Dear Sudhakar,

The following are the three approaches generally used to investigate the mechanism of action of  unknown drug:

1-Microscopy-based methods

Bioactive compounds induce phenotypic changes in target cells, changes that are observable by microscopy, and which can give insight into the mechanism of action of the compound. With antibacterial agents, for example, the conversion of target cells to spheroplasts can be an indication that peptidoglycan synthesis is being targeted, andfilamentation of target cells can be an indication that FtsZ or DNA is being targeted. In the case of anticancer agents, bleb formation can be an indication that the compound is disrupting the plasma membrane. A current limitation of this approach is the time required to manually generate and interpret data, but advances in automated microscopy and image analysis software may help resolve this.

2-Direct biochemical methods

Direct biochemical methods include methods in which a protein or a small molecule, such as a drug candidate, is labeled and is traced throughout the body. This proves to be the most direct approach to find target protein that will bind to small targets of interest, such as a basic representation of a drug outline, in order to identify the pharmacophore of the drug. Due to the physical interactions between the labeled molecule and a protein, biochemical methods can be used to determine the toxicity, efficacy, and the mechanism of action of the drug.

3-Computation inference methods

Typically, computation inference methods are primarily used to predict protein targets for small molecule drugs based on computer based pattern recognition. However, this method could also be used for finding new targets for existing or newly developed drugs. By identifying the pharmacophore of the drug molecule, the profiling method of pattern recognition can be carried out where a new target is identified. This provides an insight at a possible mechanism of action, as it is known what certain functional components of the drug are responsible for interacting with a certain area on a protein, thus, leading to a therapeutic effect.

References:

Fetz, V.; Prochnow, H.; Brönstrup, M.; Sasse, F. (2016). "Target identification by image analysis". Natural Product Reports 33 (5): 655–667. 

Cushnie, T.P.; O’Driscoll, N.H.; Lamb, A.J. (2016). "Morphological and ultrastructural changes in bacterial cells as an indicator of antibacterial mechanism of action". Cellular and Molecular Life Sciences. 

Dubovskii, P.V.; Vassilevski, A.A.; Kozlov, S.A.; Feofanov, A.V.; Grishin, E.V.; Efremov, R.G. (2015). "Latarcins: versatile spider venom peptides". Cellular and Molecular Life Sciences 72 (23): 4501–4522. doi:10.1007/s00018-015-2016-x. PMID 26286896.

Schenone, Monica; Dančík, Vlado; Wagner, Bridget K.; Clemons, Paul A. (2013-04-01). "Target identification and mechanism of action in chemical biology and drug discovery". Nature Chemical Biology 9 (4): 232–240.

Hoping this will be helpful,

Rafik

thank you Dr. Rafik Karaman.

I think you can use RNA-Seq or ITRAQ technology to find out the changed gene or protein and related signaling pawhways. Good luck!

Hello Sudhakar,

I am completely agree with Dr. Rafik Karaman. by those approaches any one can get a basic idea that drug molecules activity in vitro. for more details you have go for blocking the signalling pathway and keep on tract. And finnaly if you can tag the molecules so bio distribution assay in animal can help you to understand the basic mechanisms.

thanks.

thank you Dr. Guangfeng Zhao and Dr Siddikuzzaman