamics and single virus tracing etc. In this review our focus is to summarize some of the recent developments in single molecule studies and manipulation as mentioned above in chemical biology and nanosciences.

Chemical biology (CB) is a scientific discipline spanning the fields of chemistry and biology involving the application of chemical techniques and tools, often natural products or small chemical compounds produced through synthetic chemistry, to the study and manipulation of biological systems. CB is providing new tools for deciphering protein modification and activity. Designer small molecules as probes of protein and cellular function are becoming the method of choice for careful profiling and development of biological processes in areas such as drug discovery, neurochemistry and molecular genetics. CB studies consists of three methodologies, chemical libraries with small molecules, high-throughput screening, and computational database. Combinatorial synthetic methods combined with high-throughput screening provided large numbers of potential lead compounds. CB reach is expanding into a vide range of fields and there is need to introduce CB to professional chemists working in biotechnology, pharmaceutical, agrochemical and other relevant sectors. Inorganic/organometallic/bioinorganic chemistry-chemical biology interface, biomolecular interactions (protein-protein, protein-carbohydrate), fluorescent quantum dots, biocongugation techniques, boronic acid-based chemosensors, click chemistry and artificial enzymes are described. CB aspects in aging, microfluidics, neurodegenerative diseases, human immunodeficiency virus as well as PROteolysis TArgeting Chimeric moleculeS (PROTACS) are reported. Research on the structural and energetic factors that distinguish specific protein interfaces should be strengthened. Exploration of protein networks should be actively pursued. Chemical biology new technologies may accelerate the discovery of still elusive cures to neurodegenerative diseases.

A facile synthesis and characterisation of novel dispiro-oxindolopyrrolidines is delineated. The results of the anti-microbial studies of novel dispiro-oxindolopyrrolidines are correlated with the docking calculations performed on protein S12 from 30S ribosomal subunit.