Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach

The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are inter...
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Autor*in:	Nurisyah [verfasserIn] Dwi Syah Fitra Ramadhan [verfasserIn] Ratnasari Dewi [verfasserIn] Asyhari asikin [verfasserIn] Dwi Rachmawaty Daswi [verfasserIn] Adriyani adam [verfasserIn] Chaerunnimah [verfasserIn] Sunarto [verfasserIn] Rafika [verfasserIn] Artati [verfasserIn] Taufik Muhammad Fakih [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2024

Schlagwörter:	Marine-natural products EGFR Allosteric inhibitor

Übergeordnetes Werk:	In: Current Research in Structural Biology - Elsevier, 2020, 7(2024), Seite 100125-
Übergeordnetes Werk:	volume:7 ; year:2024 ; pages:100125-

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1016/j.crstbi.2024.100125

Katalog-ID:	DOAJ097686824

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520			\|a The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor.
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allfields	10.1016/j.crstbi.2024.100125 doi (DE-627)DOAJ097686824 (DE-599)DOAJfe14fc6a73ca4fe2bf989c6b46002425 DE-627 ger DE-627 rakwb eng QH301-705.5 Nurisyah verfasserin aut Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor. Marine-natural products EGFR Allosteric inhibitor Biology (General) Dwi Syah Fitra Ramadhan verfasserin aut Ratnasari Dewi verfasserin aut Asyhari asikin verfasserin aut Dwi Rachmawaty Daswi verfasserin aut Adriyani adam verfasserin aut Chaerunnimah verfasserin aut Sunarto verfasserin aut Rafika verfasserin aut Artati verfasserin aut Taufik Muhammad Fakih verfasserin aut In Current Research in Structural Biology Elsevier, 2020 7(2024), Seite 100125- (DE-627)1681860821 2665928X nnns volume:7 year:2024 pages:100125- https://doi.org/10.1016/j.crstbi.2024.100125 kostenfrei https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 kostenfrei http://www.sciencedirect.com/science/article/pii/S2665928X24000023 kostenfrei https://doaj.org/toc/2665-928X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 7 2024 100125-
spelling	10.1016/j.crstbi.2024.100125 doi (DE-627)DOAJ097686824 (DE-599)DOAJfe14fc6a73ca4fe2bf989c6b46002425 DE-627 ger DE-627 rakwb eng QH301-705.5 Nurisyah verfasserin aut Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor. Marine-natural products EGFR Allosteric inhibitor Biology (General) Dwi Syah Fitra Ramadhan verfasserin aut Ratnasari Dewi verfasserin aut Asyhari asikin verfasserin aut Dwi Rachmawaty Daswi verfasserin aut Adriyani adam verfasserin aut Chaerunnimah verfasserin aut Sunarto verfasserin aut Rafika verfasserin aut Artati verfasserin aut Taufik Muhammad Fakih verfasserin aut In Current Research in Structural Biology Elsevier, 2020 7(2024), Seite 100125- (DE-627)1681860821 2665928X nnns volume:7 year:2024 pages:100125- https://doi.org/10.1016/j.crstbi.2024.100125 kostenfrei https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 kostenfrei http://www.sciencedirect.com/science/article/pii/S2665928X24000023 kostenfrei https://doaj.org/toc/2665-928X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 7 2024 100125-
allfields_unstemmed	10.1016/j.crstbi.2024.100125 doi (DE-627)DOAJ097686824 (DE-599)DOAJfe14fc6a73ca4fe2bf989c6b46002425 DE-627 ger DE-627 rakwb eng QH301-705.5 Nurisyah verfasserin aut Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor. Marine-natural products EGFR Allosteric inhibitor Biology (General) Dwi Syah Fitra Ramadhan verfasserin aut Ratnasari Dewi verfasserin aut Asyhari asikin verfasserin aut Dwi Rachmawaty Daswi verfasserin aut Adriyani adam verfasserin aut Chaerunnimah verfasserin aut Sunarto verfasserin aut Rafika verfasserin aut Artati verfasserin aut Taufik Muhammad Fakih verfasserin aut In Current Research in Structural Biology Elsevier, 2020 7(2024), Seite 100125- (DE-627)1681860821 2665928X nnns volume:7 year:2024 pages:100125- https://doi.org/10.1016/j.crstbi.2024.100125 kostenfrei https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 kostenfrei http://www.sciencedirect.com/science/article/pii/S2665928X24000023 kostenfrei https://doaj.org/toc/2665-928X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 7 2024 100125-
allfieldsGer	10.1016/j.crstbi.2024.100125 doi (DE-627)DOAJ097686824 (DE-599)DOAJfe14fc6a73ca4fe2bf989c6b46002425 DE-627 ger DE-627 rakwb eng QH301-705.5 Nurisyah verfasserin aut Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor. Marine-natural products EGFR Allosteric inhibitor Biology (General) Dwi Syah Fitra Ramadhan verfasserin aut Ratnasari Dewi verfasserin aut Asyhari asikin verfasserin aut Dwi Rachmawaty Daswi verfasserin aut Adriyani adam verfasserin aut Chaerunnimah verfasserin aut Sunarto verfasserin aut Rafika verfasserin aut Artati verfasserin aut Taufik Muhammad Fakih verfasserin aut In Current Research in Structural Biology Elsevier, 2020 7(2024), Seite 100125- (DE-627)1681860821 2665928X nnns volume:7 year:2024 pages:100125- https://doi.org/10.1016/j.crstbi.2024.100125 kostenfrei https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 kostenfrei http://www.sciencedirect.com/science/article/pii/S2665928X24000023 kostenfrei https://doaj.org/toc/2665-928X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 7 2024 100125-
allfieldsSound	10.1016/j.crstbi.2024.100125 doi (DE-627)DOAJ097686824 (DE-599)DOAJfe14fc6a73ca4fe2bf989c6b46002425 DE-627 ger DE-627 rakwb eng QH301-705.5 Nurisyah verfasserin aut Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach 2024 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor. Marine-natural products EGFR Allosteric inhibitor Biology (General) Dwi Syah Fitra Ramadhan verfasserin aut Ratnasari Dewi verfasserin aut Asyhari asikin verfasserin aut Dwi Rachmawaty Daswi verfasserin aut Adriyani adam verfasserin aut Chaerunnimah verfasserin aut Sunarto verfasserin aut Rafika verfasserin aut Artati verfasserin aut Taufik Muhammad Fakih verfasserin aut In Current Research in Structural Biology Elsevier, 2020 7(2024), Seite 100125- (DE-627)1681860821 2665928X nnns volume:7 year:2024 pages:100125- https://doi.org/10.1016/j.crstbi.2024.100125 kostenfrei https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 kostenfrei http://www.sciencedirect.com/science/article/pii/S2665928X24000023 kostenfrei https://doaj.org/toc/2665-928X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2110 GBV_ILN_2112 GBV_ILN_2122 GBV_ILN_2129 GBV_ILN_2143 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4393 GBV_ILN_4700 AR 7 2024 100125-
language	English
source	In Current Research in Structural Biology 7(2024), Seite 100125- volume:7 year:2024 pages:100125-
sourceStr	In Current Research in Structural Biology 7(2024), Seite 100125- volume:7 year:2024 pages:100125-
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Marine-natural products EGFR Allosteric inhibitor Biology (General)
isfreeaccess_bool	true
container_title	Current Research in Structural Biology
authorswithroles_txt_mv	Nurisyah @@aut@@ Dwi Syah Fitra Ramadhan @@aut@@ Ratnasari Dewi @@aut@@ Asyhari asikin @@aut@@ Dwi Rachmawaty Daswi @@aut@@ Adriyani adam @@aut@@ Chaerunnimah @@aut@@ Sunarto @@aut@@ Rafika @@aut@@ Artati @@aut@@ Taufik Muhammad Fakih @@aut@@
publishDateDaySort_date	2024-01-01T00:00:00Z
hierarchy_top_id	1681860821
id	DOAJ097686824
language_de	englisch
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callnumber-first	Q - Science
author	Nurisyah
spellingShingle	Nurisyah misc QH301-705.5 misc Marine-natural products misc EGFR misc Allosteric inhibitor misc Biology (General) Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach
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topic_title	QH301-705.5 Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach Marine-natural products EGFR Allosteric inhibitor
topic	misc QH301-705.5 misc Marine-natural products misc EGFR misc Allosteric inhibitor misc Biology (General)
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title	Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach
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title_full	Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach
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author_browse	Nurisyah Dwi Syah Fitra Ramadhan Ratnasari Dewi Asyhari asikin Dwi Rachmawaty Daswi Adriyani adam Chaerunnimah Sunarto Rafika Artati Taufik Muhammad Fakih
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title_sort	targeting egfr allosteric site with marine-natural products of clathria sp.: a computational approach
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title_auth	Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach
abstract	The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor.
abstractGer	The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor.
abstract_unstemmed	The EGFR-C797S resistance mutation to third-generation drugs has been overcome by fourth-generation inhibitors, allosteric inhibitors, namely EAI045 and has reached phase 3 clinical trials, so the Allosteric Site is currently an attractive target for development. In this study, researchers are interested in knowing the activity of metabolite compounds from marine natural ingredients Clathria Sp. against the Allosteric Site of EGFR computationally. The methods used include molecular docking using Autodock4 software and Molecular Dynamics simulation performed using GROMACS software. The research began with the preparation of metabolite samples from Clathria Sp. through the KnapSack database site and the preparation of EGFR receptors that have been complexed with allosteric inhibitors, namely proteins with PDB code 5D41. Each compound was docked to the Allosteric Site of the natural ligand and then molecular dynamics simulations were performed on the compound with the best docking energy compared to the natural ligand. From the docking results, the Clathrin_A compound showed the lowest binding energy compared to other metabolites, and the value was close to the natural ligand. Then from the molecular dynamics results, the clathrin_A compound shows good stability and resembles the natural ligand, which is analyzed through RMSD, RMSF, SASA, Rg, and PCA, and shows the binding free energy from MMPBSA analysis which is close to the natural ligand. It can be concluded, Clathrin_A compound has potential as an allosteric inhibitor.
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title_short	Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach
url	https://doi.org/10.1016/j.crstbi.2024.100125 https://doaj.org/article/fe14fc6a73ca4fe2bf989c6b46002425 http://www.sciencedirect.com/science/article/pii/S2665928X24000023 https://doaj.org/toc/2665-928X
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up_date	2024-07-04T02:11:31.256Z
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Targeting EGFR allosteric site with marine-natural products of Clathria Sp.: A computational approach

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