Target Identification: A Challenging Step in Forward Chemical Genetics

Abstract

SYNOPSISInvestigation of the genetic functions in complex biological systems is a challenging step in recent year. Hence, several valuable and interesting research projects have been developed with novel ideas to find out the unknown functions of genes or proteins. To validate the applicability of their novel ideas, various approaches are built up. To date, the most promising and commonly used approach for discovering the target proteins from biological system using small molecule is well known a forward chemical genetics which is considered to be more convenient than the classical genetics. Although, the forward chemical genetics consists of the three basic components, the target identification is the most challenging step to chemical biology researchers. Hence, the diverse target identification methods have been developed and adopted to disclose the small molecule bound protein. Herein, in this review, we briefly described the first two parts chemical toolbox and screening, and then the target identifications in forward chemical genetics are thoroughly described along with the illustrative real example case study. In the tabular form, the different biological active small molecules which are the successful examples of target identifications are accounted in this research review.

Chemical genetics strategies for identification of molecular targets

“…15 step 3) (usually E. coli) for amplification ( Fig. 15 step 4) (Das et al 2011;Terstappen et al 2007). Phage populations obtained are re-exposed to immobilized SMs and are subjected to several rounds of affinity enrichment (Fig.…”

“…As in classical genetics, two approaches can be taken to chemical genetics ( Fig. 1) (Das et al 2011): Forward chemical genetics (Chang 2009;Burdine and Kodadek 2004) and reverse chemical genetics (Blackwell and Zhao 2003;Neumann et al 2003).…”

“…Over the last several years a great variety of target identification methods have been developed, ranging from biochemical to genetic, which have received a number of excellent reviews (Das et al 2011;Hübel et al 2008;Leslie and Hergenrother 2008;Roti and Stegmaier 2012;Sleno and Emili 2008;Terstappen et al 2007). We will classify these approaches as: affinitybased methods, genetic methods and other methods.…”

Affinity purification in target identification: the specificity challenge

“…(Koteva et al 2010;Eirich et al 2011). We refer the reader to a number of excellent reviews for more specific examples (Burdine and Kodadek 2004;Leslie and Hergenrother 2008;Sato et al 2010;Das et al 2011;Lomenick et al 2011b;Futamura et al 2013;Schenone et al 2013;Su et al 2013;Ziegler et al 2013;Kawatani and Osada 2014).…”

“…In principle, one may accomplish a target ID project with any of these methods, but in practice, people have realized an integrated approach, combining multiple strategies and methods are instrumental to success. Details of various target identification strategies and methods, their respective advantages and limitations, and representative examples have been extensively covered by numerous excellent reviews (Lindsay 2003;Burdine and Kodadek 2004;Parsons et al 2004;Hart 2005;Luesch et al 2005;Parsons et al 2006;Boshoff and Dowd 2007;Perlstein et al 2007;Terstappen et al 2007; Leslie and Hergenrother 2008;Sleno and Emili 2008;Bantscheff et al 2009;Rix and Superti-Furga 2009;Bottcher et al 2010;Chan et al 2010;Sato et al 2010;Chidley et al 2011a;Das et al 2011;Lomenick et al 2011b;Raida 2011;Wierzba et al 2011;Cho and Kwon 2012;Cong et al 2012;Sakamoto et al 2012;Futamura et al 2013;Lee and Bogyo 2013;Park et al 2013;Su et al 2013;Sumranjit and Chung 2013;Ziegler et al 2013;Blagg and Workman 2014;Kawatani and Osada 2014). Here we elect to only focus on the classic biochemical method: affinity purification.…”