1
|
Ashiru MA, Ogunyemi SO, Temionu OR, Ajibare AC, Cicero-Mfon NC, Ihekuna OA, Jagun MO, Abdulmumin L, Adisa QK, Asibor YE, Okorie CJ, Lawal MO, Babalola MO, Abdulrasaq IT, Salau LB, Olatunji IO, Bankole MA, Daud AB, Adeyemi AO. Identification of EGFR inhibitors as potential agents for cancer therapy: pharmacophore-based modeling, molecular docking, and molecular dynamics investigations. J Mol Model 2023; 29:128. [PMID: 37016200 DOI: 10.1007/s00894-023-05531-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/24/2023] [Indexed: 04/06/2023]
Abstract
CONTEXT As a member of a large family of proteins that together regulate various aspects of cell growth and development, the epidermal growth factor receptor (EGFR) is a validated target for the development of new drugs. Herein, we compiled a library of 62 compounds from the PubChem database with similar pharmacophores as osimertinib, which to our knowledge represents the only drug capable of overcoming EGFR-T790M-mutated NSCLC until date. Subsequently, we launched a docking-based virtual screening campaign against the EGFR kinase with the compiled chemical entities. The virtual screen identified 3 hit candidates (CID_126667097, CID_137660592, and CID_137659061) with lower binding energy/higher affinity (- 8.7 kcal/mol, - 8.6 kcal/mol, and - 8.5 kcal/mol, respectively) than the standard osimertinib (- 8.4 kcal/mol). Molecular dynamics metrics such as RMSD, RMSF, ROG, and intermolecular H-bond were used to substantiate the stability of the promising drug candidates at the binding pocket of EGFR after 100,000 ps production run. Overall, our molecular modeling study portrayed CID_126667097, CID_137660592, and CID_137659061 as lead-like drug candidates that may be further developed for the treatment of EGFR-associated cancer disease. METHODS Molecular docking was conducted with Autodock Vina. A total of 62 compounds were compiled for the docking screen, which were then downloaded in SMILE format and converted to Protein Data Bank (PDB) format using the Openbabel online server. Finally, Gromacs 2022.3 was used to perform MD simulation to substantiate the stability of the hit candidates.
Collapse
Affiliation(s)
- Mojeed Ayoola Ashiru
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Sciences, Fountain University, Osogbo, Osun State, Nigeria
| | - Sherif Olabisi Ogunyemi
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Oluwakemi Rita Temionu
- Department of Medical Laboratory Technology, Lagos State College of Health Technology, Lagos, Lagos State, Nigeria
| | - Abosede Christina Ajibare
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Nsikak Cicerella Cicero-Mfon
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Ogechi Augustina Ihekuna
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Monsurat Olatoun Jagun
- Department of Medical Laboratory Technology, Lagos State College of Health Technology, Lagos, Lagos State, Nigeria
| | - Latifatu Abdulmumin
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Quadri Kolawole Adisa
- Department of Chemical Sciences, Biochemistry Unit, College of Natural and Applied Sciences, Fountain University, Osogbo, Osun State, Nigeria
| | - Yemisi Elizabeth Asibor
- Faculty of Science, Department of Pure & Applied Chemistry, Osun State University, Osogbo, Osun State, Nigeria
| | - Chika Joseph Okorie
- Faculty of Physical Sciences, Department of Pure & Industrial Chemistry, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria
| | - Mariam Omowumi Lawal
- Faculty of Basic Medical Sciences, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Musa Oladayo Babalola
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Ibrahim Tope Abdulrasaq
- Faculty of Basic Medical Sciences, Department of Biochemistry, College of Medicine, University of Lagos, Lagos, Lagos State, Nigeria
| | - Latifat Bukola Salau
- Faculty of Basic Medical Science, Department of Physiology, University of Lagos, Lagos, Nigeria
| | - Idayat Omotolani Olatunji
- Faculty of Basic Medical Sciences, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Memunat Alake Bankole
- Faculty of Basic Medical Sciences, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Abibat Bisola Daud
- Faculty of Basic Medical Sciences, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | |
Collapse
|
2
|
Belal A, Abdel Gawad NM, Mehany ABM, Abourehab MAS, Elkady H, Al-Karmalawy AA, Ismael AS. Design, synthesis and molecular docking of new fused 1 H-pyrroles, pyrrolo[3,2- d]pyrimidines and pyrrolo[3,2- e][1, 4]diazepine derivatives as potent EGFR/CDK2 inhibitors. J Enzyme Inhib Med Chem 2022; 37:1884-1902. [PMID: 35801486 PMCID: PMC9272933 DOI: 10.1080/14756366.2022.2096019] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A new series of 1H-pyrrole (6a-c, 8a-c), pyrrolo[3,2-d]pyrimidines (9a-c) and pyrrolo[3,2-e][1, 4]diazepines (11a-c) were designed and synthesised. These compounds were designed to have the essential pharmacophoric features of EGFR Inhibitors, they have shown anticancer activities against HCT116, MCF-7 and Hep3B cancer cells with IC50 values ranging from 0.009 to 2.195 µM. IC50 value of doxorubicin is 0.008 µM, compounds 9a and 9c showed IC50 values of 0.011 and 0.009 µM respectively against HCT-116 cells. Compound 8b exerted broad-spectrum activity against all tested cell lines with an IC50 value less than 0.05 µM. Compound 8b was evaluated against a panel of kinases. This compound potently inhibited CDK2/Cyclin A1, DYRK3 and GSK3 alpha kinases with 10-23% compared to imatinib (1-10%). It has also arrested the cell cycle of MCF-7 cells at the S phase. Its antiproliferative activity was further augmented by molecular docking into the active sites of EGFR and CDK2 cyclin A1.
Collapse
Affiliation(s)
- Amany Belal
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Nagwa M Abdel Gawad
- Medicinal Chemistry Department, Faculty of Pharmacy, Cairo University, Giza, Egypt
| | - Ahmed B M Mehany
- Department of Zoology, Faculty of Science, Al-Azhar University, Nasr City, Egypt
| | - Mohammed A S Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Minia University, Minia, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University- Egypt, New Damietta, Egypt
| | - Ahmed S Ismael
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| |
Collapse
|
4
|
Azeez RFA, Zara S, Ricci A, Dev S, Vengamthodi A, Kavully FS, Abdu RA, Kalathil KT, Abdelgawad MA, Mathew B, Carradori S. Integrating N-alkyl amide in the chalcone framework: synthesis and evaluation of its anti-proliferative potential against AGS cancer cell line. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04864-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|