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Suriñach A, Hospital A, Westermaier Y, Jordà L, Orozco-Ruiz S, Beltrán D, Colizzi F, Andrio P, Soliva R, Municoy M, Gelpí JL, Orozco M. High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. J Chem Inf Model 2023; 63:321-334. [PMID: 36576351 DOI: 10.1021/acs.jcim.2c01344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mutations in the kinase domain of the epidermal growth factor receptor (EGFR) can be drivers of cancer and also trigger drug resistance in patients receiving chemotherapy treatment based on kinase inhibitors. A priori knowledge of the impact of EGFR variants on drug sensitivity would help to optimize chemotherapy and design new drugs that are effective against resistant variants before they emerge in clinical trials. To this end, we explored a variety of in silico methods, from sequence-based to "state-of-the-art" atomistic simulations. We did not find any sequence signal that can provide clues on when a drug-related mutation appears or the impact of such mutations on drug activity. Low-level simulation methods provide limited qualitative information on regions where mutations are likely to cause alterations in drug activity, and they can predict around 70% of the impact of mutations on drug efficiency. High-level simulations based on nonequilibrium alchemical free energy calculations show predictive power. The integration of these "state-of-the-art" methods into a workflow implementing an interface for parallel distribution of the calculations allows its automatic and high-throughput use, even for researchers with moderate experience in molecular simulations.
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Affiliation(s)
- Aristarc Suriñach
- Nostrum Biodiscovery, Av. Josep Tarradellas 8-10, 08029 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Yvonne Westermaier
- Nostrum Biodiscovery, Av. Josep Tarradellas 8-10, 08029 Barcelona, Spain
| | - Luis Jordà
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Sergi Orozco-Ruiz
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Daniel Beltrán
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Pau Andrio
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
| | - Robert Soliva
- Nostrum Biodiscovery, Av. Josep Tarradellas 8-10, 08029 Barcelona, Spain
| | - Martí Municoy
- Nostrum Biodiscovery, Av. Josep Tarradellas 8-10, 08029 Barcelona, Spain
| | - Josep Lluís Gelpí
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain.,Department Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona 08029, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Department Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona 08029, Spain
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Wang WJ, Zhang T. Integration of traditional Chinese medicine and Western medicine in the era of precision medicine. JOURNAL OF INTEGRATIVE MEDICINE-JIM 2018; 15:1-7. [PMID: 28088253 DOI: 10.1016/s2095-4964(17)60314-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Precision medicine has received growing recognition from clinicians, health systems, and the pharmaceutical industry, as well as patients and policymakers, which will leave a major impact on the practice of medicine. Interestingly, traditional Chinese medicine (TCM) provides personalized medical treatment based on the theory of TCM characterized by holistic concept and pattern differentiation. This, to some extent, is similar to the personalized medical treatment of precision medicine. In China, TCM as well as Western medicine (WM) plays an important role in healthcare. In this article, the authors summarized the influence of precision medicine on current medical directions, the advantages of TCM in disease treatment, further development of precision medicine and the strategies for integration of TCM and WM under this new treatment approach. In addition, the authors discuss the perspective of precise medical diagnosis and treatment, precise prevention, and the complementary advantages of the integration of TCM and WM. Finally, the authors give their perspectives on the challenges and opportunities presented by precision medicine, in the context of further research toward the integration of TCM and WM.
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Affiliation(s)
- Wen-Jian Wang
- Institute of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.,Clinical Research Institute of Chinese Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai 200437, China
| | - Teng Zhang
- Clinical Research Institute of Chinese Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai 200437, China.,Yueyang Hospital of Chinese Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
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Cho KM, Keam B, Kim TM, Lee SH, Kim DW, Heo DS. Clinical efficacy of erlotinib, a salvage treatment for non-small cell lung cancer patients following gefitinib failure. Korean J Intern Med 2015; 30:891-8. [PMID: 26552465 PMCID: PMC4642019 DOI: 10.3904/kjim.2015.30.6.891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/29/2014] [Accepted: 12/05/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND/AIMS The purpose of this study was to identify predictive factors for erlotinib treatment in non-small cell lung cancer (NSCLC) patients following gefitinib failure. METHODS Forty-five patients with NSCLC who were treated with erlotinib following gefitinib failure at Seoul National University Hospital between August 2005 and November 2011 were enrolled. Epidermal growth factor receptor (EGFR) mutation status, pathologic findings and other clinical factors, including response to tyrosine kinase inhibitors (TKIs) and progression-free survival (PFS), were evaluated. RESULTS Of the 45 patients, 40 patients (88.8%) had adenocarcinoma. The following EGFR mutations were observed: five patients with a deletion of exon 19, six patients with an L858R mutation, three patients with wild-type EGFR, and 31 patients with unknown mutations. The response rate of erlotinib was 4.4%, and stable disease was 42.2%. The median PFS for erlotinib was 2.6 months (95% confidence interval, 1.4 to 3.7). Patients with a PFS ≥ 4 months during previous gefitinib treatment had a significantly longer PFS with erlotinib (3.3 months vs. 1.6 months, respectively; p < 0.01) than patients with PFS < 4 months with gefitinib. According to multivariate analyses, PFS ≥ 4 months for previous gefitinib treatment was significantly associated with prolonged PFS with erlotinib (p = 0.04). However, the response rate of gefitinib and treatment sequence were not associated with prolonged PFS with erlotinib (p = 0.28 and p = 0.67, respectively). CONCLUSIONS Following rechallenge with the EGFR TKI erlotinib following gefitinib failure, patients who showed prolonged PFS with gefitinib benefit from erlotinib. However, further prospective studies are needed to confirm these findings.
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Affiliation(s)
- Kyoung Min Cho
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Correspondence to Bhumsuk Keam, M.D. Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno- gu, Seoul 03080, Korea Tel: +82-2-2072-7215 Fax: +82-2-762-9662 E-mail:
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Se-Hoon Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Dae Seog Heo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Zhu N, Xiao H, Wang LM, Fu S, Zhao C, Huang H. Mutations in tyrosine kinase and tyrosine phosphatase and their relevance to the target therapy in hematologic malignancies. Future Oncol 2015; 11:659-73. [PMID: 25686120 DOI: 10.2217/fon.14.280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Protein tyrosine kinases and protein tyrosine phosphatases play pivotal roles in regulation of cellular phosphorylation and signal transduction with opposite functions. Accumulating evidences have uncovered the relevance of genetic alterations in these two family members to hematologic malignancies. This review underlines progress in understanding the pathogenesis of these genetic alterations including mutations and aberrant expression and the evolving protein tyrosine kinases and protein tyrosine phosphatases targeted therapeutic strategies in hematologic neoplasms.
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Affiliation(s)
- Ni Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, PR China
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Stewart EL, Tan SZ, Liu G, Tsao MS. Known and putative mechanisms of resistance to EGFR targeted therapies in NSCLC patients with EGFR mutations-a review. Transl Lung Cancer Res 2015; 4:67-81. [PMID: 25806347 DOI: 10.3978/j.issn.2218-6751.2014.11.06] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/04/2014] [Indexed: 12/12/2022]
Abstract
Lung cancer is the leading cause of cancer related deaths in Canada with non-small cell lung cancer (NSCLC) being the predominant form of the disease. Tumor characterization can identify cancer-driving mutations as treatment targets. One of the most successful examples of cancer targeted therapy is inhibition of mutated epidermal growth factor receptor (EGFR), which occurs in ~10-30% of NSCLC patients. While this treatment has benefited many patients with activating EGFR mutations, almost all who initially benefited will eventually acquire resistance. Approximately 50% of cases of acquired resistance (AR) are due to a secondary T790M mutation in exon 20 of the EGFR gene; however, many of the remaining mechanisms of resistance are still unknown. Much work has been done to elucidate the remaining mechanisms of resistance. This review aims to highlight both the mechanisms of resistance that have already been identified in patients and potential novel mechanisms identified in preclinical models which have yet to be validated in the patient settings.
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Affiliation(s)
- Erin L Stewart
- 1 Princess Margaret Cancer Centre, University Health Network, 2 Department of Medical Biophysics, 3 Department of Laboratory Medicine and Pathobiology, 4 Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Samuel Zhixing Tan
- 1 Princess Margaret Cancer Centre, University Health Network, 2 Department of Medical Biophysics, 3 Department of Laboratory Medicine and Pathobiology, 4 Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- 1 Princess Margaret Cancer Centre, University Health Network, 2 Department of Medical Biophysics, 3 Department of Laboratory Medicine and Pathobiology, 4 Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ming-Sound Tsao
- 1 Princess Margaret Cancer Centre, University Health Network, 2 Department of Medical Biophysics, 3 Department of Laboratory Medicine and Pathobiology, 4 Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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