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Perinbaraj S, Jayaraman M, Jeyaraman J, Girija KR. Designing novel potent oxindole derivatives as VEGFR2 inhibitors for cancer therapy: Computational insights from molecular docking, drug-likeness, DFT, and structural dynamics studies. J Mol Graph Model 2025; 138:109049. [PMID: 40239487 DOI: 10.1016/j.jmgm.2025.109049] [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: 12/02/2024] [Revised: 01/25/2025] [Accepted: 04/09/2025] [Indexed: 04/18/2025]
Abstract
Oxindole is a γ-lactam featuring a heterocyclic core, combining pyrrole and benzene rings with a carbonyl group at the second position. This scaffold is present in numerous bioactive compounds, both natural and synthetic, and has emerged as a privileged pharmacophore in medicinal chemistry due to its broad biological activity. Substitution at the 3-position of the 2-oxindole structure has been shown to enhance potency and selectivity, especially in anticancer drug development. Breast cancer, a prevalent and challenging disease affecting millions of women worldwide, underscores an urgent need for more effective treatments. Current therapies often exhibit limited efficacy, significant side effects, and resistance issues, highlighting the demand for novel drugs with improved safety profiles. This study focuses on vascular endothelial growth factor receptor-2 (VEGFR-2), an essential regulator of tumor angiogenesis, as a potential target for breast cancer therapy. Through molecular docking-based virtual screening of 360 designed oxindole derivatives, three compounds (BIATAM, CIHTAM, and IATAM) were identified as potential candidates, each demonstrating high docking scores (>7 kcal/mol) and favorable interactions, including hydrogen bonding, hydrophobic contacts, and stacking. Among these, BIATAM emerged as the lead compound due to its superior docking performance, favorable pharmacokinetic profiles, and compliance with Lipinski's Rule of Five. Density functional theory (DFT) calculations confirmed its chemical stability, while molecular dynamics simulations (MDS) revealed high structural stability. Principal component-based free energy landscape (FEL) analysis highlighted limited conformational flexibility, and MM/PBSA-based binding energy calculations reinforced its strong affinity within the VEGFR-2 binding pocket. These comprehensive computational findings suggest that BIATAM holds promising potential as a novel therapeutic option for treating breast cancer.
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Affiliation(s)
- Sowmiya Perinbaraj
- Department of Pharmaceutical Chemistry, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Sciences, (A Govt. of Puducherry Institution), Puducherry, 605 006, India
| | - Manikandan Jayaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Konda Reddy Girija
- Department of Pharmaceutical Chemistry, College of Pharmacy, Mother Theresa Post Graduate and Research Institute of Health Sciences, (A Govt. of Puducherry Institution), Puducherry, 605 006, India.
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Mushtaq A, Asif R, Humayun WA, Naseer MM. Novel isatin-triazole based thiosemicarbazones as potential anticancer agents: synthesis, DFT and molecular docking studies. RSC Adv 2024; 14:14051-14067. [PMID: 38686286 PMCID: PMC11057040 DOI: 10.1039/d4ra01937g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
Thiosemicarbazones of isatin have been found to exhibit versatile bioactivities. In this study, two distinct types of isatin-triazole hybrids 3a and 3b were accessed via copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), together with their mono and bis-thiosemicarbazone derivatives 4a-h and 5a-h. In addition to the characterization by physical, spectral and analytical data, a DFT study was carried out to obtain the optimized geometries of all thiosemicarbazones. The global reactivity values showed that among the synthesized derivatives, 4c, 4g and 5c having nitro substituents are the most soft compounds, with compound 5c having the highest electronegativity and electrophilicity index values among the synthesized series, thus possessing strong binding ability with biomolecules. Molecular docking studies were performed to explore the inhibitory ability of the selected compounds against the active sites of the anticancer protein of phosphoinositide 3-kinase (PI3K). Among the synthesized derivatives, 4-nitro substituted bisthiosemicarbazone 5c showed the highest binding energy of -10.3 kcal mol-1. These findings demonstrated that compound 5c could be used as a favored anticancer scaffold via the mechanism of inhibition against the PI3K signaling pathways.
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Affiliation(s)
- Alia Mushtaq
- Department of Chemistry, Quaid-i-Azam University Islamabad 45320 Pakistan
| | - Rabbia Asif
- Department of Chemistry, Quaid-i-Azam University Islamabad 45320 Pakistan
| | - Waqar Ahmed Humayun
- Department of Medical Oncology & Radiotherapy, King Edward Medical University Lahore 54000 Pakistan
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Khalaj M, Taherkhani M, Payen L, Klein A. A Sulfonic Acid Polyvinyl Pyridinium Ionic Liquid Catalyzes the Multi-Component Synthesis of Spiro-indoline-3,5'-pyrano[2,3- d]-pyrimidines and -Pyrazines. Molecules 2023; 28:molecules28093663. [PMID: 37175073 PMCID: PMC10180120 DOI: 10.3390/molecules28093663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/11/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
A sulfonated poly-4-vinyl pyridinium (PVPy-IL-B-SO3H) containing an acidic pyridinium/HSO3- ionic liquid moiety was prepared and used as a catalyst for the three-component reaction of malononitrile with 1-alkylindoline-2,3-diones and 1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione or methyl 5-hydroxy-1H-pyrazole-3-carboxylate, leading to methyl 6'-amino-5'-cyano-2-oxo-2'H-spiro[indoline-3,4'-pyrano[2,3-c]pyrazole]-3'-carboxylates or -3,4'-pyrano[2,3-d]pyrimidine]-6'-carbonitrile derivatives under ultrasonic irradiation conditions. The solid catalyst allows easy separation, is cheap, produces high yields under mild conditions, and does not require column chromatography for product isolation and purification.
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Affiliation(s)
- Mehdi Khalaj
- Department of Chemistry, Buinzahra Branch, Islamic Azad University, Buinzahra 1477893855, Iran
| | - Mahboubeh Taherkhani
- Department of Chemistry, Takestan Branch, Islamic Azad University, Takestan 3481949479, Iran
| | - Leo Payen
- Institute for Inorganic Chemistry, Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Greinstrasse 6, 50939 Köln, Germany
| | - Axel Klein
- Institute for Inorganic Chemistry, Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Greinstrasse 6, 50939 Köln, Germany
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Thongni A, Phanrang PT, Pandya C, Diengdoh DF, Gannon PM, Kaminsky W, Nongkhlaw R, Kumari J, Sriram D, Sivaramakrishna A, Nongkhlaw R. Ultrasound assisted synthesis of spirooxindole analogs catalyzed by Fe3O4@PPCA NPs: Experimental, theoretical and in vitro biological studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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In Vivo Antifungal Activity and Computational Studies of Some Azole Derivatives against Candida Albicans. J CHEM-NY 2023. [DOI: 10.1155/2023/7834474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Resistance of Candida species is a major problem in the management of Candida infection. This study investigated in vivo antifungal activities of several new imidazole and triazole derivatives in a C. albicans systemic infection. The efficacy of derivatives was determined against systemic infection by C. albicans in mice with cyclophosphamide-induced immunosuppression, and the antifungal activities of the synthesized compounds were evaluated in comparison with fluconazole. Compounds 3 and 8 had the highest efficacy with minimum inhibitory concentration (MIC) values of 0.5–1 μM against the C. albicans pathogen. In vivo activities in immunosuppressed mice were also greater than fluconazole. Furthermore, docking analysis was carried out to know the binding mode of imidazole and triazole derivatives to the CYP51 active site of C. albicans and dihydrofolate reductase as a valid antifungal target. The docking study found that the antifungal results are well correlated with docking results. ADMET and in silico physicochemical parameters were also performed. This study demonstrates that compounds 3 and 8 are potential antifungal candidates against the C. albicans pathogen.
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Khabnadideh S, Solhjoo A, Heidari R, Amiri Zirtol L, Sakhteman A, Rezaei Z, Babaei E, Rahimi S, Emami L. Efficient synthesis of 1,3-naphtoxazine derivatives using reusable magnetic catalyst (GO-Fe 3O 4-Ti (IV)): anticonvulsant evaluation and computational studies. BMC Chem 2022; 16:44. [PMID: 35689296 PMCID: PMC9188075 DOI: 10.1186/s13065-022-00836-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 12/29/2022] Open
Abstract
A series of 2-aryl/alkyl-2,3-dihydro-1H-naphtho[1,2-e][1,3]oxazines (S1-S11) were synthesized with an eco-friendly and recoverable nanocatalyst (GO-Fe3O4-Ti(IV)) as an efficient magnetic composite. The new nanocatalyst was characterized by FT-IR, XRD and, EDS analysis. A conformable procedure, easy to work up and having a short reaction time with high yields are some advantages of this method. The new catalyst is also thermal-stable, reusable and, environment-friendly. The chemical structures of the synthesized 1,3-oxazine compounds were confirmed by comparing their melting points with those reported in literature. Then, the anticonvulsant activity of these compounds was assessed by the intraperitoneal pentylenetetrazole test (ipPTZ). Compounds S10 and S11 displayed considerable activity against chemically-induced seizure tests. The molecular simulation was also done to achieve their binding affinities as γ-aminobutyric acid A (GABA-A) receptor agonists as an assumptive mechanism of their anticonvulsant action. The result of molecular studies represented strongly matched with biological activity. Molecular docking simulation of the potent compound (S10) and diazepam as the positive control was performed and some critical residues like Thr262, Asn265, Met286, Phe289, and Val290 were identified. Based on the anticonvulsant results and also in silico ADME predictions, S11 can be to become a potential drug candidate as an anticonvulsant agent.
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Affiliation(s)
- Soghra Khabnadideh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Heidari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Amiri Zirtol
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Babaei
- Department of Chemistry, College of Science, Yazd University, Yazd, Iran
| | - Samaneh Rahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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