Chemical approaches to understanding biological mechanisms

A report on work with small-molecule inhibitors of cellular processes presented at the 39th Annual Meeting of the American Society for Cell Bilogy, Washington DC, December 11-15, 1999     

Chemical approaches to the lysophospholipid receptors

Both ligand-based and GPCR privileged scaffold chemical tools have recently emerged to provide new insights into the function and physiology of the GPCR lysophospholipid receptors both in vitro and in vivo. Both rational, design-based approaches as well as hybrid approaches where high throughput screening has been coupled to an understanding of critical molecular interactions have been productive in advancing understanding of physiology and potential therapeutics in this field. It is now feasible to identify reasonably potent and selective small molecules that provide chemical proof-of-concept in vivo directly from high throughput screening. These developments, coupled with the availability of receptor knock-out mice, presage rapid progress in the field.     

Chemical genetic screening approaches to neurobiology

Chemical genetics is an emerging technology for revealing the signaling networks that regulate biological phenotypes using exogenous reagents such as small organic molecules. To study neurobiology using chemical genetics, high-throughput cell and organismal assays can be created to identify compounds and proteins that regulate diverse neuronal phenotypes, such as cell viability, gene expression level, protein association, protein aggregation, glutamate uptake, membrane polarization, mitochondrial function, neurite outgrowth, and growth cone composition. This powerful set of tools will enable the molecular dissection of complex processes that occur within the nervous system.     

Chemical genetic approaches to probing cell death

Chemical genetics has arisen as a tool for the discovery of pathways and proteins in mammalian systems. This approach, comprising small-molecule screening combined with biochemical and genomic target identification methods, enables one to assess which proteins are involved in regulating a particular phenotype. Applied to cell death, this strategy can reveal novel targets and pathways regulating the demise of mammalian cells. Numerous diseases have been linked to the loss of regulation of cell death. Defining the mechanisms governing cell death in these diseases might lead to the discovery of therapeutic agents and targets and provide a richer understanding of the mortality of living systems. Recent advances include the discovery of novel small molecules regulating cell death pathways -- necrostatin and erastin -- as well as the elucidation of the mechanism of death induced in cancer cells by the cytotoxic agent Apratoxin A.     

Mathematical approaches to differentiation and gene regulation

We consider some mathematical issues raised by the modelling of gene networks. The expression of genes is governed by a complex set of regulations, which is often described symbolically by interaction graphs. These are finite oriented graphs where vertices are the genes involved in the biological system of interest and arrows describe their interactions: a positive (resp. negative) arrow from a gene to another represents an activation (resp. inhibition) of the expression of the latter gene by some product of the former. Once such an interaction graph has been established, there remains the difficult task to decide which dynamical properties of the gene network can be inferred from it, in the absence of precise quantitative data about their regulation. There mathematical tools, among others, can be of some help. In this paper we discuss a rule proposed by Thomas according to which the possibility for the network to have several stationary states implies the existence of a positive circuit in the corresponding interaction graph. We prove that, when properly formulated in rigorous terms, this rule becomes a theorem valid for several different types of formal models of gene networks. This result is already known for models of differential [C. Soulé, Graphic requirements for multistationarity, ComPlexUs 1 (2003) 123-133] or Boolean [E. Rémy, P. Ruet, D. Thieffry, Graphic requirements for multistability and attractive cycles in a boolean dynamical framework, 2005, Preprint] type. We show here that a stronger version of it holds in the differential setup when the decay of protein concentrations is taken into account. This allows us to verify also the validity of Thomas' rule in the context of piecewise-linear models. We then discuss open problems.     

Chemical and instrumental approaches to treat hyperpigmentation

Many modalities of treatment for acquired skin hyperpigmentation are available including chemical agents or physical therapies, but none are completely satisfactory. Depigmenting compounds should act selectively on hyperactivated melanocytes, without short- or long-term side-effects, and induce a permanent removal of undesired pigment. Since 1961 hydroquinone, a tyrosinase inhibitor, has been introduced and its therapeutic efficacy demonstrated, and other whitening agents specifically acting on tyrosinase by different mechanisms have been proposed. Compounds with depigmenting activity are now numerous and the classification of molecules, based on their mechanism of action, has become difficult. Systematic studies to assess both the efficacy and the safety of such molecules are necessary. Moreover, the evidence that bleaching compounds are fairly ineffective on dermal accumulation of melanin has prompted investigations on the effectiveness of physical therapies, such as lasers. This review which describes the different approaches to obtain depigmentation, suggests a classification of whitening molecules on the basis of the mechanism by which they interfere with melanogenesis, and confirms the necessity to apply standardized protocols to evaluate depigmenting treatments.     

Chemical approaches to deciphering the glycosaminoglycan code

Glycosaminoglycans are sulfated biopolymers with rich chemical diversity and complex functions in vivo, contributing to processes ranging from cell growth and neuronal development to viral invasion and neurodegenerative disease. Recent studies suggest that glycosaminoglycans may encode information in the form of a 'sulfation code,' whereby discrete modifications to the polysaccharide backbone may direct the location or activities of proteins.     

Modern non-drug approaches to human sleep regulation

Existing approaches to non-drug regulation and induction of human sleep are analyzed with an attempt of their classification. The main attention is paid to the methods that utilize modern computer technologies of registration and analysis of various characteristics of human organism functioning, basically to the electroencephalogram (EEG). Normal human sleep EEG correlates and their changes during different sleep stages are reviewed. Modern opportunities to regulate and induce human sleep via utilization of different EEG characteristics are analyzed.