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Wang JL, Liu MS, Fu YD, Kan QB, Li CY, Ma R, Fang ZW, Liu HX, Li MX, Lv JL, Sang P, Zhang C, Li HW. Exploring the conformational dynamics and thermodynamics of EGFR S768I and G719X + S768I mutations in non-small cell lung cancer: An in silico approaches. Open Life Sci 2023; 18:20220768. [PMID: 38035047 PMCID: PMC10685407 DOI: 10.1515/biol-2022-0768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is often driven by mutations in the epidermal growth factor receptor (EGFR) gene. However, rare mutations such as G719X and S768I lack standard anti-EGFR targeted therapies. Understanding the structural differences between wild-type EGFR and these rare mutants is crucial for developing EGFR-targeted drugs. We performed a systematic analysis using molecular dynamics simulations, essential dynamics (ED), molecular mechanics Poisson-Boltzmann surface area, and free energy calculation methods to compare the kinetic properties, molecular motion, and free energy distribution between wild-type EGFR and the rare mutants' structures G719X-EGFR, S768I-EGFR, and G719X + S768I-EGFR. Our results showed that S768I-EGFR and G719X + S768I-EGFR have higher global and local conformational flexibility and lower thermal and global structural stability than WT-EGFR. ED analysis revealed different molecular motion patterns between S768I-EGFR, G719X + S768I-EGFR, and WT-EGFR. The A-loop and αC-helix, crucial structural elements related to the active state, showed a tendency toward active state development, providing a molecular mechanism explanation for NSCLC caused by EGFR S768I and EGFR G719C + S768I mutations. The present study may be helpful in the development of new EGFR-targeted drugs based on the structure of rare mutations. Our findings may aid in developing new targeted treatments for patients with EGFR S768I and EGFR G719X + S768I mutations.
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Affiliation(s)
- Jun-Ling Wang
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Ming-Sheng Liu
- Department of Urological Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Yu-Dong Fu
- Department of Thoracic Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Qiang-Bo Kan
- Department of Thoracic Surgery, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Chun-Yan Li
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Rong Ma
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Zhe-Wei Fang
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Hong-Xia Liu
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Meng-Xian Li
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Jia-Ling Lv
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Peng Sang
- School of Life Science, Dali University, Dali671003, China
| | - Chao Zhang
- Department of Oncology, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
| | - Hong-Wei Li
- Clinical Laboratory, Kunming Medical University Affiliated Qujing Hospital, Qujing655000, China
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Todsaporn D, Zubenko A, Kartsev V, Aiebchun T, Mahalapbutr P, Petrou A, Geronikaki A, Divaeva L, Chekrisheva V, Yildiz I, Choowongkomon K, Rungrotmongkol T. Discovery of Novel EGFR Inhibitor Targeting Wild-Type and Mutant Forms of EGFR: In Silico and In Vitro Study. Molecules 2023; 28:molecules28073014. [PMID: 37049777 PMCID: PMC10096398 DOI: 10.3390/molecules28073014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
Targeting L858R/T790M and L858R/T790M/C797S mutant EGFR is a critical challenge in developing EGFR tyrosine kinase inhibitors to overcome drug resistance in non-small cell lung cancer (NSCLC). The discovery of next-generation EGFR tyrosine kinase inhibitors (TKIs) is therefore necessary. To this end, a series of furopyridine derivatives were evaluated for their EGFR-based inhibition and antiproliferative activities using computational and biological approaches. We found that several compounds derived from virtual screening based on a molecular docking and solvated interaction energy (SIE) method showed the potential to suppress wild-type and mutant EGFR. The most promising PD13 displayed strong inhibitory activity against wild-type (IC50 of 11.64 ± 1.30 nM), L858R/T790M (IC50 of 10.51 ± 0.71 nM), which are more significant than known drugs. In addition, PD13 revealed a potent cytotoxic effect on A549 and H1975 cell lines with IC50 values of 18.09 ± 1.57 and 33.87 ± 0.86 µM, respectively. The 500-ns MD simulations indicated that PD13 formed a hydrogen bond with Met793 at the hinge region, thus creating excellent EGFR inhibitory activity. Moreover, the binding of PD13 in the hinge region of EGFR was the major determining factor in stabilizing the interactions via hydrogen bonds and van der Waals (vdW). Altogether, PD13 is a promising novel EGFR inhibitor that could be further clinically developed as fourth-generation EGFR-TKIs.
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Hameduh T, Mokry M, Miller AD, Adam V, Heger Z, Haddad Y. A rotamer relay information system in the epidermal growth factor receptor-drug complexes reveals clues to new paradigm in protein conformational change. Comput Struct Biotechnol J 2021; 19:5443-5454. [PMID: 34667537 PMCID: PMC8511715 DOI: 10.1016/j.csbj.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 11/04/2022] Open
Abstract
Cancer cells can escape the effects of chemotherapy through mutations and upregulation of a tyrosine kinase protein called the epidermal growth factor receptor (EGFR). In the past two decades, four generations of tyrosine kinase inhibitors targeting EGFR have been developed. Using comparative structure analysis of 116 EGFR-drug complex crystal structures, cluster analysis produces two clans of 73 and 43 structures, respectively. The first clan of 73 structures is larger and is comprised mostly of the C-helix-IN conformation while the second clan of 43 structures correlates with the C-helix-OUT conformation. A deep rotamer analysis identifies 43 residues (18%) of the total of 237 residues spanning the kinase structures under investigation with significant rotamer variations between the C-helix-IN and C-helix-OUT clans. The locations of these rotamer variations take on the appearance of side chain conformational relays extending out from points of EGFR mutation to different regions of the EGFR kinase. Accordingly, we propose that key EGFR mutations act singly or together to induce drug resistant conformational changes in EGFR that are communicated via these side chain conformational relays. Accordingly, these side chain conformational relays appear to play a significant role in the development of tumour resistance. This phenomenon also suggests a new paradigm in protein conformational change that is mediated by supportive relays of rotamers on the protein surface, rather than through conventional backbone movements.
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Affiliation(s)
- Tareq Hameduh
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
| | - Michal Mokry
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Andrew D. Miller
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
- KP Therapeutics (Europe) s.r.o., Purkyňova 649/127, Brno CZ-61200, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Purkynova 656/123, 612 00 Brno, Czech Republic
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Aiebchun T, Mahalapbutr P, Auepattanapong A, Khaikate O, Seetaha S, Tabtimmai L, Kuhakarn C, Choowongkomon K, Rungrotmongkol T. Identification of Vinyl Sulfone Derivatives as EGFR Tyrosine Kinase Inhibitor: In Vitro and In Silico Studies. Molecules 2021; 26:molecules26082211. [PMID: 33921332 PMCID: PMC8069501 DOI: 10.3390/molecules26082211] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/17/2023] Open
Abstract
Epidermal growth factor receptor (EGFR), overexpressed in many types of cancer, has been proved as a high potential target for targeted cancer therapy due to its role in regulating proliferation and survival of cancer cells. In the present study, a series of designed vinyl sulfone derivatives was screened against EGFR tyrosine kinase (EGFR-TK) using in silico and in vitro studies. The molecular docking results suggested that, among 78 vinyl sulfones, there were eight compounds that could interact well with the EGFR-TK at the ATP-binding site. Afterwards, these screened compounds were tested for the inhibitory activity towards EGFR-TK using ADP-Glo™ kinase assay, and we found that only VF16 compound exhibited promising inhibitory activity against EGFR-TK with the IC50 value of 7.85 ± 0.88 nM. In addition, VF16 showed a high cytotoxicity with IC50 values of 33.52 ± 2.57, 54.63 ± 0.09, and 30.38 ± 1.37 µM against the A431, A549, and H1975 cancer cell lines, respectively. From 500-ns MD simulation, the structural stability of VF16 in complex with EGFR-TK was quite stable, suggesting that this compound could be a novel small molecule inhibitor targeting EGFR-TK.
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Affiliation(s)
- Thitinan Aiebchun
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Atima Auepattanapong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10700, Thailand; (A.A.); (O.K.); (C.K.)
| | - Onnicha Khaikate
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10700, Thailand; (A.A.); (O.K.); (C.K.)
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand;
| | - Lueacha Tabtimmai
- Department of Biotechnology, Faculty of Applied Science, King Mongkut’s University of Technology of North Bangkok, Bangkok 10800, Thailand;
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok 10700, Thailand; (A.A.); (O.K.); (C.K.)
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand;
- Correspondence: (K.C.); (T.R.); Tel.: +66-2218-5426 (T.R.); Fax: +66-2218-5418 (T.R.)
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (K.C.); (T.R.); Tel.: +66-2218-5426 (T.R.); Fax: +66-2218-5418 (T.R.)
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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The Value of Next-Generation Sequencing for Treatment in Non-Small Cell Lung Cancer Patients: The Observational, Real-World Evidence in China. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9387167. [PMID: 32047821 PMCID: PMC7003276 DOI: 10.1155/2020/9387167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/09/2019] [Indexed: 12/17/2022]
Abstract
Background Great success has been made in the targeting therapy of advanced non-small cell lung cancer (NSCLC). Nowadays, next generation sequencing (NGS) is acquirable and affordable in developed area of China. Using this feasible and accurate method of detecting therapeutic genes would help to select optimal treatments to extend patients survival. Here, we identified somatic mutations by NGS and analyzed the value for treatment of NSCLC in a real-world clinical setting. Methods NGS was carried out on biopsy samples obtained from 66 advanced unresectable NSCLC patients who had not received any treatment. 23 patients received liquid biopsy after failure of first-line targeted treatment. The mutation profiling as well as associations between mutations and clinicopathological characters was analyzed. The study also assessed the values of NGS for choosing treatment options and predicting prognosis in NSCLC patients. Results 152 somatic mutations were identified in 45 (68.18%) tissue samples. The most frequently mutated genes were EGFR (42.42%), TP53 (31.82%) and KRAS (15.15%). Specifically, the most frequent EGFR (42.42%), EGFR (42.42%), p = 0.046). In addition, in the smoking group, patients with EGFR (42.42%), p = 0.046). In addition, in the smoking group, patients with EGFR (42.42%), EGFR (42.42%), p = 0.046). In addition, in the smoking group, patients with Conclusions The observational study from real-world demonstrated that using NGS in routine clinical detection may be useful in guiding the therapy decisions and benefit more Chinese NSCLC patients.
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J CP, D TK, P S, R S, W CEJ, C GPD, Zayed H. An integrative bioinformatics pipeline to demonstrate the alteration of the interaction between the ALDH2*2 allele with NAD + and Disulfiram. J Cell Biochem 2019; 120:17030-17041. [PMID: 31104322 DOI: 10.1002/jcb.28964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/07/2019] [Accepted: 03/15/2019] [Indexed: 11/07/2022]
Abstract
Alcohol use disorder (AUD) is a multifactorial psychiatric behavior disorder. Disulfiram is the first approved drug by the Food and Drug Administration for alcohol-dependent patients, which targets the ALDH2 enzyme. Several genes are known to be involved in alcohol metabolism; mutations in any of these genes are known to be associated with AUD. The E504K mutation in the ALDH2 of the precursor protein or the E487K of the mature protein (E504K/E487K; ALDH2*2 allele) is carried by approximately 8% of the world population. In this study, we aimed to test the known inactive allele ALDH2*2, to validate the use of our extensive computational pipeline (in silico tools, molecular modeling, and molecular docking) for testing the interaction between the ALDH2*2 allele, NAD+, and Disulfiram. In silico predictions showed that the E504K variant of ALDH2 to be pathogenic and destabilizing with the maximum number of prediction in silico tools. Consequently, we studied the effect of this mutation mainly on the interaction between NAD+ -E504K and Disulfiram-E504K complexes using molecular docking technique, and molecular dynamics (MD) analysis. From the molecular docking analysis with NAD+ , we observed that the interaction affinity of the NAD+ decreases with the impact of E504K variant. On the other hand, the drug Disulfiram showed similar interaction in both the native and mutant ALDH2 proteins. Further, the comprehensive MD analysis predicted that the E504K destabilizes the protein and influences the NAD+ and Disulfiram interactions. Our findings reveal that the interaction of NAD+ to the protein is disturbed by the E504K/E487K variant whereas the drug Disulfiram has a similar effect as both native ALDH2 and ALDH2 bearing E504K/E487K variant. This study provides a platform to understand the effect of E504K/E487K on the molecular interaction with NAD+ and Disulfiram.
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Affiliation(s)
- Christy Priyadharshini J
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Thirumal Kumar D
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Sneha P
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Siva R
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Charles Emmanuel Jebaraj W
- Department of Biotechnology, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai-600116, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, P. O. Box:2713, Qatar
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Sangpheak K, Tabtimmai L, Seetaha S, Rungnim C, Chavasiri W, Wolschann P, Choowongkomon K, Rungrotmongkol T. Biological Evaluation and Molecular Dynamics Simulation of Chalcone Derivatives as Epidermal Growth Factor-Tyrosine Kinase Inhibitors. Molecules 2019; 24:molecules24061092. [PMID: 30897725 PMCID: PMC6471738 DOI: 10.3390/molecules24061092] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/02/2022] Open
Abstract
Targeted cancer therapy has become a high potential cancer treatment. Epidermal growth factor receptor (EGFR), which plays an important role in cell signaling, enhanced cell survival and proliferation, has been suggested as molecular target for the development of novel cancer therapeutics. In this study, a series of chalcone derivatives was screened by in vitro cytotoxicity against the wild type (A431 and A549) and mutant EGFR (H1975 and H1650) cancer cell lines, and, subsequently, tested for EGFR-tyrosine kinase (TK) inhibition. From the experimental screening, all chalcones seemed to be more active against the A431 than the A549 cell line, with chalcones 1c, 2a, 3e, 4e, and 4t showing a more than 50% inhibitory activity against the EGFR-TK activity and a high cytotoxicity with IC50 values of < 10 µM against A431 cells. Moreover, these five chalcones showed more potent on H1975 (T790M/L858R mutation) than H1650 (exon 19 deletion E746-A750) cell lines. Only three chalcones (1c, 2a and 3e) had an inhibitory activity against EGFR-TK with a relative inhibition percentage that was close to the approved drug, erlotinib. Molecular dynamics studies on their complexes with EGFR-TK domain in aqueous solution affirmed that they were well-occupied within the ATP binding site and strongly interacted with seven hydrophobic residues, including the important hinge region residue M793. From the above information, as well as ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties, all three chalcones could serve as lead compounds for the development of EGFR-TK inhibitors.
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Affiliation(s)
- Kanyani Sangpheak
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10903, Thailand.
| | - Supaphorn Seetaha
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10903, Thailand.
| | - Chompoonut Rungnim
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand.
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna 1090, Austria.
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria.
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10903, Thailand.
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
- Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Strategies to overcome acquired resistance to EGFR TKI in the treatment of non-small cell lung cancer. Clin Transl Oncol 2019; 21:1287-1301. [PMID: 30864018 DOI: 10.1007/s12094-019-02075-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/26/2019] [Indexed: 02/08/2023]
Abstract
Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR TKI) represents a paradigm shift in the treatment of non-small cell lung cancer (NSCLC) patients and has been the first-line therapy in clinical practice. While erlotinib, gefitinib and afatinib have achieved superior efficacy in terms of progression-free survival and overall survival compared with conventional chemotherapy in NSCLC patients, most people inevitably develop acquired resistance to them, which presents another challenge in the treatment of NSCLC. The mechanisms of acquired resistance can be classified as three types: target gene mutation, bypass signaling pathway activation and histological transformation. And the most common mechanism is T790M which accounts for approximately 50% of all subtypes. Many strategies have been explored to overcome the acquired resistance to EGFR TKI. Continuation of EGFR TKI beyond progressive disease is confined to patients in asymptomatic stage when the EGFR addiction is still preserved in some subclones. While the combination of EGFR TKI and chemotherapy or other targeted agents has improved the survival benefit in EGFR TKI resistant patients, there are controversies within them. The next-generation EGFR TKI and immunotherapy represent two novel directions for overcoming acquired resistance and have achieved promising efficacy. Liquid biopsy provides surveillance of the EGFR mutation by disclosing the entire genetic landscape but tissue biopsy is still indispensable because of the considerable rate of false-negative plasma.
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10
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Zarezade V, Abolghasemi M, Rahim F, Veisi A, Behbahani M. In silico assessment of new progesterone receptor inhibitors using molecular dynamics: a new insight into breast cancer treatment. J Mol Model 2018; 24:337. [DOI: 10.1007/s00894-018-3858-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023]
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Cavuturu BM, Bhandare VV, Ramaswamy A, Arumugam N. Molecular dynamics of interaction of Sesamin and related compounds with the cancer marker β-catenin: an in silico study. J Biomol Struct Dyn 2018; 37:877-891. [DOI: 10.1080/07391102.2018.1442250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bindu Madhuri Cavuturu
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | | | - Amutha Ramaswamy
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | - Neelakantan Arumugam
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
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Bharate JB, McConnell N, Naresh G, Zhang L, Lakkaniga NR, Ding L, Shah NP, Frett B, Li HY. Rational Design, Synthesis and Biological Evaluation of Pyrimidine-4,6-diamine derivatives as Type-II inhibitors of FLT3 Selective Against c-KIT. Sci Rep 2018; 8:3722. [PMID: 29487300 PMCID: PMC5829162 DOI: 10.1038/s41598-018-21839-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/12/2018] [Indexed: 12/19/2022] Open
Abstract
FMS-like Tyrosine Kinase 3 (FLT3) is a clinically validated target for acute myeloid leukemia (AML). Inhibitors targeting FLT3 have been evaluated in clinical studies and have exhibited potential to treat FLT3-driven AML. A frequent, clinical limitation is FLT3 selectivity, as concomitant inhibition of FLT3 and c-KIT is thought to cause dose-limiting myelosuppression. Through a rational design approach, novel FLT3 inhibitors were synthesized employing a pyridine/pyrimidine warhead. The most potent compound identified from the studies is compound 13a, which exhibited an IC50 value of 13.9 ± 6.5 nM against the FLT3 kinase with high selectivity over c-KIT. Mechanism of action studies suggested that 13a is a Type-II kinase inhibitor, which was also supported through computer aided drug discovery (CADD) efforts. Cell-based assays identified that 13a was potent on a variety of FLT3-driven cell lines with clinical relevance. We report herein the discovery and therapeutic evaluation of 4,6-diamino pyrimidine-based Type-II FLT3 inhibitors, which can serve as a FLT3-selective scaffold for further clinical development.
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Affiliation(s)
- Jaideep B Bharate
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Nicholas McConnell
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA.,Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Gunaganti Naresh
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Lingtian Zhang
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Lucky Ding
- Division of Hematology/Oncology, University of California, San Francisco, CA, 94143, USA
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, CA, 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94115, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, 72205, USA.
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Liu M, Xu S, Wang Y, Li Y, Li Y, Zhang H, Liu H, Chen J. PD 0332991, a selective cyclin D kinase 4/6 inhibitor, sensitizes lung cancer cells to treatment with epidermal growth factor receptor tyrosine kinase inhibitors. Oncotarget 2018; 7:84951-84964. [PMID: 27825114 PMCID: PMC5356711 DOI: 10.18632/oncotarget.13069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/27/2016] [Indexed: 01/29/2023] Open
Abstract
Acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) is a major challenge to targeted therapy for non-small cell lung cancer (NSCLC). We investigated whether a cyclin D kinase 4/6 (CDK4/6) inhibitor, PD 0332991, could reverse EGFR-TKI resistance in human lung cancer cells and explored the underlying mechanisms. We found that PD 0332991 potentiated gefitinib-induced growth inhibition in both EGFR-TKI-sensitive (PC-9) and EGFR-TKI-resistant (PC-9/AB2) cells by down-regulating proliferation and inducing apoptosis and G0/G1 cell cycle arrest. Tumor xenografts were then used to verify the effects of PD 0332991 in vivo. Mice treated with a combination of PD 0332991 and gefitinib had the fastest tumor regression and delayed relapse. Tumors from mice receiving the combination treatment exhibited down-regulated proliferation, up-regulated apoptosis, and less angiogenesis. Finally, lung adenocarcinoma patients with acquired resistance to EGFR-TKIs were given an exploratory treatment of PD 0332991. One patient with gefitinib resistance exhibited clinical remission after treatment with PD 0332991. These findings suggest PD 0332991 reverses acquired EGFR-TKI-resistance in NSCLC cells, and may provide a novel treatment strategy for NSLSC patients with EGFR-TKI resistance.
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Affiliation(s)
- Minghui Liu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Song Xu
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China.,Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Yuli Wang
- Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Ying Li
- Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Yongwen Li
- Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Hongbing Zhang
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Hongyu Liu
- Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
| | - Jun Chen
- Department of Lung Cancer Surgery, Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China.,Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, 300052, Tianjin, China
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14
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Peng XN, Wang J, Zhang W. Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma. Oncol Lett 2017; 14:2249-2253. [PMID: 28789446 PMCID: PMC5530049 DOI: 10.3892/ol.2017.6387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/21/2017] [Indexed: 11/23/2022] Open
Abstract
Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.
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Affiliation(s)
- Xiao-Nu Peng
- Department of Thoracic Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Jing Wang
- Intensive Care Unit, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Wei Zhang
- Department of Thoracic Surgery, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
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15
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Martínez-Jiménez F, Overington JP, Al-Lazikani B, Marti-Renom MA. Rational design of non-resistant targeted cancer therapies. Sci Rep 2017; 7:46632. [PMID: 28436422 PMCID: PMC5402386 DOI: 10.1038/srep46632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022] Open
Abstract
Drug resistance is one of the major problems in targeted cancer therapy. A major cause of resistance is changes in the amino acids that form the drug-target binding site. Despite of the numerous efforts made to individually understand and overcome these mutations, there is a lack of comprehensive analysis of the mutational landscape that can prospectively estimate drug-resistance mutations. Here we describe and computationally validate a framework that combines the cancer-specific likelihood with the resistance impact to enable the detection of single point mutations with the highest chance to be responsible of resistance to a particular targeted cancer therapy. Moreover, for these treatment-threatening mutations, the model proposes alternative therapies overcoming the resistance. We exemplified the applicability of the model using EGFR-gefitinib treatment for Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Cancer (LSCC) and the ERK2-VTX11e treatment for melanoma and colorectal cancer. Our model correctly identified the phenotype known resistance mutations, including the classic EGFR-T790M and the ERK2-P58L/S/T mutations. Moreover, the model predicted new previously undescribed mutations as potentially responsible of drug resistance. Finally, we provided a map of the predicted sensitivity of alternative ERK2 and EGFR inhibitors, with a particular highlight of two molecules with a low predicted resistance impact.
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Affiliation(s)
- Francisco Martínez-Jiménez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John P. Overington
- Medicines Discovery Catapult Block 35, Mereside, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK
| | | | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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16
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Li K, Yang M, Liang N, Li S. Determining EGFR-TKI sensitivity of G719X and other uncommon EGFR mutations in non-small cell lung cancer: Perplexity and solution (Review). Oncol Rep 2017; 37:1347-1358. [PMID: 28184913 PMCID: PMC5364853 DOI: 10.3892/or.2017.5409] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/19/2017] [Indexed: 01/20/2023] Open
Abstract
Mutations in epidermal growth factor receptor (EGFR) play critical roles in the pathogenesis of non-small cell lung cancer (NSCLC), and they are highly associated with sensitivity to tyrosine kinase inhibitors (TKIs). While the pathogenic and pharmacological characteristics of common mutations in EGFR have been thoroughly investigated, those of uncommon mutations remain to be elucidated. Traditional approaches to study common mutations by randomized controlled trials are not feasible for uncommon mutations owing to their rarity. Therefore, by systematically reviewing laboratory and clinical studies of the G719X mutation, one of the uncommon mutations, we concluded that the G719X mutation was intermediately sensitive to TKIs, with an average response rate of 35.1% (47/134). Moreover, accordingly, we proposed a comprehensive model to investigate uncommon mutations in EGFR. The model involves both basic and clinical components, composed of structural analyses, functional alterations, cell viabilities and animal models with various types of clinical studies. In this review, we systematically reviewed studies of the G719X mutation and put forward a research model that could be generalized to explore uncommon mutations in diseases associated with gene mutations.
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Affiliation(s)
- Kaidi Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Maojun Yang
- Key Laboratory for Protein Sciences of Ministry of Education, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
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17
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García-Godoy MJ, López-Camacho E, García-Nieto J, Nebro AJ, Aldana-Montes JF. Molecular Docking Optimization in the Context of Multi-Drug Resistant and Sensitive EGFR Mutants. Molecules 2016; 21:molecules21111575. [PMID: 27869781 PMCID: PMC6274512 DOI: 10.3390/molecules21111575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/13/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022] Open
Abstract
The human Epidermal Growth Factor (EGFR) plays an important role in signaling pathways, such as cell proliferation and migration. Mutations like G719S, L858R, T790M, G719S/T790M or T790M/L858R can alter its conformation, and, therefore, drug responses from lung cancer patients. In this context, candidate drugs are being tested and in silico studies are necessary to know how these mutations affect the ligand binding site. This problem can be tackled by using a multi-objective approach applied to the molecular docking problem. According to the literature, few studies are related to the application of multi-objective approaches by minimizing two or more objectives in drug discovery. In this study, we have used four algorithms (NSGA-II, GDE3, SMPSO and MOEA/D) to minimize two objectives: the ligand-receptor intermolecular energy and the RMSD score. We have prepared a set of instances that includes the wild-type EGFR kinase domain and the same receptor with somatic mutations, and then we assessed the performance of the algorithms by applying a quality indicator to evaluate the convergence and diversity of the reference fronts. The MOEA/D algorithm yields the best solutions to these docking problems. The obtained solutions were analyzed, showing promising results to predict candidate EGFR inhibitors by using this multi-objective approach.
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Affiliation(s)
- María Jesús García-Godoy
- Khaos Research Group, Departament of Computer Sciences, University of Málaga (UMA), ETSI Informática, Campus de Teatinos, 29071 Málaga, Spain.
| | - Esteban López-Camacho
- Khaos Research Group, Departament of Computer Sciences, University of Málaga (UMA), ETSI Informática, Campus de Teatinos, 29071 Málaga, Spain.
| | - José García-Nieto
- Khaos Research Group, Departament of Computer Sciences, University of Málaga (UMA), ETSI Informática, Campus de Teatinos, 29071 Málaga, Spain.
| | - Antonio J Nebro
- Khaos Research Group, Departament of Computer Sciences, University of Málaga (UMA), ETSI Informática, Campus de Teatinos, 29071 Málaga, Spain.
| | - José F Aldana-Montes
- Khaos Research Group, Departament of Computer Sciences, University of Málaga (UMA), ETSI Informática, Campus de Teatinos, 29071 Málaga, Spain.
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18
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Choe C, Shin YS, Kim C, Choi SJ, Lee J, Kim SY, Cho YB, Kim J. Crosstalk with cancer-associated fibroblasts induces resistance of non-small cell lung cancer cells to epidermal growth factor receptor tyrosine kinase inhibition. Onco Targets Ther 2015; 8:3665-78. [PMID: 26676152 PMCID: PMC4676617 DOI: 10.2147/ott.s89659] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although lung cancers with activating mutations in the epidermal growth factor receptor (EGFR) are highly sensitive to selective EGFR tyrosine kinase inhibitors (TKIs), these tumors invariably develop acquired drug resistance. Host stromal cells have been found to have a considerable effect on the sensitivity of cancer cells to EGFR TKIs. Little is known, however, about the signaling mechanisms through which stromal cells contribute to the response to EGFR TKI in non-small cell lung cancer. This work examined the role of hedgehog signaling in cancer-associated fibroblast (CAF)-mediated resistance of lung cancer cells to the EGFR TKI erlotinib. PC9 cells, non-small cell lung cancer cells with EGFR-activating mutations, became resistant to the EGFR TKI erlotinib when cocultured in vitro with CAFs. Polymerase chain reaction and immunocytochemical assays showed that CAFs induced epithelial to mesenchymal transition phenotype in PC9 cells, with an associated change in the expression of epithelial to mesenchymal transition marker proteins including vimentin. Importantly, CAFs induce upregulation of the 7-transmembrane protein smoothened, the central signal transducer of hedgehog, suggesting that the hedgehog signaling pathway is active in CAF-mediated drug resistance. Indeed, downregulation of smoothened activity with the smoothened antagonist cyclopamine induces remodeling of the actin cytoskeleton independently of Gli-mediated transcriptional activity in PC9 cells. These findings indicate that crosstalk with CAFs plays a critical role in resistance of lung cancer to EGFR TKIs through induction of the epithelial to mesenchymal transition and may be an ideal therapeutic target in lung cancer.
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Affiliation(s)
- Chungyoul Choe
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Yong-Sung Shin
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Changhoon Kim
- Department of Biomedical Science, Graduate School of Biomedical & Engineering, Hanyang University, Seoul, Republic of Korea
| | - So-Jung Choi
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Jinseon Lee
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - So Young Kim
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
| | - Jhingook Kim
- Samsung Biomedical Research Institute, Samsung Medical Center Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea ; Department of Thoracic Surgery, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Republic of Korea
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19
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N N, Zhu H, Liu J, V K, C GPD, Chakraborty C, Chen L. Analysing the Effect of Mutation on Protein Function and Discovering Potential Inhibitors of CDK4: Molecular Modelling and Dynamics Studies. PLoS One 2015; 10:e0133969. [PMID: 26252490 PMCID: PMC4529227 DOI: 10.1371/journal.pone.0133969] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/03/2015] [Indexed: 11/18/2022] Open
Abstract
The cyclin-dependent kinase 4 (CDK4)-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1) and protein-ligand (CDK4-flavopiridol) interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL) _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment.
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Affiliation(s)
- Nagasundaram N
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Hailong Zhu
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- * E-mail:
| | - Jiming Liu
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Karthick V
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - George Priya Doss C
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Chiranjib Chakraborty
- Department of Computer Sciences, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- Department of Bioinformatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, Uttra Pradesh, India
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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20
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Chikan NA, Bukhari S, Shabir N, Amin A, Shafi S, Qadri RA, Patel TNC. Atomic Insight into the Altered O6-Methylguanine-DNA Methyltransferase Protein Architecture in Gastric Cancer. PLoS One 2015; 10:e0127741. [PMID: 26011121 PMCID: PMC4444098 DOI: 10.1371/journal.pone.0127741] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/19/2015] [Indexed: 11/22/2022] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) is one of the major DNA repair protein that counteracts the alkalyting agent-induced DNA damage by replacing O6-methylguanine (mutagenic lesion) back to guanine, eventually suppressing the mismatch errors and double strand crosslinks. Exonic alterations in the form of nucleotide polymorphism may result in altered protein structure that in turn can lead to the loss of function. In the present study, we focused on the population feared for high exposure to alkylating agents owing to their typical and specialized dietary habits. To this end, gastric cancer patients pooled out from the population were selected for the mutational screening of a specific error prone region of MGMT gene. We found that nearly 40% of the studied neoplastic samples harbored missense mutation at codon151 resulting into Serine to Isoleucine variation. This variation resulted in bringing about the structural disorder, subsequently ensuing into a major stoichiometric variance in recognition domain, substrate binding and selectivity loop of the active site of the MGMT protein, as observed under virtual microscope of molecular dynamics simulation (MDS). The atomic insight into MGMT protein by computational approach showed a significant change in the intra molecular hydrogen bond pattern, thus leading to the observed structural anomalies. To further examine the mutational implications on regulatory plugs of MGMT that holds the protein in a DNA-Binding position, a MDS based analysis was carried out on, all known physically interacting amino acids essentially clustered into groups based on their position and function. The results generated by physical-functional clustering of protein indicated that the identified mutation in the vicinity of the active site of MGMT protein causes the local and global destabilization of a protein by either eliminating the stabilizing salt bridges in cluster C3, C4, and C5 or by locally destabilizing the “protein stabilizing hing” mapped on C3-C4 cluster, preceding the active site.
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Affiliation(s)
- Naveed Anjum Chikan
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Shoiab Bukhari
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Nadeem Shabir
- Department of Animal Biotechnology, College of Veterinary Sciences, Anand Agricultural University, Anand, Gujarat, India, 388 001
| | - Asif Amin
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Sheikh Shafi
- Department of Clinical Biochemistry, Sher-i- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, 190011, India
| | - Raies Ahmad Qadri
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Trupti Navin Chandra Patel
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- * E-mail:
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