Opportunities at the interface of chemistry and biology

The combination of the tools and principles of chemistry, together with the tools of modern molecular biology, allow us to create complex synthetic and natural molecules, and processes with novel biological, chemical and physical properties. This article illustrates the tremendous opportunity that lies at this interface of chemistry and biology by describing a number of examples, ranging from efforts to expand the genetic code of living organisms to the use of combinatorial methods to generate biologically active synthetic molecules.     

Opportunities at the interface of chemistry and biology

The combination of the tools and principles of chemistry, together with the tools of modern molecular biology, allow us to create complex synthetic and natural molecules, and processes with novel biological, chemical and physical properties. This article illustrates the tremendous opportunity that lies at this interface of chemistry and biology by describing a number of examples, ranging from efforts to expand the genetic code of living organisms to the use of combinatorial methods to generate biologically active synthetic molecules.     

Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry

Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions.     

Exploration of the central dogma at the interface of chemistry and biology: 2010 Yale Chemical Biology Symposium

Ever since the term "central dogma" was coined in 1958, researchers have sought to control information flow from nucleic acids to proteins. Talks delivered by Drs. Anna Pyle and Hiroaki Suga at this year's Chemical Biology Symposium at Yale in May 2010 applauded recent advances in this area, at the interface between chemistry and biology.     

Bionanoscience at the plant virus-inorganic chemistry interface

Bionanoscience is an inter-disciplinary area of research that sits at the interface of chemistry, biology, materials science, engineering and medicine. During the past 10 years the suitability and applicability of using plant viruses as building blocks, synthons, scaffolds or templates in bionanoscience/technology have begun to be explored. This short review describes how the plant Cowpea mosaic virus can be functionalised on its outer surface to form electroactive nanoparticles, can be used to construct monolayers on solid surfaces and multilayer arrays by a bottom-up, layer-by-layer approach, and how it can template mineralization processes to give new routes to monodisperse nanoparticles. Potential applications of virus-derived nanoparticles include nanoelectronics, sensory devices, catalysis, photonics and medical applications from imaging to the targeting and delivery of therapeutic agents.     

Recent progress in ellagitannin chemistry

Continuing studies on the total synthesis of ellagitannin plant metabolites have led to the preparation of the dimeric antitumor compound, coriariin A, as well as designed structural analogues. In related investigations, the synthesis of a 2,4-hexahydroxydiphenoyl (HHDP)-bearing glucopyranose structure has been achieved. This species is related to the geraniin family of ellagitannins, and its subsequent chemistry is suggestive of a mechanistic rationale for the observation that the HHDP units within (3,6-bridged)2,4-HHDP-containing ellagitannins invariably are oxidized further in vivo. Companion studies designed to assay the immunomodulatory properties of coriariin A and analogues have led to the thesis that tumor necrosis factor alpha (TNFalpha) serves as a mediator of this ellagitannin's tumor remissive activity. Furthermore, certain tannins and tannin analogues appear to act in an immunosuppressive capacity with peripheral blood monocytes that were exposed to the bacterially derived septic shock inducing agent lipid A.     

Role of surface chemistry in protein remodeling at the cell-material interface

Background

The cell-material interaction is a complex bi-directional and dynamic process that mimics to a certain extent the natural interactions of cells with the extracellular matrix. Cells tend to adhere and rearrange adsorbed extracellular matrix (ECM) proteins on the material surface in a fibril-like pattern. Afterwards, the ECM undergoes proteolytic degradation, which is a mechanism for the removal of the excess ECM usually approximated with remodeling. ECM remodeling is a dynamic process that consists of two opposite events: assembly and degradation.

Methodology/Principal Findings

This work investigates matrix protein dynamics on mixed self-assembled monolayers (SAMs) of –OH and –CH₃ terminated alkanethiols. SAMs assembled on gold are highly ordered organic surfaces able to provide different chemical functionalities and well-controlled surface properties. Fibronectin (FN) was adsorbed on the different surfaces and quantified in terms of the adsorbed surface density, distribution and conformation. Initial cell adhesion and signaling on FN-coated SAMs were characterized via the formation of focal adhesions, integrin expression and phosphorylation of FAKs. Afterwards, the reorganization and secretion of FN was assessed. Finally, matrix degradation was followed via the expression of matrix metalloproteinases MMP2 and MMP9 and correlated with Runx2 levels. We show that matrix degradation at the cell material interface depends on surface chemistry in MMP-dependent way.

Conclusions/Significance

This work provides a broad overview of matrix remodeling at the cell-material interface, establishing correlations between surface chemistry, FN adsorption, cell adhesion and signaling, matrix reorganization and degradation. The reported findings improve our understanding of the role of surface chemistry as a key parameter in the design of new biomaterials. It demonstrates the ability of surface chemistry to direct proteolytic routes at the cell-material interface, which gains a distinct bioengineering interest as a new tool to trigger matrix degradation in different biomedical applications.     

At the crossroads of chemistry and biology

The life sciences are molecular and the harnessing of information gleaned from genomics and proteomics will require interdisciplinary research integrating chemistry and biology. This approach is illustrated by the synthesis and biological evaluation of lipidated peptides and proteins and the delineation of a concept arguing for natural product guided combinatorial chemistry.     

The biology and chemistry of hyperlipidemia

Coronary arterial diseases are responsible for more deaths than all other associated causes combined. Elevated serum cholesterol levels leading to atherosclerosis can cause coronary heart disease (CHD). Reduction in serum cholesterol levels reduces the risk for CHD, substantially. Medicinal chemists all around the world have been designing, synthesizing, and evaluating a variety of new bioactive molecules for lowering lipid levels. This review summarizes the disorders associated with elevation of lipids in blood and the current strategies to control them. The emphasis has been laid in particular on the new potential biological targets and the possible treatments as well as the current ongoing research status in the field of lipid lowering agents.     

Creating parts that allow for rational design: Synthetic biology and the problem of context-sensitivity

The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins’ account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.     

Molecular biology and the control of viral vaccines

Abstract The live attenuated vaccines against poliomyelitis developed by Sabin are among the safest and most effective antiviral vaccines in current use and have eliminated poliomyelitis as a public health problem in many countries. They form the main basis of the WHO intention to eliminate poliomyelitis from the world by the year 2000, and the molecular basis of their attenuated phenotype and some of its virological consequences are increasingly clear. Nonetheless, the data reviewed here show how poorly understood their mechanism of action is in use. Our studies raise the possibility of in vitro neurovirulence tests and may help to identify features of particular importance in the attenuation of the virus for human rather than simian recipients. On the other hand it is clear that when a live virus is used as a vaccine it is not possible to control it in the same way that genetically engineered products may be controlled in so far as replication in the recipient makes it possible for the live vaccine strain to alter in ways which may or may not be undesirable.     

A career at the interface of cell and developmental biology: a view from the crest

Just as neural crest cells migrate great distances through the embryo, my journey has taken me from a childhood in a distant land to a career as a biologist. My mentoring relationships have shaped not only the careers of my trainees, but also the trajectory of my own science. One of the most satisfying aspects of mentoring comes from helping to empower the next generation of scientists to do more tomorrow than is possible today. This, together with a passion for discovery and learning new things, motivates me and makes science such a rewarding career.First, let me say how honored I am to receive the Women in Cell Biology Senior Award. I am particularly thankful to my former postdoctoral fellows and students. I have learned as much, or more, from them as they have from me and take great pride and vicarious pleasure from their successes. My goal as a mentor has been to impart an enthusiasm for science and for the satisfaction it can bring at both a professional and personal level. It is the pleasure of discovery and the bonds of collegiality that make being a scientist not only a worthwhile and interesting but also a very fulfilling career.When looking back upon my life as a biologist, many of the “choices” made along my career path were more of a random walk than a premeditated trajectory. Perhaps the most important and constant influences come from my family background, wonderful friends and colleagues, and an inherent interest in the natural world. For me, these were mixed with a good deal of luck and the generous mentorship of valued colleagues.     

Recent progress in the biology, chemistry and structural biology of DNA glycosylases

Since the discovery in 1974 of uracil DNA glycosylase (UDG), the first member of the family of enzymes involved in base excision repair (BER), considerable progress has been made in the understanding of DNA glycosylases, the polypeptides that remove damaged or mispaired DNA bases from DNA. We also know the enzymes that act downstream of the glycosylases, in the processing of abasic sites, in gap filling and in DNA ligation. This article covers the most recent developments in our understanding of BER, with particular emphasis on the mechanistic aspects of this process, which have been made possible by the elucidation of the crystal structures of several glycosylases in complex with their respective substrates, substrate analogues and products. The biological importance of individual BER pathways is also being appreciated through the inactivation of key BER genes in knockout mouse models.     

The chemistry and biology of nitroxide compounds

Cyclic nitroxides are a diverse group range of stable free radicals that have unique antioxidant properties. Because of their ability to interact with free radicals, they have been used for many years as biophysical tools. During the past 15-20 years, however, many interesting biochemical interactions have been discovered and harnessed for therapeutic applications. Biologically relevant effects of nitroxides have been described, including their ability to degrade superoxide and peroxide, inhibit Fenton reactions, and undergo radical-radical recombination. Cellular studies defined the activity of nitroxides in vitro. By modifying oxidative stress and altering the redox status of tissues, nitroxides have been found to interact with and alter many metabolic processes. These interactions can be exploited for therapeutic and research use, including protection against ionizing radiation, as probes in functional magnetic resonance imaging, cancer prevention and treatment, control of hypertension and weight, and protection from damage resulting from ischemia/reperfusion injury. Although much remains to be done, many applications have been well studied and some are currently being tested in clinical trials. The therapeutic and research uses of nitroxide compounds are reviewed here with a focus on the progress from initial development to modern trials.