Gefitinib and AMP
Biochemical software
Joint analysis of the effect of key mutations in the EGFR protein on binding to gefitinib and AMP
Joint analysis of the effect of key mutations in the EGFR protein on binding to gefitinib and AMP
Our method aims to develop software that will make it possible, based on the three-dimensional structures of interacting reagents (protein and small chemical molecule) already known, to determine the stability of the molecular complex which affects the affinity of the components and which will also affect the cellular response.
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.
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.
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.
Fig. 1. Diagram showing the general appearance of the experimental graph (a) and the calculated graph (b), which was obtained using our software.
Direction of affinity change
A value lg(cond(W)) that shows the stability of a biological complex and shows the direction of change in the affinity of a dimer under various mutations.
Gefitinib (iressa) is an orally active TK inhibitor (TKI) that blocks signal transduction pathways implicated in cancers. The structures of the L858R and G719S mutants complexed with either AMPPNP or the inhibitors, gefitinib and AEE788, revealed that the overall conformation and ligand-binding modes are very similar to those of the wild-type EGFR-TK in the active conformation.
Gefitinib (iressa) is an orally active TK inhibitor (TKI) that blocks signal transduction pathways implicated in cancers. The structures of the L858R and G719S mutants complexed with either AMPPNP or the inhibitors, gefitinib and AEE788, revealed that the overall conformation and ligand-binding modes are very similar to those of the wild-type EGFR-TK in the active conformation. The T790M mutation of EGFR increases the ATP affinity of the G719S mutant, explaining the acquired drug resistance of the double mutant. Structural analyses of the G719S/T790M double mutant, as well as the wild type and the G719S and L858R mutants, revealed that the T790M mutation stabilizes the hydrophobic spine of the active EGFR-TK conformation. Determined the IC50 (half maximal inhibitory concentration) value of the G719S/T790M double mutant EGFR-TK domain and compared its gefitinib sensitivity with those of the wild-type and G719S mutant proteins.
Three-dimensional structure of the dimeric complex gefitinib-EGFR (PDB 3UG2 [28] a) and AMPPNP-EGFR (PDB: 3VJN) [33] b), small molecules gefitinib and AMPPNP compete for one binding site in the EGFR molecule [32]
PLOTS OF KD CHANGE DEPENDING ON MUTATION IN EGFR INHIBITOR DISSOCIATION CONSTANTS FOR THE WT AND MUTANT EGFR KINASES [51] A) AND IC50 DEPENDING ON MUTATION IN EGFR PROTEIN. [35]
Software that allows you to get preliminary results before conducting a laboratory experiment!
Data on the calculation of the conformational mobility of small molecules
Results of numerical modeling of substitutions of amino acid residues in the EGFR protein.
For convenience, the graphs indicate the corresponding experimental results obtained.
The higher lg(cond(W)) value, the worse the affinity of the dimeric complex.
Results of numerical calculations of the dependence of the lg(cond (W)) value on the substitution of amino acid residue in EGFR upon binding to AMPPNP a) and gefitinibe b)
The higher lg(cond(W)) value, the worse the affinity of the dimeric complex.
Results of numerical calculations of the dependence of the lg(cond (W)) value on the substitution of amino acid residue in EGFR upon binding to AMPPNP a) and gefitinibe b)
Results
obtained numerical calculations on the effect of mutations in the EGFR protein on the binding affinity to two competing molecules Gefitinib and AMP-PNP
Henceforth, in the analysis of graphs, we shall bear in mind that a decrease in lg(cond(W)) value leads to an increase in the stability of molecular complexes involving one protein and one small chemical molecule, while the increase in stability leads to an increase in the affinity of mutant forms of proteins to small chemical molecules, in comparison with the interaction of wild type protein with the same
small chemical molecule. If the calculated value of lg(cond(W)) has a tendency to be higher when compared to the interaction of the wild-type protein, then we interpret this as a decrease in the stability of the dimer complex involving the mutant protein and the small chemical molecule. For convenience, in the conclusions for each small chemical molecule, we operate at once with the concept of "affinity"
1. Results of numerical simulations, we found that an additional mutation L858R to T790M significantly enhances ATP-binding affinity of the L858R mutant
2. Numerical modeling revealed that the introduction of mutations T790M and L858R / T790M are characterized by a higher affinity for ATPPMP than an increase in the affinity for gefitinib. The increased ATP affinity of the L858R / T790M mutant leads to gefitinib resistance at cellular concentrations of ATP
3. Results of numerical simulations showed the T790M mutation binds gefitinib with a higher affinity than wild-type EGFR.
4. Results of numerical simulations showed the L858R substitution is also characterized by a higher affinity for gefitinib than the wild-type protein.
5. Results of numerical simulations showed substitution G719 has a higher affinity for gefitinib than for wild-type protein.
6. Results of numerical simulations showed substitution of G719S / T790M results in a higher affinity for both gefitinib and AMAPNP.
7. Numerical analysis of the two substitutions G719S and G719S / T790M indicates that the double mutation G719S / T790M results in a greater affinity for gefitinib.
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. Application of our method will allow you to identify mutations that lead to a decrease in the affinity of components. 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.
Examples using small molecules are given below
List of Literatures
1. What are the drugs of the future?
2. A big future for small molecules: targeting the undruggable
3. Small-Molecule Drug Development: Advantages of an Integrated, Phase-Based Approach
4. https://www.marketwatch.com/press-release/small-molecule-drug-discovery-market-trend-survey-2021-with-top-countries-data-industry-growth-size-share-forecasts-analysis-company-profiles-competitive-landscape-and-key-regions-analysis-research-report-with-covid-19-analysis-2021-03-08
5. https://www.malvernpanalytical.com/en/products/measurement-type/binding-affinity
6. . Determination of half-maximal inhibitory concentration using biosensor-based protein interaction analysis
7. Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction
8. Differential binding of human immunoagents and Herceptin to the ErbB2 receptor
9. Using Electrophoretic Mobility shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System
10. Quantitative analysis of protein-RNA interactions by gel mobility shift equilibrium dialysis.
11. Determination of the Binding Parameters of Drug to Protein by Equilibrium Dialysis/Piezoelectric Quartz Crystal Sensor
12. Analytical Ultracentrifugation as a Tool to Study Nonspecific Protein–DNA Interactions
13. Use of Surface Plasmon Resonance (SPR) to Determine Binding Affinities and Kinetic Parameters Between Components Important in Fusion Machinery]
14. Structure of CD20 in complex with the therapeutic monoclonal antibody rituximab]
15. Fluorescence Titrations to Determine the Binding Affinity of Cyclic Nucleotides to SthK Ion Channels],
16. DNA binding to alkaloids
17. Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis
18. Transformation of Low-Affinity Lead Compounds into High-Affinity Protein Capture Agents
19. Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
20. Epidermal Growth Factor Receptor Cell Proliferation Signaling Pathways
21. EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib
22. Advances in studies of tyrosine kinase inhibitors and their acquired resistance
23. Structural insight into the binding mechanism of ATP to EGFR and L858R, and T790M and L858R/T790 mutants
24. Efficacy of rociletinib (CO-1686) in plasma-genotyped T790M-positive non-small cell lung cancer (NSCLC) patients (pts)
25. Synthesis and Fundamental Evaluation of Radioiodinated Rociletinib (CO-1686) as a Probe to Lung Cancer with L858R/T790M Mutations of Epidermal Growth Factor Receptor (EGFR
26. Pharmacological and Structural Characterizations of Naquotinib, a Novel Third-Generation EGFR Tyrosine Kinase Inhibitor, in EGFR-Mutated Non-Small Cell Lung Cancer
27. Structural Basis for the Regulation of PPARγ Activity by Imatinib
28. PDB https://www.rcsb.org/structure/3UG2
29. Матанство
30. https://pubchem.ncbi.nlm.nih.gov/compound/Water
31. https://pubchem.ncbi.nlm.nih.gov/compound/1%2C4-butanediol
32. https://pubchem.ncbi.nlm.nih.gov/compound/Gefitinib
33. https://www.rcsb.org/structure/3VJN
34. Nonhydrolyzable ATP analog 5'-adenylyl-imidodiphosphate (AMP-PNP) does not inhibit ATP-dependent scanning of leader sequence of mRNA
35. Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
36. https://www.rcsb.org/structure/5XDK
37. Structural basis of mutant-selectivity and drug-resistance related to CO-1686
38. https://www.selleckchem.com/products/co-1686.html
39. https://www.rcsb.org/structure/6KTN
40. Structural Basis for the Regulation of PPARγ Activity by Imatinib
41. Small Molecule Kinase Inhibitors as Anti-Cancer Therapeutics
42. Influence of chemotherapy on EGFR mutation status
43. https://www.rcsb.org/structure/5XDL
44. https://www.rcsb.org/structure/5Y9T
45. https://www.rcsb.org/structure/1M17
46. Tyrosine kinase inhibitors: Multi-targeted or single-targeted?
47. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
48. Epidermal growth factor receptor mutations and gene amplification in non-small-cell lung cancer: molecular analysis of the IDEAL/INTACT gefitinib trials
49. Advances in studies of tyrosine kinase inhibitors
50. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: Mechanism of activation and insights into differential inhibitor sensitivity
51. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP
52. Discovery of a mutant-selective covalent inhibitor of EGFR that overcomes T790M-mediated resistance in NSCLC
53. New developments in the management of non-small-cell lung cancer, focus on rociletinib: what went wrong
54. Discovery of a mutant-selective covalent inhibitor of EGFR that overcomes T790M-mediated resistance in NSCLC
55. Tjin Tham Sjin R, Lee K, Walter AO, Dubrovskiy A, SheetsM, Martin TS, Labenski MT, Zhu Z, Tester R, Karp R,Medikonda A, Chaturvedi P, Ren Y, et al. In vitro and in vivo characterization of irreversible mutant-selective EGFR inhibitors that are wild-type sparing. Mol Cancer Ther. 2014; 13:1468-1479.]
56. LiverTox: Clinical and Research Information on Drug-Induced Liver Injury
57. Yki-Jarvinen H. Thiazolidinediones. N Engl J Med (2004) 351:1106–18. doi:10.1056/NEJMra041001
58. PPAR-γ Agonists As Antineoplastic Agents in Cancers with Dysregulated
59. Novel Third-Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance
60. Markedly increased ocular side effect causing severe vision deterioration after chemotherapy using new or investigational
.
1. What are the drugs of the future?
2. A big future for small molecules: targeting the undruggable
3. Small-Molecule Drug Development: Advantages of an Integrated, Phase-Based Approach
4. https://www.marketwatch.com/press-release/small-molecule-drug-discovery-market-trend-survey-2021-with-top-countries-data-industry-growth-size-share-forecasts-analysis-company-profiles-competitive-landscape-and-key-regions-analysis-research-report-with-covid-19-analysis-2021-03-08
5. https://www.malvernpanalytical.com/en/products/measurement-type/binding-affinity
6. . Determination of half-maximal inhibitory concentration using biosensor-based protein interaction analysis
7. Titration ELISA as a Method to Determine the Dissociation Constant of Receptor Ligand Interaction
8. Differential binding of human immunoagents and Herceptin to the ErbB2 receptor
9. Using Electrophoretic Mobility shift Assays to Measure Equilibrium Dissociation Constants: GAL4-p53 Binding DNA as a Model System
10. Quantitative analysis of protein-RNA interactions by gel mobility shift equilibrium dialysis.
11. Determination of the Binding Parameters of Drug to Protein by Equilibrium Dialysis/Piezoelectric Quartz Crystal Sensor
12. Analytical Ultracentrifugation as a Tool to Study Nonspecific Protein–DNA Interactions
13. Use of Surface Plasmon Resonance (SPR) to Determine Binding Affinities and Kinetic Parameters Between Components Important in Fusion Machinery]
14. Structure of CD20 in complex with the therapeutic monoclonal antibody rituximab]
15. Fluorescence Titrations to Determine the Binding Affinity of Cyclic Nucleotides to SthK Ion Channels],
16. DNA binding to alkaloids
17. Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis
18. Transformation of Low-Affinity Lead Compounds into High-Affinity Protein Capture Agents
19. Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
20. Epidermal Growth Factor Receptor Cell Proliferation Signaling Pathways
21. EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib
22. Advances in studies of tyrosine kinase inhibitors and their acquired resistance
23. Structural insight into the binding mechanism of ATP to EGFR and L858R, and T790M and L858R/T790 mutants
24. Efficacy of rociletinib (CO-1686) in plasma-genotyped T790M-positive non-small cell lung cancer (NSCLC) patients (pts)
25. Synthesis and Fundamental Evaluation of Radioiodinated Rociletinib (CO-1686) as a Probe to Lung Cancer with L858R/T790M Mutations of Epidermal Growth Factor Receptor (EGFR
26. Pharmacological and Structural Characterizations of Naquotinib, a Novel Third-Generation EGFR Tyrosine Kinase Inhibitor, in EGFR-Mutated Non-Small Cell Lung Cancer
27. Structural Basis for the Regulation of PPARγ Activity by Imatinib
28. PDB https://www.rcsb.org/structure/3UG2
29. Матанство
30. https://pubchem.ncbi.nlm.nih.gov/compound/Water
31. https://pubchem.ncbi.nlm.nih.gov/compound/1%2C4-butanediol
32. https://pubchem.ncbi.nlm.nih.gov/compound/Gefitinib
33. https://www.rcsb.org/structure/3VJN
34. Nonhydrolyzable ATP analog 5'-adenylyl-imidodiphosphate (AMP-PNP) does not inhibit ATP-dependent scanning of leader sequence of mRNA
35. Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor
36. https://www.rcsb.org/structure/5XDK
37. Structural basis of mutant-selectivity and drug-resistance related to CO-1686
38. https://www.selleckchem.com/products/co-1686.html
39. https://www.rcsb.org/structure/6KTN
40. Structural Basis for the Regulation of PPARγ Activity by Imatinib
41. Small Molecule Kinase Inhibitors as Anti-Cancer Therapeutics
42. Influence of chemotherapy on EGFR mutation status
43. https://www.rcsb.org/structure/5XDL
44. https://www.rcsb.org/structure/5Y9T
45. https://www.rcsb.org/structure/1M17
46. Tyrosine kinase inhibitors: Multi-targeted or single-targeted?
47. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
48. Epidermal growth factor receptor mutations and gene amplification in non-small-cell lung cancer: molecular analysis of the IDEAL/INTACT gefitinib trials
49. Advances in studies of tyrosine kinase inhibitors
50. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: Mechanism of activation and insights into differential inhibitor sensitivity
51. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP
52. Discovery of a mutant-selective covalent inhibitor of EGFR that overcomes T790M-mediated resistance in NSCLC
53. New developments in the management of non-small-cell lung cancer, focus on rociletinib: what went wrong
54. Discovery of a mutant-selective covalent inhibitor of EGFR that overcomes T790M-mediated resistance in NSCLC
55. Tjin Tham Sjin R, Lee K, Walter AO, Dubrovskiy A, SheetsM, Martin TS, Labenski MT, Zhu Z, Tester R, Karp R,Medikonda A, Chaturvedi P, Ren Y, et al. In vitro and in vivo characterization of irreversible mutant-selective EGFR inhibitors that are wild-type sparing. Mol Cancer Ther. 2014; 13:1468-1479.]
56. LiverTox: Clinical and Research Information on Drug-Induced Liver Injury
57. Yki-Jarvinen H. Thiazolidinediones. N Engl J Med (2004) 351:1106–18. doi:10.1056/NEJMra041001
58. PPAR-γ Agonists As Antineoplastic Agents in Cancers with Dysregulated
59. Novel Third-Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance
60. Markedly increased ocular side effect causing severe vision deterioration after chemotherapy using new or investigational
.
