Rociletinib (CO-1686)
Rociletinib (CO-1686)
Biochemical software
Results of numerical calculations on the effect of amino acid residue substitutions in EGFR on binding to rociletinib (CO-1686)
Results of numerical calculations on the effect of amino acid residue substitutions in EGFR on binding to rociletinib (CO-1686)
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.
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.
Rociletinib (CO-1686, AVL-301) is an irreversible, mutant-selective EGFR inhibitor with Ki of 21.5 nM and 303.3 nM for EGFRL858R/T790M and EGFRWT in cell-free assays, respectively.
Rociletinib (CO-1686) is an irreversible, mutant-selective EGFR inhibitor. It is a medication developed to treat non-small cell lung carcinomas with a specific mutation. It is a third-generation epidermal growth factor receptor tyrosine kinase inhibitor. It was being developed by Clovis Oncology as a potential treatment for non-small cell lung cancer
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.
Three-dimensional structure of CO-1686-EGFR dimer with indication of key amino acid residues (PDB 5XDL). The graph shows the results of numerical calculations when the CO-1686 molecule binds to EGFR for the PDB 5XDK structure and the additional calculations conducted for the PDB 5XDL structure (Figure 1a-b).
Software Data Results
The results of numerical calculations of two different structures (5XDK and 5XDL) EGFR-Rociletinib (CO-1686) are in good agreement.
1. Substitution of L844V leads to a decrease in the stability of the mEGFR (L844V) - Rociletinib dimeric complex when analyzing the 5XDK and 5XDL sutures (the difference in the cond (W) value between the two mEGFR (L844V) - Rociletinib and wtEGFR-Rociletinib complexes was 300)
2. Replacement of T790M leads to increased resistance of mEGFR (T790M) - Rociletinib
3. Double substitution of T790M / L858R leads to a significant increase in the stability of the mEGFR dimer (T790M / L858R) - Rociletinib. Numerical calculations of the two structures showed similar results.
4. Replacement of L858R led to an increase in the stability of the mEGFR complex (L858R) - Rociletinib
Thus, our developed numerical method makes it possible to determine the range of stability changes in dimeric complexes involving a small chemical molecule and a protein molecule in the presence of a three-dimensional structure of the dimeric complex.
Applying our method will make it possible to identify mutations that lead to the decreased/increased affinity of components.
Note that a numerical analysis requires the three-dimensional structure of the studied dimer, into whose protein amino acid substitutions will be introduced. The three-dimensional structure may already contain mutations in the protein or be represented by a wild-type protein. Existing substitutions/mutations in the three-dimensional structure of proteins do not affect the results of computational accuracy.
1. Substitution of L844V leads to a decrease in the stability of the mEGFR (L844V) - Rociletinib dimeric complex when analyzing the 5XDK and 5XDL sutures (the difference in the cond (W) value between the two mEGFR (L844V) - Rociletinib and wtEGFR-Rociletinib complexes was 300)
2. Replacement of T790M leads to increased resistance of mEGFR (T790M) - Rociletinib
3. Double substitution of T790M / L858R leads to a significant increase in the stability of the mEGFR dimer (T790M / L858R) - Rociletinib. Numerical calculations of the two structures showed similar results.
4. Replacement of L858R led to an increase in the stability of the mEGFR complex (L858R) - Rociletinib
Thus, our developed numerical method makes it possible to determine the range of stability changes in dimeric complexes involving a small chemical molecule and a protein molecule in the presence of a three-dimensional structure of the dimeric complex.
Applying our method will make it possible to identify mutations that lead to the decreased/increased affinity of components.
Note that a numerical analysis requires the three-dimensional structure of the studied dimer, into whose protein amino acid substitutions will be introduced. The three-dimensional structure may already contain mutations in the protein or be represented by a wild-type protein. Existing substitutions/mutations in the three-dimensional structure of proteins do not affect the results of computational accuracy.
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
.
