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Radwan AA, Alanazi F, Al-Dhfyan A. Bioinformatics-driven discovery of novel EGFR kinase inhibitors as anti-cancer therapeutics: In silico screening and in vitro evaluation. PLoS One 2024; 19:e0298326. [PMID: 38625872 PMCID: PMC11020408 DOI: 10.1371/journal.pone.0298326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 04/18/2024] Open
Abstract
Epidermal growth factor receptor EGFR inhibitors are widely used as first line therapy for the treatment of non-small-cell lung cancer (NSCLC) in patients harboring EGFR mutation. However, the acquisition of a second-site mutation (T790 M) limited the efficacy and developed resistance. Therefore, discovery and development of specific drug target for this mutation is of urgent needs. In our study we used the ChemDiv diversity database for receptor-based virtual screening to secure EGFR-TK inhibitors chemotherapeutics. We identified four compounds that bind to the ATP-binding region of the EGFR-TK using AutoDock 4.0 and AutoDock Vina1.1.2 and post-docking investigations. The ligand showed hydrophobic interactions to the hydrophobic region of the binding site and engaged in hydrogen bonding with Met793. The ligands also explored π-cation interactions between the π-system of the ligand-phenyl ring and the positive amino group of Lys745. Molecular mechanics Poisson-Boltzmann surface area MM/PBSA per-residue energy decomposition analyses revealed that Val726, Leu792, Met793, Gly796, Cys797, Leu798, and Thr844 contributed the most to the binding energy. Biological evaluation of the retrieved hit compounds showed suppressing activity against EGFR auto phosphorylation and selective apoptosis-induced effects toward lung cancer cells harboring the EGFR L858R/T790M double mutation. Our work anticipated into novel and specific EGFR-TKIs and identified new compounds with therapeutic potential against lung cancer.
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Affiliation(s)
- Awwad A. Radwan
- Department of Pharmaceutics, Kayyli Chair for Pharmaceutical Industries, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department King Faisal Specialized Hospital and Research Center, Cell Therapy & Immunobiology, Riyadh, Saudi Arabia
| | - Fars Alanazi
- Department of Pharmaceutics, Kayyli Chair for Pharmaceutical Industries, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Al-Dhfyan
- Department King Faisal Specialized Hospital and Research Center, Cell Therapy & Immunobiology, Riyadh, Saudi Arabia
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2
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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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3
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Todsaporn D, Mahalapbutr P, Poo-Arporn RP, Choowongkomon K, Rungrotmongkol T. Structural dynamics and kinase inhibitory activity of three generations of tyrosine kinase inhibitors against wild-type, L858R/T790M, and L858R/T790M/C797S forms of EGFR. Comput Biol Med 2022; 147:105787. [PMID: 35803080 DOI: 10.1016/j.compbiomed.2022.105787] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/25/2022] [Accepted: 06/26/2022] [Indexed: 11/19/2022]
Abstract
Mutations in the tyrosine kinase domain of epidermal growth factor receptor (EGFR), including L858R/T790M double and L858R/T790M/C797S triple mutations, are major causes of acquired resistance towards EGFR targeted drugs. In this work, a combination of comprehensive molecular modeling and in vitro kinase inhibition assay was used to unravel the mutational effects of EGFR on the susceptibility of three generations of EGFR tyrosine kinase inhibitors (erlotinib, gefitinib, afatinib, dacomitinib, and osimertinib) in comparison with the wild-type EGFR. The binding affinity of all studied inhibitors towards the double and triple EGFR mutations was in good agreement with the experimental data, ranked in the order of osimertinib > afatinib > dacomitinib > erlotinib > gefitinib. Three hot-spot residues at the hinge region (M790, M793, and C797) were involved in the binding of osimertinib and afatinib, enhancing their inhibitory activity towards mutated EGFRs. Both double and triple EGFR mutations causing erlotinib and gefitinib resistance are mainly caused by the low number of H-bond occupations, the low number of surrounding atoms, and the high number of water molecules accessible to the enzyme active site. According to principal component analysis, the molecular complexation of osimertinib against the two mutated EGFRs was in a closed conformation, whereas that against wild-type EGFR was in an open conformation, resulting in drug resistance. This work paves the way for further design of the novel EGFR inhibitors to overcome drug resistance mechanisms.
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Affiliation(s)
- Duangjai Todsaporn
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, and Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Rungtiva P Poo-Arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
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4
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Matada GSP, Dhiwar PS, Abbas N, Singh E, Ghara A, Patil R, Raghavendra NM. Pharmacophore modeling, virtual screening, molecular docking and dynamics studies for the discovery of HER2-tyrosine kinase inhibitors: An in-silico approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Ashraf MA, Sayed S, Bello M, Hussain N, Chando RK, Alam S, Hasan MK. CDK4 as a phytochemical based anticancer drug target. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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6
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Cao H, Sun Y, Wang L, Pan Y, Li Z, Liang Y. In silico identification of novel inhibitors targeting the DNA-binding domain of the human estrogen receptor alpha. J Steroid Biochem Mol Biol 2021; 213:105966. [PMID: 34416373 DOI: 10.1016/j.jsbmb.2021.105966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022]
Abstract
The human estrogen receptor alpha (ERα) is an important regulator in breast cancer development and progression. The frequent ERα mutations in the ligand-binding domain (LBD) can increase the resistance of antiestrogen drugs, highlighting the need to develop new drugs to target ERα-positive breast cancer. In this study, we combined molecular docking, molecular dynamics simulations and binding free energy calculations to develop a structure-based virtual screening workflow to identify hit compounds capable of interfering with the recognition of ERα by the specific response element of DNA. A druggable pocket on the DNA binding domain (DBD) of ERα was identified as the potential binding site. The hits binding modes were further analyzed to reveal the structural characteristics of the DBD-inhibitor complexes. The core structure of the lead molecules was synthesized and was found to inhibit the E2-induced cell proliferation in MCF-7 cell lines. These findings provide an insight into the structural basis of ligand-ERα for alternate sites beyond the LBD-based pocket. The core structure proposed in this study could potentially be used as the lead molecule for further rational optimization of the antiestrogen drug structure with stronger binding of DBD and higher activity.
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Affiliation(s)
- Huiming Cao
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Yuzhen Sun
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Ling Wang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Yu Pan
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Zhunjie Li
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Yong Liang
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Institute of Environment and Health, Jianghan University, Wuhan, 430056, China.
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Balbuena-Rebolledo I, Padilla-Martínez II, Rosales-Hernández MC, Bello M. Repurposing FDA Drug Compounds against Breast Cancer by Targeting EGFR/HER2. Pharmaceuticals (Basel) 2021; 14:ph14080791. [PMID: 34451888 PMCID: PMC8401258 DOI: 10.3390/ph14080791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing studies have identified several FDA-approved compounds as potential inhibitors of the intracellular domain of epidermal growth factor receptor 1 (EGFR) and human epidermal receptor 2 (HER2). EGFR and HER2 represent important targets for the design of new drugs against different types of cancer, and recently, differences in affinity depending on active or inactive states of EGFR or HER2 have been identified. In this study, we first identified FDA-approved compounds with similar structures in the DrugBank to lapatinib and gefitinib, two known inhibitors of EGFR and HER2. The selected compounds were submitted to docking and molecular dynamics MD simulations with the molecular mechanics generalized Born surface area approach to discover the conformational and thermodynamic basis for the recognition of these compounds on EGFR and HER2. These theoretical studies showed that compounds reached the ligand-binding site of EGFR and HER2, and some of the repurposed compounds did not interact with residues involved in drug resistance. An in vitro assay performed on two different breast cancer cell lines, MCF-7, and MDA-MB-23, showed growth inhibitory activity for these repurposed compounds on tumorigenic cells at micromolar concentrations. These repurposed compounds open up the possibility of generating new anticancer treatments by targeting HER2 and EGFR.
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Affiliation(s)
- Irving Balbuena-Rebolledo
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna Ticomán, Ciudad de México 07340, Mexico;
| | - Itzia Irene Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio La Laguna Ticomán, Ciudad de México 07340, Mexico;
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón, s/n, Col. Casco de Santo Tomas, Ciudad de México 11340, Mexico;
- Correspondence: or
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8
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Topomer-CoMFA proposed as a tool to construct dual EGFR/HER-2 models. J Mol Model 2021; 27:239. [PMID: 34363097 DOI: 10.1007/s00894-021-04852-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Protein kinases (in this case, HER-2 and EGFR) are involved in cancer-related diseases. Some reports have shown unique CoMFA models using the sum of activities expressed as pIC50 (-log IC50), as the classical CoMFA technique would not be the best strategy to construct models for multitarget therapy considering that the molecular alignment will not be the same for different targets. An alternative for this problem is the use of Topomer-CoMFA, a variation of CoMFA, which does not require the alignment step in the generation of 3D models. In this study, we propose the combined use of the sum of activities and Topomer-CoMFA for the construction of a unique dual 3D model considering the inhibitory activities against EGFR and HER-2. For this, 88 compounds from the literature were divided into two groups: training (71) and test (17) sets. The biological activity of each compound, expressed as IC50 for EGFR and HER-2, was transformed into pIC50, summed, and used as the dependent variable in the Topomer-CoMFA analyses. The obtained model was considered statistically robust in the prediction of the dual activity of new compounds. Finally, based on the obtained model, we proposed structural modifications to some of the compounds used to improve the biological data. From the 3D model, we suggested new derivative compounds with improved biological activity for both targets. Therefore, the combination of the techniques proposed in this study proves to be a good strategy to construct better statistical models that can predict biological activities in multitarget systems.
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9
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Abdelgawad MA, Musa A, Almalki AH, Alzarea SI, Mostafa EM, Hegazy MM, Mostafa-Hedeab G, Ghoneim MM, Parambi DGT, Bakr RB, Al-Muaikel NS, Alanazi AS, Alharbi M, Ahmad W, Bukhari SNA, Al-Sanea MM. Novel Phenolic Compounds as Potential Dual EGFR and COX-2 Inhibitors: Design, Semisynthesis, in vitro Biological Evaluation and in silico Insights. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:2325-2337. [PMID: 34103896 PMCID: PMC8178614 DOI: 10.2147/dddt.s310820] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022]
Abstract
Introduction Epidermal growth factor receptor (EGFR) inhibition is an imperative therapeutic approach targeting various types of cancer including colorectal, lung, breast, and pancreatic cancer types. Moreover, cyclooxygenase-2 (COX-2) is frequently overexpressed in different types of cancers and has a role in the promotion of malignancy, apoptosis inhibition, and metastasis of tumor cells. Combination therapy has been emerged to improve the therapeutic benefit against cancer and curb intrinsic and acquired resistance. Methods Three semi-synthetic series of compounds (C1-4, P1-4, and G1-4) were prepared and evaluated biologically as potential dual epidermal growth factor receptor (EGFR) and COX-2 inhibitors. The main phenolic constituents of Amaranthus spinosus L. (p-coumaric, caffeic and gallic) acids have been isolated and subsequently subjected to diazo coupling with various amines to get novel three chemical scaffolds with potential anticancer activities. Results Compounds C4 and G4 showed superior inhibitory activity against EGFR (IC50: 0.9 and 0.5 µM, respectively) and displayed good COX-2 inhibition (IC50: 4.35 and 2.47 µM, respectively). Moreover, the final compounds were further evaluated for their cytotoxic activity against human colon cancer (HT-29), pancreatic cancer (PaCa-2), human malignant melanoma (A375), lung cancer (H-460), and pancreatic ductal cancer (Panc-1) cell lines. Interestingly, compounds C4 and G4 exhibited the highest cytotoxic activity with average IC50 values of 1.5 µM and 2.8 µM against H-460 and Panc-1, respectively. The virtual docking study was conducted to gain proper understandings of the plausible-binding modes of target compounds within EGFR and COX-2 binding sites. Discussion The NMR of prepared compounds showed characteristic peaks that confirmed the structure of the target compounds. The synthesized benzoxazolyl scaffold containing compounds showed inhibitory activities for both COXs and EGFR which are consistent with the virtual docking study.
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Affiliation(s)
- Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, 21944, Saudi Arabia.,Addiction and Neuroscience Research Unit, Taif University, Taif, 21944, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Ehab M Mostafa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Mostafa M Hegazy
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt
| | - Gomaa Mostafa-Hedeab
- Department of Pharmacology, Medical College, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Mohammed M Ghoneim
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Cairo, 11371, Egypt.,Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah, 13713, Saudi Arabia
| | - Della G T Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Rania B Bakr
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Nayef S Al-Muaikel
- Department of Chemistry, College of Science, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Abdullah S Alanazi
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia.,Health Sciences Research Unit, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Waqas Ahmad
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Syed N A Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
| | - Mohammad M Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, 72341, Saudi Arabia
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10
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Martiniano B. Molecular recognition of tak-285 and lapatinib by inactive, active, and middle active-inactive HER2. J Mol Model 2021; 27:105. [PMID: 33686576 DOI: 10.1007/s00894-021-04720-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Experimental and theoretical studies have provided structural information regarding the shift from inactive to active EGFR, throughout which both conformations are linked via binding to specific tyrosine kinase inhibitors. For HER2, an intermediate active-inactive receptor conformation is present in the PDB, which has been co-crystallized with tak-285. The affinity of HER2 in monomeric state to tak-285 has been previously reported. However, the lack of structural knowledge of HER2 limits our capacity to understand whether tak-285, or other known HER2 inhibitors, selectively bind active, inactive, or intermediate forms of HER2. To elucidate mechanisms by which tak-285 binds to HER2, we first obtained information regarding the structural features of the active state of HER2 via microsecond MD simulations from the crystallized intermediate structure previously determined. Based on these HER2 conformers, together with the inactive HER2 conformer obtained in a previous study, we used docking and MD simulations coupled to MMGBSA approach to assess binding of tak-285 and lapatinib, known HER2/EGFR dual inhibitors, to HER2. Structural and energetic studies revealed that tak-285 binds with a greater affinity than lapatinib to active and intermediate active-inactive forms of HER2. This is in accordance with experimental findings that showed the tak-285 inhibitor has increased activity relative to lapatinib in breast cancer cell lines.
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Affiliation(s)
- Bello Martiniano
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, CP: 11340, Mexico City, Mexico.
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11
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Sixto-López Y, Correa-Basurto J, Bello M, Landeros-Rivera B, Garzón-Tiznado JA, Montaño S. Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Sci Rep 2021; 11:4659. [PMID: 33633229 PMCID: PMC7907372 DOI: 10.1038/s41598-021-84053-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/11/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly emerged coronavirus responsible for coronavirus disease 2019 (COVID-19); it become a pandemic since March 2020. To date, there have been described three lineages of SARS-CoV-2 circulating worldwide, two of them are found among Mexican population, within these, we observed three mutations of spike (S) protein located at amino acids H49Y, D614G, and T573I. To understand if these mutations could affect the structural behavior of S protein of SARS-CoV-2, as well as the binding with S protein inhibitors (cepharanthine, nelfinavir, and hydroxychloroquine), molecular dynamic simulations and molecular docking were employed. It was found that these punctual mutations affect considerably the structural behavior of the S protein compared to wild type, which also affect the binding of its inhibitors into their respective binding site. Thus, further experimental studies are needed to explore if these affectations have an impact on drug-S protein binding and its possible clinical effect.
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Affiliation(s)
- Yudibeth Sixto-López
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | - Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón S/N, Casco de Santo Tomás, 11340, Mexico, Mexico
| | | | - Jose Antonio Garzón-Tiznado
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Sarita Montaño
- Laboratorio de Bioinformática y Simulación Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico.
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Wang C, Ding S, Wang S, Shi Z, Pandey NK, Chudal L, Wang L, Zhang Z, Wen Y, Yao H, Lin L, Chen W, Xiong L. Endogenous tumor microenvironment-responsive multifunctional nanoplatforms for precision cancer theranostics. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213529] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Guadarrama-García C, Bello M, Soriano-Ursúa M. Molecular insights into how SHBG dimerization exerts changes on ligand molecular recognition. J Steroid Biochem Mol Biol 2020; 197:105502. [PMID: 31689504 DOI: 10.1016/j.jsbmb.2019.105502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/28/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
Sex hormone binding globulin (SHBG) is a homodimeric glycoprotein and is the major carrier protein for sex steroids in plasma, regulating sex hormone availability in most vertebrate groups. Although it was initially thought that human dimeric SHBG bound a single ligand at the homodimer interface, studies demonstrated that dimeric SHBG binds a ligand to each subunit with similar affinity. In fact, the findings from recent experimental studies suggest that ligand binding to the SHBG dimer involves a complex allosteric mechanism involving conformational changes that limit observations of the presence of allosteric regulation. Therefore, we combined structural data with molecular dynamics simulations using Molecular Mechanics Generalized-Born Surface Area (MMGBSA) to dissect the structural and energetic basis for molecular recognition between five ligands whose affinities and binding positions on SHBG are known, i.e., 3β,17α-diol; 3β,17β-diol; DHT; norgestrel (NOG); and estradiol (E2), and monomeric and dimeric SHBG. Protein-ligand complexes, involving dimeric SHBG saturated with two ligands on each subunit, reproduce the experimental affinity tendency and allow the observation that dimerization exerts disparate effects on binding affinity, characteristic of negative cooperativity for E2, DHT, and NOG, whereas 3β-17α-diol and 3β-17β-diol lack allostery.
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Affiliation(s)
- Concepción Guadarrama-García
- Laboratorio de Modelado Molecular y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México City, Mexico
| | - Martiniano Bello
- Laboratorio de Modelado Molecular y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México City, Mexico.
| | - Marvin Soriano-Ursúa
- Departamento de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 México City, Mexico
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Bello M, Guadarrama-García C, Rodriguez-Fonseca RA. Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2. J Comput Aided Mol Des 2019; 34:293-303. [DOI: 10.1007/s10822-019-00270-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/06/2019] [Indexed: 01/22/2023]
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15
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Ye L, Zhao T, Du W, Li A, Gao W, Li J, Wang L, Chen W. Discovery of aminopyridine-containing spiro derivatives as EGFR mutations inhibitors. J Enzyme Inhib Med Chem 2019; 34:1233-1246. [PMID: 31286784 PMCID: PMC6691816 DOI: 10.1080/14756366.2019.1634704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Neratinib is an oral pan HER inhibitor, that irreversibly inhibits EGFR and HER2 and was proven to be effective against multiple EGFR mutations. In previous study, we reported spiro [indoline-3, 4′-piperidine]-2-ones as anticancer agents. In this study, we designed aminopyridine-containing spiro [indoline-3,4′-piperidine] derivatives A1-A4 using Neratinib and spiro [indoline-3, 4′-piperidine]-2-one compound patented as lead structure, then replaced piperidine with cyclopropane to obtain B1-B7 and replaced indoline with benzmorpholine to get C1-C4 and D1-D2. We synthesized these compounds and evaluated their residual activities under 0.5 M drug concentration on EGFR and ERBB2. Most of compounds showed stronger inhibition on EGFR-wt and ERBB2, in which A1-A4 showed excellent inhibitory activity with inhibition percentage on EGFR-wt kinase of 7%, 6%, 19%, 27%, respectively and 9%, 5%, 12%, 34% on ERBB2 kinase compared with 2% and 6% of Neratinib.
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Affiliation(s)
- Lianbao Ye
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Tao Zhao
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Wenjun Du
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | - Anhu Li
- b Esa Biotech Co., LTD. , Guangzhou , China
| | - Wei Gao
- a School of Pharmacy , Guangdong Pharmaceutical University , Guangzhou , China
| | | | - Ling Wang
- d Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering , South China University of Technology , Guangzhou , China
| | - Weiqiang Chen
- c School of Basic Courses , Guangdong Pharmaceutical University , Guangzhou , China
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16
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Saldaña-Rivera L, Bello M, Méndez-Luna D. Structural insight into the binding mechanism of ATP to EGFR and L858R, and T790M and L858R/T790 mutants. J Biomol Struct Dyn 2019; 37:4671-4684. [PMID: 30558477 DOI: 10.1080/07391102.2018.1558112] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The L858R mutation in EGFR is particularly responsive to small tyrosine kinase inhibitors (TKIs) such as gefitinib and erlotinib. This efficacy decreases due to drug resistance conferred by a second mutation, T790M, which subsequently produces a double mutant, L858R/T790M. Although this resistance was initially attributed to steric blocking by the T790M mutation, experimental studies have demonstrated that differences in the binding affinities of TKIs to T790M and L858R/T790M mutants are more a result of the increased sensitivity of these mutants to ATP than to a decrease in the affinity to TKIs. Regrettably, detailed information at the atomic level on the origins of the increased binding affinity of mutants for ATP is lacking. In this study, we have combined structural data and molecular dynamics simulations with the MMGBSA approach to determine how the L858R, T790M and L858R/T790 mutations impact the binding mechanism of ATP with respect to wild-type EGFR. Structural and energetic analyses provided novel information that helps to explain the increased affinity of ATP to T790M and L858R/T790 mutants with respect to L858R and wild-type systems. In addition, it was observed that dimerization of the wild-type and mutant systems exerts dissimilar effects on the ATP binding affinity characteristic of negative cooperativity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lucia Saldaña-Rivera
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Díaz Mirón S/N, Col. Casco de Santo Tomas , México City , México
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Díaz Mirón S/N, Col. Casco de Santo Tomas , México City , México
| | - David Méndez-Luna
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Díaz Mirón S/N, Col. Casco de Santo Tomas , México City , México
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17
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Tu J, Song LT, Zhai HL, Wang J, Zhang XY. Selective mechanisms and molecular design of 2,4 Diarylaminopyrimidines as ALK inhibitors. Int J Biol Macromol 2018; 118:1149-1156. [PMID: 30001602 DOI: 10.1016/j.ijbiomac.2018.06.192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/30/2018] [Accepted: 06/30/2018] [Indexed: 12/30/2022]
Abstract
As an attractive therapeutic target for non-small-cell lung cancer (NSCLC), anaplastic lymphoma kinase (ALK) has got increased attention, and the selectivity of ALK inhibitors is an enormous challenge. Recently, 2,4-Diarylaminopyrimidines with high inhibitory activity over InsR/IGF1R were reported as ALK inhibitors, which harboring phosphine oxide moiety. In this work, it is the first time to reveal that the incorporation of dimethylphosphine oxide moiety and the smaller active pocket of ALK is key factor in the selectivity of inhibitor 11q toward ALK over IGF1R/InsR. The results of molecular simulation indicate that the subtle change in the binding pocket of ALK is mainly associated with the flexibility of P-loop and the own residues K1150 and D1270. The replacement of the dimethylphosphine oxide and methylpiperazine of inhibitor 11q would alter the major inhibitory effects of binding and activation. The results further combined 3D-QSAR can not only profile the binding mechanism between the 2,4-Diarylaminopyrimidines inhibitors and ALK, but also supply the useful information for the rational design of a more potential small molecule inhibitor bound to ALK receptor.
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Affiliation(s)
- Jing Tu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Li Ting Song
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China.
| | - Juan Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Xiao Yun Zhang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
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Bello M. Binding mechanism of kinase inhibitors to EGFR and T790M, L858R and L858R/T790M mutants through structural and energetic analysis. Int J Biol Macromol 2018; 118:1948-1962. [PMID: 30017980 DOI: 10.1016/j.ijbiomac.2018.07.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/12/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023]
Abstract
Experimental studies have demonstrated that L858R mutation in the EGF receptor (EGFR) confers tumor sensitivity whereas T790M and L858R/T790M mutations cause resistance to tyrosine kinase inhibitors in patients with non-small cell lung cancer. Theoretical studies have been carried out to try to clarify the structural and energetic details linked to acquired resistance to Gefitinib, Erlotinib or Lapatinib, however, some of these studies are contradictory with each other and with experimental reports and did not mention whether the study was performed by considering the inactive or active EGFR states. In this study, we combined structural data and molecular dynamic simulations coupled to a molecular mechanics generalized Born surface area approach to provide insight into the binding mechanism between three FDA-approved drugs (Erlotinib, Gefitinib and Lapatinib) that target the wild-type and T790M, L858R and L858R/T790M mutants of EGFR. Structural analysis showed that the drugs impact differently the conformational space of active and inactive EGFR. Energetic analysis pointed out that some ligands have better affinity for the inactive EGFR than the active EGFR state. Comparative analysis of the molecular recognition of Gefitinib, Erlotinib and Lapatinib provided insight into the drug sensitivity or resistance observed for the three FDA-approved drugs evaluated.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Díaz Mirón S/N, Col. Casco de Santo Tomas, México City 11340, Mexico.
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