One of the first steps during new drugs development is known to be the screening of library of potential compounds. The method of this procedure optimization was developed in our laboratory. This method represents development of kinetic model of concerned biochemical systems, finding of all available quantitative experimental data, which characterizing their functioning and regulation, and taking all these data into model account. Such approach allows not only collect together all the information available about the concerned biochemical system, but also use it effectively on the pre-clinical stages of new drugs development, in particular, during the search of protein target and effective clinical candidates optimization. The method of information processing, given in the framework of this approach, allows finding effective inhibitors not only for one protein target but also in that case when biotarget is represented by the part of metabolic or signal way.

Problem: to optimize antyphemonia drugs screening using kinetic modeling.

Subject of inquiry: inhibitors of Streptococcus pneumoniae aromatic amino acids biosynthesis.

Approach

	Result №1. Kinetic model taking into account functioning of the part of aromatic amino acids biosynthesis (four-enzyme section of shikimate pathway) in Streptococcus pneumoniae have been developed.
	Result №2. Kinetic model have been verified using different types of the quantitative experimental data both in vitro (enzyme kinetics) and in vivo (LC-MC metabolomics).
	Result №3. The model of the four-enzyme section of shikimate pathway has been employed to design an inhibition-sensitive reconstituted pathway for a high-throughput screening effort on the shikimate pathway. It was demonstrated that using the model it was possible to optimize this reconstituted pathway in such a way to provide equal sensitivity of the enzymes to inhibition.

Conclusions

Performing high-throughput screening campaigns against bacterial biosynthetic pathways may yield new chemical entities that have potent inhibitory effects on the pathway as a whole despite rather weaker effects on any one isolated enzyme. It may not always be possible to set up a working, robust assay for screening a pathway, and so separate screens may have to be considered. For whichever case, the availability of a validated kinetic model for the pathway allows predictions to be made on the cumulative effect of several single enzyme inhibitions. Information provided by experiment on the mode and potency of inhibition of any pathway enzymes can be input to both the pathwaymodel and thewhole cell model to predict the global cellular impact of the inhibitor.

Publications

You can find more information about this project in our publucation –  Michael Noble, Yugesh Sinha, Aleksey Kolupaev, Oleg Demin, David Earnshaw, Frank Tobin, Joshua West, John D. Martin, Chunyan Qiu, Wu-Schyong Liu, Walter E. DeWolf Jr., David Tew, Igor I. Goryanin. The kinetic model of the shikimate pathway as a tool to optimize enzyme assays for high-throughput screening. Biotechnology and Bioengineering. Volume 95, Issue 4, Date: 5 November 2006, Pages: 560-571.