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Azzouzi M, Azougagh O, Ouchaoui AA, El hadad SE, Mazières S, Barkany SE, Abboud M, Oussaid A. Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2- a]pyrimidine-Schiff Base Derivative: ( E)-2-Phenyl- N-(thiophen-2-ylmethylene)imidazo[1,2- a]pyrimidin-3-amine. ACS OMEGA 2024; 9:837-857. [PMID: 38222514 PMCID: PMC10785637 DOI: 10.1021/acsomega.3c06841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/17/2023] [Indexed: 01/16/2024]
Abstract
In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.
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Affiliation(s)
- Mohamed Azzouzi
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Omar Azougagh
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Abderrahim Ait Ouchaoui
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Salah eddine El hadad
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Stéphane Mazières
- Laboratory
of IMRCP, University Paul Sabatier, CNRS
UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Soufian El Barkany
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Mohamed Abboud
- Catalysis
Research Group (CRG), Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Adyl Oussaid
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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Ding Y, Liu K, Zhao X, Lv Y, Yu R, Kang C. Design, synthesis, and antitumor activity of novel benzoheterocycle derivatives as inhibitors of vascular endothelial growth factor receptor-2 tyrosine kinase. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519819899067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The vascular endothelial growth factor receptor-2 signaling pathway promotes the formation of new blood vessels, and vascular endothelial growth factor receptor-2 tyrosine kinase exists in both active and inactive conformations. Novel indole–benzimidazole and indole–benzothiazole derivatives joined by different linkers are designed and synthesized as inhibitors of vascular endothelial growth factor receptor-2 tyrosine kinase. All the synthesized compounds were evaluated for their cytotoxicity against four human cancer cell lines (HeLa, HT29, A549, and MDA-MB-435) and human umbilical vein endothelial cell. Meanwhile, the inhibitory activities against vascular endothelial growth factor receptor-2 are estimated in vitro and the binding interactions with dual conformations of vascular endothelial growth factor receptor-2 tyrosine kinase are evaluated by molecular docking. Compounds 5a–c and 14 show inhibitory activity against vascular endothelial growth factor receptor-2 tyrosine kinase and promising cytotoxicity, specifically with IC50 values ranging between 0.1 and 1 μM, which imply broad-spectrum antitumor activity. These results provide a deep insight into potential structural modifications for developing potent vascular endothelial growth factor receptor-2 tyrosine kinase inhibitors.
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Affiliation(s)
- Yangyang Ding
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P.R. China
| | - Kai Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P.R. China
| | - Xinyu Zhao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P.R. China
| | - Yingtao Lv
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, P.R. China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, P.R. China
| | - Congmin Kang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, P.R. China
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Molecular Modeling of ALK L1198F and/or G1202R Mutations to Determine Differential Crizotinib Sensitivity. Sci Rep 2019; 9:11390. [PMID: 31388026 PMCID: PMC6684801 DOI: 10.1038/s41598-019-46825-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/17/2019] [Indexed: 01/29/2023] Open
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that has been recognized as a therapeutic target for EML4-ALK fusion-positive nonsmall cell lung cancer (NSCLC) treatment using type I kinase inhibitors such as crizotinib to take over the ATP binding site. According to Shaw’s measurements, ALK carrying G1202R mutation shows reduced response to crizotinib (IC50 = 382 nM vs. IC50 = 20 nM for wild-type), whereas L1198F mutant is more responsive (IC50 = 0.4 nM). Interestingly, the double mutant L1198F/G1202R maintains a similar response (IC50 = 31 nM) to the wild-type. Herein we conducted molecular modeling simulations to elucidate the varied crizotinib sensitivities in three mutants carrying L1198F and/or G1202R. Both L1198 and G1202 are near the ATP pocket. Mutation G1202R causes steric hindrance that blocks crizotinib accessibility, which greatly reduces efficacy, whereas mutation L1198F enlarges the binding pocket entrance and hydrophobically interacts with crizotinib to enhance sensitivity. With respect to the double mutant L1198F/G1202R, F1198 indirectly pulls R1202 away from the binding entrance and consequently alleviates the steric obstacle introduced by R1202. These results demonstrated how the mutated residues tune the crizotinib response and may assist kinase inhibitor development especially for ALK G1202R, analogous to the ROS1 G2302R and MET G1163R mutations that are also resistant to crizotinib treatment in NSCLC.
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Abstract
Interest in the application of molecular dynamics (MD) simulations has increased in the field of protein kinase (PK) drug discovery. PKs belong to an important drug target class because they are directly involved in a number of diseases, including cancer. MD methods simulate dynamic biological and chemical events at an atomic level. This information can be combined with other in silico and experimental methods to efficiently target selected receptors. In this review, we present common and advanced methods of MD simulations and we focus on the recent applications of MD-based methodologies that provided significant insights into the elucidation of biological mechanisms involving PKs and into the discovery of novel kinase inhibitors.
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