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Mohammadi Y, Emadi R, Maddahi A, Shirdel S, Morowvat MH. Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: A molecular docking and dynamics approach. Comput Biol Chem 2024; 111:108095. [PMID: 38805865 DOI: 10.1016/j.compbiolchem.2024.108095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
Emerging as a promising drug target for Alzheimer's disease (AD) therapy, glycogen synthase kinase 3β (GSK-3β) has garnered attention. This study sought to rigorously scrutinize a compendium of natural compounds retrieved from the ZINC database through pharmacodynamic experiments, employing a 1 H-indazole-3-carboxamide (INDZ) scaffold, to identify compounds capable of inhibiting the GSK-3β protein. Utilizing a multi-step approach, the study involved pharmacophore analysis, followed by molecular docking to select five promising ligands for further investigation. Subsequently, ESMACS simulations were employed to assess the stability of the ligand-protein interactions. Evaluation of the binding modes and free energy of the ligands revealed that five compounds (2a-6a) exhibited crucial interactions with the active site residues. Furthermore, various methodologies, including hydrogen bond and clustering analyses, were utilized to ascertain their inhibitory potential and elucidate the factors contributing to ligand binding in the protein's active site. The findings from MMPBSA/GBSA analysis indicated that these five selected small molecules closely approached the IC50 value of the reference ligand (OH8), yielding energy values of -34.85, -32.58, -31.71, and -30.39 kcal/mol, respectively. Additionally, an assessment of the interactions using hydrogen bond and dynamic analyses delineated the effective binding of the ligands with the binding pockets in the protein. Through computational analysis, we obtained valuable insights into the molecular mechanisms of GSK-3β, aiding in the development of more potent inhibitors.
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Affiliation(s)
- Yasaman Mohammadi
- Faculty of Dentistry, Islamic Azad University, Shiraz Branch, Shiraz, Iran
| | - Reza Emadi
- Department of Biochemistry, Institute of Biochemistry & Biophsysics (IBB), University of Tehran, Tehran, Iran
| | - Arman Maddahi
- Department of Microbiology, Islamic Azad University, Shiraz Branch, Shiraz, Iran
| | - Shiva Shirdel
- Department of Psychology, Faculty of Education and Psychology, University of Tabriz, Tabriz, Iran
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Farasati Far B, Safaei M, Mokhtari F, Fallahi MS, Naimi-Jamal MR. Fundamental concepts of protein therapeutics and spacing in oncology: an updated comprehensive review. Med Oncol 2023; 40:166. [PMID: 37147486 DOI: 10.1007/s12032-023-02026-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Current treatment regimens in cancer cases cause significant side effects and cannot effectively eradicate the advanced disease. Hence, much effort has been expended over the past years to understand how cancer grows and responds to therapies. Meanwhile, proteins as a type of biopolymers have been under commercial development for over three decades and have been proven to improve the healthcare system as effective medicines for treating many types of progressive disease, such as cancer. Following approving the first recombinant protein therapeutics by FDA (Humulin), there have been a revolution for drawing attention toward protein-based therapeutics (PTs). Since then, the ability to tailor proteins with ideal pharmacokinetics has provided the pharmaceutical industry with an important noble path to discuss the clinical potential of proteins in oncology research. Unlike traditional chemotherapy molecules, PTs actively target cancerous cells by binding to their surface receptors and the other biomarkers particularly associated with tumorous or healthy tissue. This review analyzes the potential and limitations of protein therapeutics (PTs) in the treatment of cancer as well as highlighting the evolving strategies by addressing all possible factors, including pharmacology profile and targeted therapy approaches. This review provides a comprehensive overview of the current state of PTs in oncology, including their pharmacology profile, targeted therapy approaches, and prospects. The reviewed data show that several current and future challenges remain to make PTs a promising and effective anticancer drug, such as safety, immunogenicity, protein stability/degradation, and protein-adjuvant interactions.
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Affiliation(s)
- Bahareh Farasati Far
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Narmak, Tehran, Iran
| | - Maryam Safaei
- Department of Pharmacology, Faculty of Pharmacy, Eastern Mediterranean University, Via Mersin 10, TR. North Cyprus, Famagusta, Turkey
| | - Fatemeh Mokhtari
- Department of Chemistry, Faculty of Basic Science, Azarbaijan Shahid Madani (ASMU), Tabriz, 53751-71379, Iran
| | | | - Mohammad Reza Naimi-Jamal
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Narmak, Tehran, Iran.
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Le QH, Far BF, Sajadi SM, Jahromi BS, Kaspour S, Cakir B, Abdelmalek Z, Inc M. Analysis of Conocurvone, Ganoderic acid A and Oleuropein molecules against the main protease molecule of COVID-19 by in silico approaches: Molecular dynamics docking studies. ENGINEERING ANALYSIS WITH BOUNDARY ELEMENTS 2023; 150:583-598. [PMID: 36875283 PMCID: PMC9968613 DOI: 10.1016/j.enganabound.2023.02.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Traditional medicines against COVID-19 have taken important outbreaks evidenced by multiple cases, controlled clinical research, and randomized clinical trials. Furthermore, the design and chemical synthesis of protease inhibitors, one of the latest therapeutic approaches for virus infection, is to search for enzyme inhibitors in herbal compounds to achieve a minimal amount of side-effect medications. Hence, the present study aimed to screen some naturally derived biomolecules with anti-microbial properties (anti-HIV, antimalarial, and anti-SARS) against COVID-19 by targeting coronavirus main protease via molecular docking and simulations. Docking was performed using SwissDock and Autodock4, while molecular dynamics simulations were performed by the GROMACS-2019 version. The results showed that Oleuropein, Ganoderic acid A, and conocurvone exhibit inhibitory actions against the new COVID-19 proteases. These molecules may disrupt the infection process since they were demonstrated to bind at the coronavirus major protease's active site, affording them potential leads for further research against COVID-19.
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Affiliation(s)
- Quynh Hoang Le
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Medicine and Pharmacy, Duy Tan University, Da Nang, Vietnam
| | - Bahareh Farasati Far
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - S Mohammad Sajadi
- Department of Nutrition, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Bahar Saadaie Jahromi
- Biological Science Department, Western Michigan University, 1903W Michigan Avenue, Kalamazoo, MI 49008-5410, United States
| | - Sogand Kaspour
- Department of Paramed, Tehran University of Medical Science, Tehran, Iran
| | - Bilal Cakir
- Halal Food R&D Center, İstanbul S. Zaim University (İZÜ), Halkalı, Küçükçekmece, İstanbul, Turkey
- İZÜ Food and Agricultural Research Center (GTUAM), Halkalı Campus,, Küçükçekmece, İstanbul 34303, Turkey
| | - Zahra Abdelmalek
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Medicine and Pharmacy, Duy Tan University, Da Nang, Vietnam
| | - Mustafa Inc
- Science Faculty, Department of Mathematics, Firat University, Elazig 23119, Turkey
- Department of Medical Research, China Medical University, Taichung 40402, Taiwan
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Multi-responsive chitosan-based hydrogels for controlled release of vincristine. Commun Chem 2023; 6:28. [PMID: 36765265 PMCID: PMC9918727 DOI: 10.1038/s42004-023-00829-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/02/2023] [Indexed: 02/12/2023] Open
Abstract
As medical research progresses, the derivation and development of biological materials such as hydrogels have steadily gained more interest. The biocompatibility and non-toxicity of chitosan make chitosan hydrogels potential carriers for drug delivery. This work aims to develop two multi-reactive, safe, and highly swellable bio-hydrogels consisting of chitosan-graft-glycerol (CS-g-gly) and carboxymethyl chitosan-graft-glycerol (CMCS-g-gly), for sustained and controlled drug release, improved bioavailability along with entrapment in nanocarriers, which reduces side effects of vincristine sulphate. CS-g-gly and CMCS-g-gly are successfully prepared and fully characterized using analytical techniques. Under various conditions, the prepared hydrogels exhibit a high swelling ratio. Vincristine-loaded CS-g-gly (VCR/CS-g-gly), and CMCS-g-gly (VCR/CMCS-g-gly) show high encapsulation efficiency between 72.28-89.97%, and 56.97-71.91%, respectively. VCR/CS-g-gly show a sustained release behavior, and the maximum release of VCR from hydrogels reached 82% after 120 h of incubation. MCF-7 (breast cancer cell line) and MCF-10 (normal breast cell line) are evaluated for cell viability and apoptosis induction. The in-vitro anti-tumor efficacy is investigated using flow cytometry. The tetrazolium-based MTT assay of hydrogels shows no evidence of significant cytotoxicity in MCF-7 and MCF-10 cells. According to these findings, these hydrogels can effectively deliver drugs to MCF-7 and other breast cancer cells.
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Folate-Targeted Curcumin-Loaded Niosomes for Site-Specific Delivery in Breast Cancer Treatment: In Silico and In Vitro Study. Molecules 2022; 27:molecules27144634. [PMID: 35889513 PMCID: PMC9322601 DOI: 10.3390/molecules27144634] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
As the most common cancer in women, efforts have been made to develop novel nanomedicine-based therapeutics for breast cancer. In the present study, the in silico curcumin (Cur) properties were investigated, and we found some important drawbacks of Cur. To enhance cancer therapeutics of Cur, three different nonionic surfactants (span 20, 60, and 80) were used to prepare various Cur-loaded niosomes (Nio-Cur). Then, fabricated Nio-Cur were decorated with folic acid (FA) and polyethylene glycol (PEG) for breast cancer suppression. For PEG-FA@Nio-Cur, the gene expression levels of Bax and p53 were higher compared to free drug and Nio-Cur. With PEG-FA-decorated Nio-Cur, levels of Bcl2 were lower than the free drug and Nio-Cur. When MCF7 and 4T1 cell uptake tests of PEG-FA@Nio-Cur and Nio-Cur were investigated, the results showed that the PEG-FA-modified niosomes exhibited the most preponderant endocytosis. In vitro experiments demonstrate that PEG-FA@Nio-Cur is a promising strategy for the delivery of Cur in breast cancer therapy. Breast cancer cells absorbed the prepared nanoformulations and exhibited sustained drug release characteristics.
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Formulation and Characterization of Poly (Ethylene Glycol)-Coated Core-Shell Methionine Magnetic Nanoparticles as a Carrier for Naproxen Delivery: Growth Inhibition of Cancer Cells. Cancers (Basel) 2022; 14:cancers14071797. [PMID: 35406569 PMCID: PMC8997395 DOI: 10.3390/cancers14071797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Naproxen was loaded onto a magnetic nanoparticle coated with polyethylene glycol. Magnetic nanoparticles (MNPs) were used in this study to develop a smart naproxen delivery system. One of the most potent COX-1 and COX-2 inhibitors is naproxen, which belongs to the NSAID family of drugs. Although this drug has a short half-life, it has considerable toxicities and side effects on gastrointestinal tissues. The significant potential of our proposed nanocarrier for biomedical applications has been widely recognized; we modified MNPs to attach to this drug via disulfide bonds, promote the selective release of naproxen in inflammatory cells, and prevent adverse effects on the digestive system. It was found that the cytotoxicity of the drug was lowered by this change, which prevented unspecific protein binding. Abstract An efficient and selective drug delivery vehicle for cancer cells can remarkably improve therapeutic approaches. In this study, we focused on the synthesis and characterization of magnetic Ni1−xCoxFe2O4 nanoparticles (NPs) coated with two layers of methionine and polyethylene glycol to increase the loading capacity and lower toxicity to serve as an efficient drug carrier. Ni1−xCoxFe2O4@Methionine@PEG NPs were synthesized by a reflux method then characterized by FTIR, XRD, FESEM, TEM, and VSM. Naproxen was used as a model drug and its loading and release in the vehicles were evaluated. The results for loading efficiency showed 1 mg of Ni1−xCoxFe2O4@Methionine@PEG NPs could load 0.51 mg of the naproxen. Interestingly, Ni1−xCoxFe2O4@Methionine@PEG showed a gradual release of the drug, achieving a time-release up to 5 days, and demonstrated that a pH 5 release of the drug was about 20% higher than Ni1−xCoxFe2O4@Methionine NPs, which could enhance the intracellular drug release following endocytosis. At pH 7.4, the release of the drug was slower than Ni1−xCoxFe2O4@Methionine NPs; demonstrating the potential to minimize the adverse effects of anticancer drugs on normal tissues. Moreover, naproxen loaded onto the Ni1−xCoxFe2O4@Methionine@PEG NPs for breast cancer cell lines MDA-MB-231 and MCF-7 showed more significant cell death than the free drug, which was measured by an MTT assay. When comparing both cancer cells, we demonstrated that naproxen loaded onto the Ni1−xCoxFe2O4@Methionine@PEG NPs exhibited greater cell death effects on the MCF-7 cells compared with the MDA-MB-231 cells. The results of the hemolysis test also showed good hemocompatibility. The results indicated that the prepared magnetic nanocarrier could be suitable for controlled anticancer drug delivery.
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