Biochemical software. Examples of calculated data obtained for Naquotinib
The purpose of this work is to develop and test a new biophysical approach, which is implemented as a software package to determine changes in the direction of affinity changes for various amino acid residue substitutions in the protein when binding to various small chemical molecules.
Small molecule drugs accounted for 84% of the total pharmaceutical industry revenue in 2014. In 2015, a total of 45 new molecular entities were approved in the United States, out of which 33 were small molecules. The versatility of small molecule drugs (which can range from global blockbusters to targeted therapies to orphan drugs), and their ability to be formulated into pills and tablets are driving the demand for these drugs. In 2015, the revenues of Contract Research Organizations (CROs) and CDMOs, focusing on the development of small molecules, increased by 15-20% . On average, the cost of drug development ranges between USD 1.5-3 billion and has an average cost of around USD 2.6 billion. This high cost of drug development is a result of the high failure rate of experiments and relatively low-efficiency figures involved in the initial phases of drug discovery. Most of the small molecule drug discovery cost lies in the same bracket. Thus, developing such drugs always involves high costs, which cannot be borne by new entrants or small-scale laboratories; this is limiting the market scope. Therefore, developing a method to reduce the cost of preclinical studies on small molecules is particularly relevant at the present time.
The results of applying our technique can be of good help for the pre-experimental determination of such quantities as the affinity expressed by the dissociation constant or the half maximal inhibitory concentration (IC50).
Note that the results of numerical calculations, which are given in the article, can be applied in the following biochemical studies:
Inhibitory potency and binding ability of small molecules.
Inhibitor dissociation constants for the wt and mutant kinases.
Enzyme kinetic parameters.
Explanation of the enhanced drug sensitivity of different mutants.
Changing in the binding site caused by the mutation on the enzyme's binding affinity for TKIs.
Enzyme kinetic assays and IC50 determinations.
Inhibitor binding constants; the drug resistance provides important information for the development of more potent and selective drugs for use in resistant individuals.
Methods to measure binding affinity
One can also measure binding affinity when modifying a molecule as a way to see how changing its binding properties relates to the pathway or process under study. Our developed software allows us to determine the direction of the change in affinity during the mutations of amino acid chains during interaction with small chemical molecules. In this study, we will show how it is possible to determine the range of changes in the affinity of small chemical molecules only using information about the threedimensional structure of such a complex. The calculated data, which was obtained using our developed software package and is given in graphs, directly enables us to obtain information about the nature and direction of changes in affinity.
Fig. 1. Diagram showing the general appearance of the experimental graph (a) and the calculated graph (b), which was obtained using our software.
Naquotinib is an orally available, irreversible, third-generation, mutant-selective, epidermal growth factor receptor (EGFR) inhibitor
ASP8273 is a novel, small molecule, irreversible TKI that inhibits EGFR activity in patients with exon 19 deletions, L858R substitutions in exon 21, as well as T790M resistance mutations. This section will present a joint analysis of previously obtained experimental and computational data on the binding of naquotinib (ASP8273) to different mutant forms of the EGFR protein.
Therefore, for clarity, we present experimental data in diagrams and the results of numerical calculations in graphs. Note that Fig. 2 c)-d) is arranged as two linked experimental and calculated plots, with no IC50 value for the T790M mutation when naquotinib binds, but, as previously reported, naquotinib inhibits the mutant form of EGFR T790M. The calculated value of lg(cond(W)) for the T790M EGFR mutation when binding to naquatinib is lower than that for the wtEGFR interaction with naquatinib. Two subsequent L858R/T790M and L858R substitutions show a decrease in the two parameters IC50 and lg(cond(W)) in the experimental and calculated plots, respectively.
Drug Discovery Research
Fig.2.Tree-dimensional structure of the naquatinib-EGFR dimer indicating the key amino acid residues a) and chemical formula of naquatinib b) Three-dimensional structure was used PDB 5Y9T,results of numerical calculations and experimental IC50 values (nmol/L) of EGFR-TKIs for Ba/F3 cells harboring EGFR mutations c) and dependence of lg(cond(W)) value on amino acid residue replacement in EGFR when binding to naquatinib d)