Erlotinib
Biochemical software.
Medicinal Chemistry.
Examples of calculated data obtained for Erlotinib
Medicinal Chemistry.
Examples of calculated data obtained for Erlotinib
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.
Introduction
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.
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.
Erlotinib
Erlotinib is used to treat certain types of non-small cell lung cancer that has spread to nearby tissues or to other parts of the body in patients who have already been treated with at least one other chemotherapy medication and have not gotten better. Erlotinib is also used in combination with another medication (gemcitabine [Gemzar]) to treat pancreatic cancer that has spread to nearby tissues or to other parts of the body and cannot be treated with surgery. Erlotinib is in a class of medications called kinase inhibitors. It works by blocking the action of an abnormal protein that signals cancer cells to multiply. This helps slow or stop the spread of cancer cells.
Note that the results of numerical calculations, which are given in the article, can be applied in the following biochemical studies:
1
Inhibitory potency and binding ability of small molecules.
2
Inhibitor dissociation constants for the wt and mutant kinases.
3
Enzyme kinetic parameters.
4
Explanation of the enhanced drug sensitivity of different mutants.
5
Changing in the binding site caused by the mutation on the enzyme's binding affinity for TKIs.
6
Enzyme kinetic assays and IC50 determinations.
7
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.
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.
Receptor tyrosine kinases (RTKs), the protein kinases which catalyse phosphorylation of hydroxyl groups on tyrosine residues, predominantly following activation by an extracellular ligand, have proved to be a particularly tractable class of drug target involved in a wide range of cellular signalling pathways. Inhibitors of protein kinases most commonly target the ATP binding site of the activated kinase, although binding to an adjacent allosteric site or to an inactive form of the kinase has also been exploited.
In this section, we present the numerical results on the interaction between erlotinib and
various mutant forms of EGFR. The numerical results are presented as graphs, which we have combined with the experimental graphs obtained earlier. Erlotinib is in a class of medications called kinase inhibitors. It works by blocking the action of an abnormal protein that signals cancer cells to multiply. This helps to slow or stop the spread of cancer cells. Fig.1 shows the experimental results (a) and numerical results b).
The numerical results correspond well to the previously obtained IC50 values; namely, the L858R substitutions in EGFR lead to a decrease in the two values of IC50 and lg(cond(W)) when interacting with erlotinib. The double substitution of T790M/L858R in EGFR leads to an increase in the experimental and calculated values of IC50 and lg(cond(W)). At the same time, we interpret the increase in lg(cond(W)), when the system switches from the wild-type to a mutant form of mEGFR (T790M/L858R)-erlotinib, as a decrease in dimer stability, which is reflected in the decrease in the affinity of the mutant form of the protein to erlotinib.
In this section, we present the numerical results on the interaction between erlotinib and
various mutant forms of EGFR. The numerical results are presented as graphs, which we have combined with the experimental graphs obtained earlier. Erlotinib is in a class of medications called kinase inhibitors. It works by blocking the action of an abnormal protein that signals cancer cells to multiply. This helps to slow or stop the spread of cancer cells. Fig.1 shows the experimental results (a) and numerical results b).
The numerical results correspond well to the previously obtained IC50 values; namely, the L858R substitutions in EGFR lead to a decrease in the two values of IC50 and lg(cond(W)) when interacting with erlotinib. The double substitution of T790M/L858R in EGFR leads to an increase in the experimental and calculated values of IC50 and lg(cond(W)). At the same time, we interpret the increase in lg(cond(W)), when the system switches from the wild-type to a mutant form of mEGFR (T790M/L858R)-erlotinib, as a decrease in dimer stability, which is reflected in the decrease in the affinity of the mutant form of the protein to erlotinib.
Chemical structure of Erlotinib-EGFR dimer with indication of key amino acid residues
Chemical structure of Erlotinib
Chemical structure of erlotinib molecule showing atoms and charges
[Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain ] L834Rmutated NSCLC tumours respond to first-generation TKIs (like erlotinib)
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).
Results of numerical calculations and comparison with the obtained experimental data
The first graph (red) shows the dependence of the value IC50 on the mutation in the EGFR protein, the second graph (blue) shows the results of the calculations using the software developed by us, which shows the direction of the change in affinity for mutations in proteins
The numerical results correspond well to the previously obtained IC50 values; namely, the L858R substitutions in EGFR lead to a decrease in the two values of IC50 and lg(cond(W)) when interacting with erlotinib. The double substitution of T790M/L858R in EGFR leads to an increase in the experimental and calculated values of IC50 and lg(cond(W)). At the same time, we interpret the increase in lg(cond(W)), when the system switches from the wild-type to a mutant form of mEGFR (T790M/L858R)-erlotinib as a decrease in dimer stability which is reflected in the decrease in the affinity of the mutant form of the protein to erlotinib.
The experimental values were taken [In vitro modeling to determine mutation specificity of EGFR tyrosine kinase inhibitors against clinically relevant EGFR mutants in non-small-cell lung cancer]
1. Thus, the numerical method developed by us makes it possible to determine the range of changes in the stability of dimeric complexes with the participation of a small chemical molecule and a protein molecule.
2. Application of our method will allow us to identify mutations that lead to a decrease in the affinity of components.
3. Numerical analysis requires a three-dimensional structure of the dimer under study, in the protein component of which substitutions of amino acid residues will be introduced.
The experimental values were taken [In vitro modeling to determine mutation specificity of EGFR tyrosine kinase inhibitors against clinically relevant EGFR mutants in non-small-cell lung cancer]
1. Thus, the numerical method developed by us makes it possible to determine the range of changes in the stability of dimeric complexes with the participation of a small chemical molecule and a protein molecule.
2. Application of our method will allow us to identify mutations that lead to a decrease in the affinity of components.
3. Numerical analysis requires a three-dimensional structure of the dimer under study, in the protein component of which substitutions of amino acid residues will be introduced.
