Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis
Abstract Background Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity varies for less common and rare EGFR mutations. There are various explanat...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-03-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2093-6 |
| _version_ | 1811325934651834368 |
|---|---|
| author | Bin Zou Victor H. F. Lee Hong Yan |
| author_facet | Bin Zou Victor H. F. Lee Hong Yan |
| author_sort | Bin Zou |
| collection | DOAJ |
| description | Abstract Background Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity varies for less common and rare EGFR mutations. There are various explanations for the low sensitivity of EGFR exon 20 insertions and the exon 20 T790 M point mutation to gefitinib/erlotinib. However, few studies discuss, from a structural perspective, why less common mutations, like G719X and L861Q, have moderate sensitivity to gefitinib/erlotinib. Results To decode the drug sensitivity/selectivity of EGFR mutants, it is important to analyze the interaction between EGFR mutants and EGFR inhibitors. In this paper, the 30 most common EGFR mutants were selected and the technique of protein-ligand interaction fingerprint (IFP) was applied to analyze and compare the binding modes of EGFR mutant-gefitinib/erlotinib complexes. Molecular dynamics simulations were employed to obtain the dynamic trajectory and a matrix of IFPs for each EGFR mutant-inhibitor complex. Multilinear Principal Component Analysis (MPCA) was applied for dimensionality reduction and feature selection. The selected features were further analyzed for use as a drug sensitivity predictor. The results showed that the accuracy of prediction of drug sensitivity was very high for both gefitinib and erlotinib. Targeted Projection Pursuit (TPP) was used to show that the data points can be easily separated based on their sensitivities to gefetinib/erlotinib. Conclusions We can conclude that the IFP features of EGFR mutant-TKI complexes and the MPCA-based tensor object feature extraction are useful to predict the drug sensitivity of EGFR mutants. The findings provide new insights for studying and predicting drug resistance/sensitivity of EGFR mutations in NSCLC and can be beneficial to the design of future targeted therapies and innovative drug discovery. |
| first_indexed | 2024-04-13T14:42:02Z |
| format | Article |
| id | doaj.art-f7027bd88c0c4fce9acdfc604defb23a |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T14:42:02Z |
| publishDate | 2018-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-f7027bd88c0c4fce9acdfc604defb23a2022-12-22T02:42:53ZengBMCBMC Bioinformatics1471-21052018-03-0119111310.1186/s12859-018-2093-6Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysisBin Zou0Victor H. F. Lee1Hong Yan2Department of Electronic Engineering, City University of Hong KongDepartment of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong KongDepartment of Electronic Engineering, City University of Hong KongAbstract Background Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity varies for less common and rare EGFR mutations. There are various explanations for the low sensitivity of EGFR exon 20 insertions and the exon 20 T790 M point mutation to gefitinib/erlotinib. However, few studies discuss, from a structural perspective, why less common mutations, like G719X and L861Q, have moderate sensitivity to gefitinib/erlotinib. Results To decode the drug sensitivity/selectivity of EGFR mutants, it is important to analyze the interaction between EGFR mutants and EGFR inhibitors. In this paper, the 30 most common EGFR mutants were selected and the technique of protein-ligand interaction fingerprint (IFP) was applied to analyze and compare the binding modes of EGFR mutant-gefitinib/erlotinib complexes. Molecular dynamics simulations were employed to obtain the dynamic trajectory and a matrix of IFPs for each EGFR mutant-inhibitor complex. Multilinear Principal Component Analysis (MPCA) was applied for dimensionality reduction and feature selection. The selected features were further analyzed for use as a drug sensitivity predictor. The results showed that the accuracy of prediction of drug sensitivity was very high for both gefitinib and erlotinib. Targeted Projection Pursuit (TPP) was used to show that the data points can be easily separated based on their sensitivities to gefetinib/erlotinib. Conclusions We can conclude that the IFP features of EGFR mutant-TKI complexes and the MPCA-based tensor object feature extraction are useful to predict the drug sensitivity of EGFR mutants. The findings provide new insights for studying and predicting drug resistance/sensitivity of EGFR mutations in NSCLC and can be beneficial to the design of future targeted therapies and innovative drug discovery.http://link.springer.com/article/10.1186/s12859-018-2093-6Epidermal growth factor receptor mutationMolecular dynamics simulationsInteraction fingerprintsMultilinear principal component analysis |
| spellingShingle | Bin Zou Victor H. F. Lee Hong Yan Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis BMC Bioinformatics Epidermal growth factor receptor mutation Molecular dynamics simulations Interaction fingerprints Multilinear principal component analysis |
| title | Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis |
| title_full | Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis |
| title_fullStr | Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis |
| title_full_unstemmed | Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis |
| title_short | Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis |
| title_sort | prediction of sensitivity to gefitinib erlotinib for egfr mutations in nsclc based on structural interaction fingerprints and multilinear principal component analysis |
| topic | Epidermal growth factor receptor mutation Molecular dynamics simulations Interaction fingerprints Multilinear principal component analysis |
| url | http://link.springer.com/article/10.1186/s12859-018-2093-6 |
| work_keys_str_mv | AT binzou predictionofsensitivitytogefitiniberlotinibforegfrmutationsinnsclcbasedonstructuralinteractionfingerprintsandmultilinearprincipalcomponentanalysis AT victorhflee predictionofsensitivitytogefitiniberlotinibforegfrmutationsinnsclcbasedonstructuralinteractionfingerprintsandmultilinearprincipalcomponentanalysis AT hongyan predictionofsensitivitytogefitiniberlotinibforegfrmutationsinnsclcbasedonstructuralinteractionfingerprintsandmultilinearprincipalcomponentanalysis |