Additional file 5: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Identification of Novel Potential VEGFR-2 Inhibitors Using a Combination of Computational Methods for Drug Discovery

Mohammad M. Al-Sanea
Garri Chilingaryan
Narek Abelyan
Arsen Sargsyan
Sargis Hovhannisyan
Hayk Gasparyan
Smbat Gevorgyan
Sarah Albogami
Mohammed M. Ghoneim
Ahmed K. Farag
Ahmed A. B. Mohamed
Ashraf K. El-Damasy

October 2021

The vascular endothelial growth factor receptor 2 (VEGFR-2) is largely recognized as a potent therap...

Additional file 2: of The small organic molecule C19 binds and strengthens the KRAS4b-PDEδ complex and inhibits growth of colorectal cancer cells in vitro and in vivo

Pedro Cruz-Nova (5919875)
Michael Schnoor (419644)
José Correa-Basurto (472076)
Martiniano Bello (152281)
Paola Briseño-Diaz (5919893)
Arturo Rojo-Domínguez (5919902)
Carlos Ortiz-Mendoza (5919911)
Jorge Guerrero-Aguirre (5919917)
Francisco García-Vázquez (5919923)
Rosaura Hernández-Rivas (510505)
María del Rocío Thompson-Bonilla (3342392)
Miguel Vargas (85521)

November 2018

Table S2. MD simulation results of the first populated site of the C19 compound in the KRAS4b-PDEδ c...

Additional file 5: Table S3. of Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

Pavithra Balasubramanian (3840235)
Anand Balupuri (685904)
Hee-Young Kang (3840238)
Seung Cho (3840241)

March 2017

Experimental and predicted pIC50 values with their residuals of selected COMSIA model. (DOCX 14 kb

Additional file 2: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Cocrystal re-dock results of 4AG8. Overlapping of the co-crystal (cyan) onto the docked pose (orange...

Additional file 4: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the Hit compound and 4AG8. Detailed molecular interactions of the H...

Additional file 3: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the the reference compound and 4AG8. Detailed molecular interaction...

Additional file 9: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Active sites comparison. Comparison of the active site residues of 4AG8 and 1UMR. (DOCX 13Â kb

Additional file 7: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the reference compound and 1URW. Molecular interaction details of t...

Additional file 8: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the Hit compound and 1URW. Molecular interaction details of the Hit...

Additional file 1: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Test set assessment. Assessing the test set values for estimated and the experimental activities by ...

Discovery of Small Molecules That Target Vascular Endothelial Growth Factor Receptor-2 Signalling Pathway Employing Molecular Modelling Studies

Shailima Rampogu
Ayoung Baek
Chanin Park
Minky Son
Shraddha Parate
Saravanan Parameswaran
Yohan Park
Baji Shaik
Ju Hyun Kim
Seok Ju Park
Keun Woo Lee

March 2019

Angiogenesis is defined as the formation of new blood vessels and is a key phenomenon manifested in ...

MOESM1 of KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Aeri Lee (2014732)
Seungpyo Hong (182769)
Dongsup Kim (50568)

April 2018

Additional file 1: Table S1. Re-docking of five ligands co-crystalized with CDK2 to the five Rosetta...

Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations

Munoz, C.
Adasme, F.
Alzate-Morales, J.H.
Vergara-Jaque, A.
Kniess, T.
Caballero, J.

January 2012

Caballero, J (reprint author), Univ Talca, Ctr Bioinformat & Simulac Mol, 2 Norte 685,Casilla 721, T...

Additional file 1: of Targeting the Tie2–αvβ3 integrin axis with bi-specific reagents for the inhibition of angiogenesis

Tomer Shlamkovich (5642744)
Lidan Aharon (5642747)
Dana Koslawsky (5642750)
Yulia Einav (390895)
Niv Papo (3096837)

August 2018

Figures S1–S5, Tables S1–S2. Figure S1. Production and purification of soluble Ang2-BD bi-specific v...

Additional file 2: Figure S2. of Chronic myeloid leukemia: the paradigm of targeting oncogenic tyrosine kinase signaling and counteracting resistance for successful cancer therapy

Simona Soverini (148501)
Manuela Mancini (495234)
Luana Bavaro (4862191)
Michele Cavo (463532)
Giovanni Martinelli (148520)

February 2018

Cartoon representation of the ABL1 kinase domain in complex with the five ATP-competitive inhibitors...

Identification of Novel Potential VEGFR-2 Inhibitors Using a Combination of Computational Methods for Drug Discovery

Mohammad M. Al-Sanea
Garri Chilingaryan
Narek Abelyan
Arsen Sargsyan
Sargis Hovhannisyan
Hayk Gasparyan
Smbat Gevorgyan
Sarah Albogami
Mohammed M. Ghoneim
Ahmed K. Farag
Ahmed A. B. Mohamed
Ashraf K. El-Damasy

October 2021

The vascular endothelial growth factor receptor 2 (VEGFR-2) is largely recognized as a potent therap...

Additional file 2: of The small organic molecule C19 binds and strengthens the KRAS4b-PDEδ complex and inhibits growth of colorectal cancer cells in vitro and in vivo

Pedro Cruz-Nova (5919875)
Michael Schnoor (419644)
José Correa-Basurto (472076)
Martiniano Bello (152281)
Paola Briseño-Diaz (5919893)
Arturo Rojo-Domínguez (5919902)
Carlos Ortiz-Mendoza (5919911)
Jorge Guerrero-Aguirre (5919917)
Francisco García-Vázquez (5919923)
Rosaura Hernández-Rivas (510505)
María del Rocío Thompson-Bonilla (3342392)
Miguel Vargas (85521)

November 2018

Table S2. MD simulation results of the first populated site of the C19 compound in the KRAS4b-PDEδ c...

Additional file 5: Table S3. of Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

Pavithra Balasubramanian (3840235)
Anand Balupuri (685904)
Hee-Young Kang (3840238)
Seung Cho (3840241)

March 2017

Experimental and predicted pIC50 values with their residuals of selected COMSIA model. (DOCX 14 kb

Additional file 2: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Cocrystal re-dock results of 4AG8. Overlapping of the co-crystal (cyan) onto the docked pose (orange...

Additional file 4: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the Hit compound and 4AG8. Detailed molecular interactions of the H...

Additional file 3: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the the reference compound and 4AG8. Detailed molecular interaction...

Additional file 9: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Active sites comparison. Comparison of the active site residues of 4AG8 and 1UMR. (DOCX 13Â kb

Additional file 7: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the reference compound and 1URW. Molecular interaction details of t...

Additional file 8: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

2D interaction representation of the Hit compound and 1URW. Molecular interaction details of the Hit...

Additional file 1: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Shailima Rampogu (3856018)
Ayoung Baek (503198)
Amir Zeb (4921021)
Keun Lee (3539810)

March 2018

Test set assessment. Assessing the test set values for estimated and the experimental activities by ...

Discovery of Small Molecules That Target Vascular Endothelial Growth Factor Receptor-2 Signalling Pathway Employing Molecular Modelling Studies

Shailima Rampogu
Ayoung Baek
Chanin Park
Minky Son
Shraddha Parate
Saravanan Parameswaran
Yohan Park
Baji Shaik
Ju Hyun Kim
Seok Ju Park
Keun Woo Lee

March 2019

Angiogenesis is defined as the formation of new blood vessels and is a key phenomenon manifested in ...

MOESM1 of KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking

Aeri Lee (2014732)
Seungpyo Hong (182769)
Dongsup Kim (50568)

April 2018

Additional file 1: Table S1. Re-docking of five ligands co-crystalized with CDK2 to the five Rosetta...

Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations

Munoz, C.
Adasme, F.
Alzate-Morales, J.H.
Vergara-Jaque, A.
Kniess, T.
Caballero, J.

January 2012

Caballero, J (reprint author), Univ Talca, Ctr Bioinformat & Simulac Mol, 2 Norte 685,Casilla 721, T...

Additional file 1: of Targeting the Tie2–αvβ3 integrin axis with bi-specific reagents for the inhibition of angiogenesis

Tomer Shlamkovich (5642744)
Lidan Aharon (5642747)
Dana Koslawsky (5642750)
Yulia Einav (390895)
Niv Papo (3096837)

August 2018

Figures S1–S5, Tables S1–S2. Figure S1. Production and purification of soluble Ang2-BD bi-specific v...

Additional file 2: Figure S2. of Chronic myeloid leukemia: the paradigm of targeting oncogenic tyrosine kinase signaling and counteracting resistance for successful cancer therapy

Simona Soverini (148501)
Manuela Mancini (495234)
Luana Bavaro (4862191)
Michele Cavo (463532)
Giovanni Martinelli (148520)

February 2018

Cartoon representation of the ABL1 kinase domain in complex with the five ATP-competitive inhibitors...

Identification of Novel Potential VEGFR-2 Inhibitors Using a Combination of Computational Methods for Drug Discovery

Mohammad M. Al-Sanea
Garri Chilingaryan
Narek Abelyan
Arsen Sargsyan
Sargis Hovhannisyan
Hayk Gasparyan
Smbat Gevorgyan
Sarah Albogami
Mohammed M. Ghoneim
Ahmed K. Farag
Ahmed A. B. Mohamed
Ashraf K. El-Damasy

October 2021

The vascular endothelial growth factor receptor 2 (VEGFR-2) is largely recognized as a potent therap...

Additional file 2: of The small organic molecule C19 binds and strengthens the KRAS4b-PDEδ complex and inhibits growth of colorectal cancer cells in vitro and in vivo

Pedro Cruz-Nova (5919875)
Michael Schnoor (419644)
José Correa-Basurto (472076)
Martiniano Bello (152281)
Paola Briseño-Diaz (5919893)
Arturo Rojo-Domínguez (5919902)
Carlos Ortiz-Mendoza (5919911)
Jorge Guerrero-Aguirre (5919917)
Francisco García-Vázquez (5919923)
Rosaura Hernández-Rivas (510505)
María del Rocío Thompson-Bonilla (3342392)
Miguel Vargas (85521)

November 2018

Table S2. MD simulation results of the first populated site of the C19 compound in the KRAS4b-PDEδ c...

Additional file 5: Table S3. of Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

Pavithra Balasubramanian (3840235)
Anand Balupuri (685904)
Hee-Young Kang (3840238)
Seung Cho (3840241)

March 2017

Experimental and predicted pIC50 values with their residuals of selected COMSIA model. (DOCX 14 kb

Additional file 5: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Abstract

Extracted data

Additional file 5: of Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations

Abstract

Extracted data

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