Target identification strategies in plant chemical biology

One of the most important steps in developing a new drug is target identification and validation. Target-based drug discovery has become the prevailing paradigm used by pharmaceutical and biotechnology companies. This approach is appealing because it holds the promise of identifying more efficacious compounds with fewer undesirable side effects. Good target identification and validation enables increased confidence in the relationship between target and disease and allows the exploration of whether target modulation will lead to mechanism-based side effects. Email: marketing@medicilon.com.cn web: www.medicilon.com

The current needs to understand gene function in plant biology increasingly require more dynamic and conditional approaches opposed to classic genetic strategies. Gene redundancy and lethality can substantially complicate research, which might be solved by applying a chemical genetics approach. Now understood as the study of small molecules and their effect on biological systems with subsequent target identification, chemical genetics is a fast developing field with a strong history in pharmaceutical research and drug discovery. In plant biology however, chemical genetics is still largely in the starting blocks, with most studies relying on forward genetics and phenotypic analysis for target identification, whereas studies including direct target identification are limited. Here, we provide an overview of recent advances in chemical genetics in plant biology with a focus on target identification. Furthermore, we discuss different strategies for direct target identification and the possibilities and challenges for plant biology. INTRODUCTION A proven way to study how something works is to perturb the process of interest in a well-defined and controlled manner. In biology, this is often accomplished by introducing alterations into the genome of an organism, such as mutations or ectopic expression. A major disadvantage of working at the gene level is that the resulting organism will live in a steady state with the induced genetic change. Additionally, perturbations of essential gene functions will lead to lethality, unless conditional, and perturbations of a gene member of a large gene family might have no effect due to redundancy. In order to address gene redundancy and lethality problems, together with the possibility to perturb a system in a more dynamic manner, chemical biology approaches can be used. In chemical biology, typically small molecules are applied to a biological system, altering the process of interest by binding target molecules. A key feature of chemical biology is its conditional nature. Small molecules can be used for any desired time and concentration, and in most cases can be washed out of the system of choice, making them an ideal tool to study dynamic processes for a certain period of time. Crucially, small molecules will not alter an organism over generations and are not restricted to bind only proteins, but can modulate a biological system by binding lipids or nucleic acids. Finally, using different approaches, the target of small molecules needs to be identified to get a better understanding of the affected process. Chemical genetics strategies in plant biology lag behind the animal field, in which drug development provided a plethora of different target identification strategies. In plant biology, most target identification strategies consist of a phenotyping approach or a forward genetics strategy based on small molecule resistance screens. A few examples exist of strategies, such as affinity purifi- cation, that were successfully applied. An important aspect of chemical biology is linking the induced phenotype to one or more targets . Usually, only the relevant target, or target with the highest affinity for the small molecule, is identified and validated, although socalled “off-targets” might contribute substantially to the overall phenotype. Therefore, it has become increasingly important to understand and generate the small molecule interactome, in order to explain the observed phenotypes. This aspect is especially important for small molecules with a commercial application in healthcare or agriculture. Several reviews have addressed the chemical genetics approaches in plant biology and the challenges and opportunities that lay ahead. Other recent reviews include a comprehensive overview of target identification strategies in mostly animal systems (Ziegler et al., 2013), and a thorough overview of small molecules with known targets and mode of action in plant biology (Tresch, 2013). Given that plant biological research uses limited target identification approaches, this review will briefly discuss the current ones, and will mostly focus on emerging new strategies, which have not found a broad application in plant biology yet (Table 1). Where applicable, examples from plant biology will be given, and benefits and shortcomings will be discussed. The ultimate aim of this review is to convince the reader to look further than the established target identification strategies when a chemical genetics approach is considered.