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Iqbal Z, Fauzia Farheen Zofair S, Ahmed S, Sharma M, Younus H, Mahmood R. Interaction of plant phenol vanillin with human hemoglobin: A spectroscopic and molecular docking study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124831. [PMID: 39024790 DOI: 10.1016/j.saa.2024.124831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Vanillin is a phenolic aldehyde widely used as a flavouring agent in the food industry. Vanillin has many health benefits and has gained attention in pharmacological industries also, due to its antioxidant properties and non-toxic nature. The interaction of vanillin with human hemoglobin (hHb), an abundant tetrameric heme protein, was investigated by several spectroscopic techniques and molecular modeling methods. UV-visible spectra showed that the binding of vanillin to hHb induces structural changes due to alterations in the micro-environment of hHb. Vanillin quenches the intrinsic fluorescence of hHb by the dynamic mechanism, which was confirmed by both temperature dependent and time resolved fluorescence studies. Vanillin binds spontaneously to hHb at a single site and the binding is stabilized by hydrogen bonds and hydrophobic interactions. The circular dichroism spectra showed that the binding of vanillin altered the secondary structure of hHb due to change in its alpha-helical content. Molecular docking identified the amino acids of hHb involved in binding to vanillin and also that the free energy change of the binding reaction is -5.5 kcal/mol. Thus, our results indicate that vanillin binds spontaneously to hHb at a single site and alters its secondary structure. This will help in understanding the potential use of vanillin and related antioxidants as therapeutic agents in various hematological disorders.
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Affiliation(s)
- Zarmin Iqbal
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Syeda Fauzia Farheen Zofair
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahbaz Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monika Sharma
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Hina Younus
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Riaz Mahmood
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, UP, India.
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Shimu MSS, Paul GK, Dutta AK, Kim C, Saleh MA, Islam MA, Acharjee UK, Kim B. Biochemical and molecular docking-based strategies of Acalypha indica and Boerhavia diffusa extract by targeting bacterial strains and cancer proteins. J Biomol Struct Dyn 2023:1-18. [PMID: 38146734 DOI: 10.1080/07391102.2023.2297011] [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: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Antibiotic-resistant microbes have emerged around the world, presenting a risk to health. Plant-derived drugs have become a potential source for the production of antibiotic-resistant drugs and cancer therapies. In this study, we investigated the antibacterial, cytotoxic and antioxidant properties of Acalypha indica and Boerhavia diffusa, and conducted in silico molecular docking experiments against EGFR and VEGFR-2 proteins. The metabolic extract of A. indica inhibited Streptococcus iniae and Staphylococcus sciuri with inhibition zones of 21.66 ± 0.57 mm and 20.33 ± 0.57 mm, respectively. The B. diffusa leaf extract produced inhibition zones of 20.3333 ± 0.5773 mm and 20.33 ± 0.57 mm against Streptococcus iniae and Edwardsiella anguillarum, respectively. A. indica and B. diffusa extracts had toxicities of 162.01 μg/ml and 175.6 μg/ml, respectively. Moreover, B. diffusa (IC50 =154.42 µg/ml) leaf extract exhibited moderately higher antioxidant activity compared with the A. indica (IC50 = 218.97 µg/ml) leaf extract. Multiple interactions were observed at Leu694, Met769 and Leu820 sites for EGFR and at Asp1046 and Cys1045 sites for VEGFR during the molecular docking study. CID-235030, CID-70825 and CID-156619353 had binding energies of -7.6 kJ/mol, -7.5 kJ/mol and -7.6 kJ/mol, respectively, with EGFR protein. VEGFR-2 protein had docking energies of -7.5 kJ/mol, -7.6 kJ/mol and -7.3 kJ/mol, respectively, for CID-6420353, CID-156619353 and CID-70825 compounds. The MD simulation trajectories revealed the hit compound; CID-235030 and EGFR complex, CID-6420353 and VEGFR-2 exhibit stable profile in the root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bond and root mean square fluctuation (RMSF) and the binding free energy by MM-PBSA method. This study indicates that methanol extracts of A. indica and B. diffusa may play a crucial role in developing antibiotic-resistant and cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mst Sharmin Sultana Shimu
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Gobindo Kumar Paul
- Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Amit Kumar Dutta
- Department of Microbiology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Changhyun Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, Korea
| | - Md Abu Saleh
- Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Md Asadul Islam
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Uzzal Kumar Acharjee
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh, India
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, Korea
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Ismail MMF, Shawer TZ, Ibrahim RS, Allam RM, Ammar YA. Novel quinoxaline-based VEGFR-2 inhibitors to halt angiogenesis. Bioorg Chem 2023; 139:106735. [PMID: 37531818 DOI: 10.1016/j.bioorg.2023.106735] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
Vascular endothelial growth factor receptor-2 is a dynamic target for therapeutic intervention in various types of cancer. This study was aimed at exploring the VEGFR-2 inhibitory activity of a novel library of quinoxalin-2-one derivatives such as 3-furoquinoxaline carboxamides, 3-pyrazolylquinoxalines, and 3-pyridopyrimidyl-quinoxalines. Among them, 6c, 7a, and 7d-f produced remarkable cytotoxicity against HCT-116 (IC50's 4.28-9.31 µM) and MCF-7 (IC50's 3.57-7.57 µM) cell lines using the MTT assay and doxorubicin (DOX) as a reference standard. Interestingly, results of cytotoxicity towards the human fibroblast cell line WI38 revealed that these hits demonstrated higher selectivity indices towards both HCT-116 (SI 8.69-23.19) and MCF-7 (SI 9.48-27.80) than DOX, SI 0.72 and 0.90, respectively. Then, these hits were subjected to a mechanistic study; they showed direct inhibition of VEGFR-2. Impressively, compound 7f displayed 1.2 times the VEGFR-2 inhibitory activity of sorafenib. The antiangiogenic potential of 7f was proved via lowering the level of VEGF-A, than that of control. It as well, exhibited scratch closure percent of 61.8%, compared with 74.5% of control at 48 hrs, indicating the potential anti-migratory effect of the compound 7f. It significantly increased the expression of tumor suppressor gene (p53) on MCF-7 cells by almost 18 folds and upregulated the caspase-3 level by 10.7 folds, compared to the control. Cell cycle analysis revealed cell cycle arrest at G2/M together with a PreG increase which indicated apoptosis induction potential. Annexin V-FITC apoptosis results proposed the two modes of cell death (apoptosis and necrosis) as an inherent mechanism of cytotoxicity of compound 7f. Molecular docking further supported the mechanism showing the affinity of target compounds for VEGFR-2 active site. Moreover, physicochemical and drug-like properties were assessed from the ADME properties.
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Affiliation(s)
- Magda M F Ismail
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), 11754 Al-Azhar University, Cairo, Egypt.
| | - Taghreed Z Shawer
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), 11754 Al-Azhar University, Cairo, Egypt
| | - Rabab S Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), 11754 Al-Azhar University, Cairo, Egypt
| | - Rasha M Allam
- Department of Pharmacology, Medical and Clinical Research Institute, National Research Centre, 12622, Dokki, Cairo, Egypt
| | - Yousry A Ammar
- Department of Chemistry, Faculty of Science, 11754 Al-Azhar University, Cairo, Egypt
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Molecular dynamics-based insight of VEGFR-2 kinase domain: a combined study of pharmacophore modeling and molecular docking and dynamics. J Mol Model 2022; 29:17. [PMID: 36550239 DOI: 10.1007/s00894-022-05427-x] [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: 06/19/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Inhibition of vascular endothelial growth factor receptor 2 (VEGFR-2) tyrosine kinase by small molecules has become a promising target in the treatment of cancer. OBJECTIVE In this study, we approached pharmacophore modeling coupled with a structure-based virtual screening workflow to identify the potent inhibitors. METHODS The top selected hit compounds have been rescored using the MM/GBSA approach. To understand the molecular reactivity, electronic properties, and stability of those inhibitors, we have employed density functional theory and molecular dynamics. Following that, the best 21 hit compounds have been further post-processed with a Quantum ligand partial charge-based rescoring process and further validated by implementing molecular dynamics simulation. RESULTS The ten hit compounds have been hypothesized and considered as potent inhibitors of VEGFR-2 tyrosine kinase. This study also signifies the contribution of QM-based ligand partial charge, which is more accurate in predicting reliable free binding energy and filtering large ligand libraries to hit optimization, rather than assigning those of the force field-based method. From the binding pattern analysis of all the complexes, amino acids, such as Glu885, Cys919, Cys1045, Thr916, Thr919, and Asp1046, were found to have comprehensive interaction with the hit compounds. CONCLUSION Hence, this could prove to be useful as a potential inhibition site of the VEGFR-2 tyrosine kinase domain for future researchers. Moreover, this study also emphasizes the conformational changes upon ATP binding, based on either the receptor's rigidity or flexibility.
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Khazaei-Poul Z, Mahmoodi NO, Taherpour Nahzomi H. Synthesis, biological evaluation and molecular docking studies of a new series of bis-chalcones. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04872-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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The use of machine learning modeling, virtual screening, molecular docking, and molecular dynamics simulations to identify potential VEGFR2 kinase inhibitors. Sci Rep 2022; 12:18825. [PMID: 36335233 PMCID: PMC9637137 DOI: 10.1038/s41598-022-22992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 10/21/2022] [Indexed: 11/08/2022] Open
Abstract
Targeting the signaling pathway of the Vascular endothelial growth factor receptor-2 is a promising approach that has drawn attention in the quest to develop novel anti-cancer drugs and cardiovascular disease treatments. We construct a screening pipeline using machine learning classification integrated with similarity checks of approved drugs to find new inhibitors. The statistical metrics reveal that the random forest approach has slightly better performance. By further similarity screening against several approved drugs, two candidates are selected. Analysis of absorption, distribution, metabolism, excretion, and toxicity, along with molecular docking and dynamics are performed for the two candidates with regorafenib as a reference. The binding energies of molecule1, molecule2, and regorafenib are - 89.1, - 95.3, and - 87.4 (kJ/mol), respectively which suggest candidate compounds have strong binding to the target. Meanwhile, the median lethal dose and maximum tolerated dose for regorafenib, molecule1, and molecule2 are predicted to be 800, 1600, and 393 mg/kg, and 0.257, 0.527, and 0.428 log mg/kg/day, respectively. Also, the inhibitory activity of these compounds is predicted to be 7.23 and 7.31, which is comparable with the activity of pazopanib and sorafenib drugs. In light of these findings, the two compounds could be further investigated as potential candidates for anti-angiogenesis therapy.
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He L, Liu Y, Xu J, Li J, Cheng G, Cai J, Dang J, Yu M, Wang W, Duan W, Liu K. Inhibitory Effects of Myriocin on Non-Enzymatic Glycation of Bovine Serum Albumin. Molecules 2022; 27:molecules27206995. [PMID: 36296589 PMCID: PMC9607541 DOI: 10.3390/molecules27206995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/12/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Advanced glycation end products (AGEs) are the compounds produced by non-enzymatic glycation of proteins, which are involved in diabetic-related complications. To investigate the potential anti-glycation activity of Myriocin (Myr), a fungal metabolite of Cordyceps, the effect of Myr on the formation of AGEs resulted from the glycation of bovine serum albumin (BSA) and the interaction between Myr and BSA were studied by multiple spectroscopic techniques and computational simulations. We found that Myr inhibited the formation of AGEs at the end stage of glycation reaction and exhibited strong anti-fibrillation activity. Spectroscopic analysis revealed that Myr quenched the fluorescence of BSA in a static process, with the possible formation of a complex (approximate molar ratio of 1:1). The binding between BSA and Myr mainly depended on van der Waals interaction, hydrophobic interactions and hydrogen bond. The synchronous fluorescence and UV-visible (UV-vis) spectra results indicated that the conformation of BSA altered in the presence of Myr. The fluorescent probe displacement experiments and molecular docking suggested that Myr primarily bound to binding site 1 (subdomain IIA) of BSA. These findings demonstrate that Myr is a potential anti-glycation agent and provide a theoretical basis for the further functional research of Myr in the prevention and treatment of AGEs-related diseases.
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Affiliation(s)
- Libo He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Liu
- Department of Central Laboratory, The First People’s Hospital of Huzhou, First Affiliated Hospital of Huzhou University, Huzhou 313000, China
| | - Junling Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jingjing Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Guohua Cheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jiaxiu Cai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jinye Dang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Meng Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Weiyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wei Duan
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Ke Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Correspondence:
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Arif A, Hashmi MA, Salam S, Younus H, Mahmood R. Interaction of the insecticide bioallethrin with human hemoglobin: biophysical, in silico and enzymatic studies. J Biomol Struct Dyn 2022:1-12. [PMID: 35950518 DOI: 10.1080/07391102.2022.2109756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Bioallethrin is an insecticide that is widely used in households resulting in human exposure. Bioallethrin is cytotoxic to human erythrocytes. Here we have studied the interaction of bioallethrin with human hemoglobin (Hb) using in silico and biophysical approaches. Incubation of Hb (5 μM) with bioallethrin (1-50 µM) led to increase in absorbance at 280 nm while the Soret band at 406 nm was slightly reduced. The intrinsic fluorescence of Hb was enhanced with the appearance of a new peak around 305 nm. Synchronous fluorescence showed that the binding of bioallethrin to Hb mainly affects the tyrosine microenvironment. The structural changes in Hb were confirmed with a significant shift in CD spectra and about 25% loss of α-helix. Molecular docking and visualisation through Discovery studio confirmed the formation of Hb-bioallethrin complex with a binding energy of -7.3 kcal/mol. Molecular simulation showed the stability and energy dynamics of the binding reaction between bioallethrin and Hb. The structural changes induced by bioallethrin led to inhibition of the esterase activity of Hb. In conclusion, this study shows that bioallethrin forms a stable complex with human Hb which may lead to loss of Hb function in the body.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amin Arif
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Md Amiruddin Hashmi
- Department of Biotechnology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Samreen Salam
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Hina Younus
- Department of Biotechnology, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Riaz Mahmood
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules 2022; 12:biom12070878. [PMID: 35883434 PMCID: PMC9312989 DOI: 10.3390/biom12070878] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer is one of the most prevalent cancer types. Although there have been breakthroughs in its treatments, a better understanding of the molecular mechanisms and genetic involvement in colorectal cancer will have a substantial role in producing novel and targeted treatments with better safety profiles. In this review, the main molecular pathways and driver genes that are responsible for initiating and propagating the cascade of signaling molecules reaching carcinoma and the aggressive metastatic stages of colorectal cancer were presented. Protein kinases involved in colorectal cancer, as much as other cancers, have seen much focus and committed efforts due to their crucial role in subsidizing, inhibiting, or changing the disease course. Moreover, notable improvements in colorectal cancer treatments with in silico studies and the enhanced selectivity on specific macromolecular targets were discussed. Besides, the selective multi-target agents have been made easier by employing in silico methods in molecular de novo synthesis or target identification and drug repurposing.
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Motahari R, Boshagh MA, Moghimi S, Peytam F, Hasanvand Z, Oghabi Bakhshaiesh T, Foroumadi R, Bijanzadeh H, Firoozpour L, Khalaj A, Esmaeili R, Foroumadi A. Design, synthesis and evaluation of novel tetrahydropyridothienopyrimidin-ureas as cytotoxic and anti-angiogenic agents. Sci Rep 2022; 12:9683. [PMID: 35690595 PMCID: PMC9188586 DOI: 10.1038/s41598-022-13515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
The novel derivatives of tetrahydropyridothienopyrimidine-based compounds have been designed and efficiently synthesized with good yields through seven steps reaction. The anticancer activity of compounds 11a-y has been evaluated against MCF-7, PC-3, HEPG-2, SW-480, and HUVEC cell lines by MTT assay. The target compounds showed IC50 values between 2.81–29.6 μg/mL and were compared with sorafenib as a reference drug. Among them, compound 11n showed high cytotoxic activity against four out of five examined cell lines and was 14 times more selective against MRC5. The flow cytometric analysis confirmed the induction of apoptotic cell death by this compound against HUVEC and MCF-7 cells. In addition, 11n caused sub-G1 phase arrest in the cell cycle arrest. Besides, this compound induced anti-angiogenesis in CAM assay and increased the level of caspase-3 by 5.2 fold. The western-blot analysis of the most active compound, 11n, revealed the inhibition of VEGFR-2 phosphorylation. Molecular docking study also showed the important interactions for compound 11n.
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Affiliation(s)
- Rasoul Motahari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Boshagh
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Peytam
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Zaman Hasanvand
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Roham Foroumadi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Bijanzadeh
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Khalaj
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran. .,Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
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Elmaaty A, Darwish KM, Chrouda A, Boseila AA, Tantawy MA, Elhady SS, Shaik AB, Mustafa M, Al-karmalawy AA. In Silico and In Vitro Studies for Benzimidazole Anthelmintics Repurposing as VEGFR-2 Antagonists: Novel Mebendazole-Loaded Mixed Micelles with Enhanced Dissolution and Anticancer Activity. ACS OMEGA 2022; 7:875-899. [PMID: 35036753 PMCID: PMC8757357 DOI: 10.1021/acsomega.1c05519] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/03/2021] [Indexed: 02/08/2023]
Abstract
Cancer is a leading cause of death worldwide and its incidence is unfortunately anticipated to rise in the next years. On the other hand, vascular endothelial growth factor receptor 2 (VEGFR-2) is highly expressed in tumor-associated endothelial cells, where it affects tumor-promoting angiogenesis. Therefore, VEGFR-2 is considered one of the most promising therapeutic targets for cancer treatment. Furthermore, some FDA-approved benzimidazole anthelmintics have already shown potential anticancer activities. Therefore, repurposing them against VEGFR-2 can provide a rapid and effective alternative that can be implicated safely for cancer treatment. Hence, 13 benzimidazole anthelmintic drugs were subjected to molecular docking against the VEGFR-2 receptor. Among the tested compounds, fenbendazole (FBZ, 1), mebendazole (MBZ, 2), and albendazole (ABZ, 3) were proposed as potential VEGFR-2 antagonists. Furthermore, molecular dynamics simulations were carried out at 200 ns, giving more information on their thermodynamic and dynamic properties. Besides, the anticancer activity of the aforementioned drugs was tested in vitro against three different cancer cell lines, including liver cancer (HUH7), lung cancer (A549), and breast cancer (MCF7) cell lines. The results depicted potential cytotoxic activity especially against both HUH7 and A549 cell lines. Furthermore, to improve the aqueous solubility of MBZ, it was formulated in the form of mixed micelles (MMs) which showed an enhanced drug release with better promising cytotoxicity results compared to the crude MBZ. Finally, an in vitro quantification for VEGFR-2 concentration in treated HUH7 cells has been conducted based on the enzyme-linked immunosorbent assay. The results disclosed that FBZ, MBZ, and ABZ significantly (p < 0.001) reduced the concentration of VEGFR-2, while the lowest inhibition was achieved in MBZ-loaded MMs, which was even much better than the reference drug sorafenib. Collectively, the investigated benzimidazole anthelmintics could be encountered as lead compounds for further structural modifications and thus better anticancer activity, and that was accomplished through studying their structure-activity relationships.
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Affiliation(s)
- Ayman
Abo Elmaaty
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
| | - Khaled M. Darwish
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Amani Chrouda
- Department
of Chemistry, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia
- Laboratory
of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University, Monastir 5000, Tunisia
| | - Amira A. Boseila
- Pharmaceutics
Department, Egyptian Drug Authority EDA
(Formerly Known as National Organization for Drug Control and Research
NODCAR) Dokki, Giza 12611, Egypt
| | - Mohamed A. Tantawy
- Hormones
Department, Medical Research Division, National
Research Centre, Dokki, Giza 12622, Egypt
- Stem
Cells Lab, Center of Excellence for Advanced Sciences, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Sameh S. Elhady
- Department
of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Afzal B. Shaik
- Department
of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University, Vadlamudi 522 213, Andhra Pradesh, India
| | - Muhamad Mustafa
- Department
of Medicinal Chemistry, Deraya University, Minia 61111, Egypt
| | - Ahmed A. Al-karmalawy
- Department of Pharmaceutical Medicinal
Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
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Abstract
Amongst the several types of brain cancers known to humankind, glioma is one of the most severe and life-threatening types of cancer, comprising 40% of all primary brain tumors. Recent reports have shown the incident rate of gliomas to be 6 per 100,000 individuals per year globally. Despite the various therapeutics used in the treatment of glioma, patient survival rate remains at a median of 15 months after undergoing first-line treatment including surgery, radiation, and chemotherapy with Temozolomide. As such, the discovery of newer and more effective therapeutic agents is imperative for patient survival rate. The advent of computer-aided drug design in the development of drug discovery has emerged as a powerful means to ascertain potential hit compounds with distinctively high therapeutic effectiveness against glioma. This review encompasses the recent advances of bio-computational in-silico modeling that have elicited the discovery of small molecule inhibitors and/or drugs against various therapeutic targets in glioma. The relevant information provided in this report will assist researchers, especially in the drug design domains, to develop more effective therapeutics against this global disease.
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Khedr F, Ibrahim MK, Eissa IH, Abulkhair HS, El-Adl K. Phthalazine-based VEGFR-2 inhibitors: Rationale, design, synthesis, in silico, ADMET profile, docking, and anticancer evaluations. Arch Pharm (Weinheim) 2021; 354:e2100201. [PMID: 34411344 DOI: 10.1002/ardp.202100201] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/07/2023]
Abstract
In the designed compounds, a new linker was inserted in the form of fragments with verified VEGFR-2 inhibitory potential, including an α,β-unsaturated ketonic fragment, pyrazole, and pyrimidine. Also, new distal hydrophobic moieties were attached to these linkers that are expected to increase the hydrophobic interaction with VEGFR-2 and, consequently, the affinity. These structural optimizations have led us to identify the novel dihydropyrazole derivative 6e as a promising hit molecule. All the new derivatives were evaluated to assess their anticancer activity against three human cancer cell lines, including HepG2, HCT-116, and MCF-7. The results of the in vitro anticancer evaluation study revealed the moderate to excellent cytotoxicity of 6c , 6e , 6g , and 7b , with IC50 values in the low micromolar range. The inhibitory activity of VEGFR-2 was investigated for 16 of the designed compounds. The enzyme assay results of the new compounds were compared with those of sorafenib as a reference VEGFR-2 inhibitor. The obtained results demonstrated that our derivatives are potent VEGFR-2 inhibitors. The most potent derivatives 6c , 6e , 6g , and 7b showed IC50 values in the range of 0.11-0.22 µM. Molecular docking and pharmacokinetic studies were also conducted to rationalize the VEGFR-2 inhibitory activity and to evaluate the ability of the most potent derivatives to be developed as good drug candidates.
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Affiliation(s)
- Fathalla Khedr
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed-Kamal Ibrahim
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.,Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
| | - Khaled El-Adl
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt.,Pharmaceutical Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
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14
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Li B, Yao J, He F, Liu J, Lin Z, Liu S, Wang W, Wu T, Huang J, Chen K, Fang M, Chen J, Zeng JZ. Synthesis, SAR study, and bioactivity evaluation of a series of Quinoline-Indole-Schiff base derivatives: Compound 10E as a new Nur77 exporter and autophagic death inducer. Bioorg Chem 2021; 113:105008. [PMID: 34089944 DOI: 10.1016/j.bioorg.2021.105008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
We previously reported 5-((8-methoxy-2-methylquinolin-4-yl)amino)-1H-indole- 2-carbohydrazide derivatives as new Nur77 modulators. In this study, we explored whether the 8-methoxy-2-methylquinoline moiety and bicyclic aromatic rings at the N'-methylene position were critical for their antitumor activity against hepatocellular carcinoma (HCC). For this purpose, a small library of 5-substituted 1H-indole-2-carbohydrazide derivatives was designed and synthesized. We found that the 8-methoxy-2-methylquinoline moiety was a fundamental structure for its biological function, while the introduction of the bicyclic aromatic ring into the N'-methylene greatly improved its anti-tumor effect. We found that the representative compound 10E had a high affinity to Nur77. The KD values were in the low micromolar (2.25-4.10 μM), which were coincident with its IC50 values against the tumor cell lines (IC50 < 3.78 μM). Compound 10E could induce autophagic cell death of liver cancer cells by targeting Nur77 to mitochondria while knocking down Nur77 greatly impaired anti-tumor effect. These findings provide an insight into the structure-activity relation of Quinoline-Indole-Schiff base derivatives and further demonstrate that antitumor agents targeting Nur77 may be considered as a promising strategy for HCC therapy.
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Affiliation(s)
- Baicun Li
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China; State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Department of Physiology, Peking Union Medical College, Beijing 100730, China
| | - Jie Yao
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China; Radiation Oncology Key Laboratory of Sichuan Province, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610000, China
| | - Fengming He
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jie Liu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zongxin Lin
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shunzhi Liu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Wang Wang
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Tong Wu
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jiangang Huang
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Kun Chen
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China
| | - Meijuan Fang
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jingwei Chen
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Jin-Zhang Zeng
- School of Pharmaceutical Sciences and School of Public Health, Xiamen University, Xiamen 361102, China.
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15
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Reddy NN, Hung SJ, Swamy MK, Sanjeev A, Rao VS, Rohini R, Raju AK, Bhaskar K, Hu A, Reddy PM. Synthesis and Rational Design of New Appended 1,2,3-Triazole-uracil Ensembles as Promising Anti-Tumor Agents via In Silico VEGFR-2 Transferase Inhibition. Molecules 2021; 26:1952. [PMID: 33808444 PMCID: PMC8037033 DOI: 10.3390/molecules26071952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/18/2022] Open
Abstract
Angiogenesis inhibition is a key step towards the designing of new chemotherapeutic agents. In a view to preparing new molecular entities for cancer treatment, eighteen 1,2,3-triazole-uracil ensembles 5a-r were designed and synthesized via the click reaction. The ligands were well characterized using 1H-, 13C-NMR, elemental analysis and ESI-mass spectrometry. The in silico binding propinquities of the ligands were studied sequentially in the active region of VEGFR-2 using the Molegro virtual docker. All the compounds produced remarkable interactions and potentially inhibitory ligands against VEGFR-2 were obtained with high negative binding energies. Drug-likeness was assessed from the ADME properties. Cytotoxicity of the test compounds was measured against HeLa and HUH-7 tumor cells and NIH/3T3 normal cells by MTT assay. Compound 5h showed higher growth inhibition activity than the positive control, 5-fluorouracil (5-FU), against both HeLa and HUH-7 cells with IC50 values of 4.5 and 7.7 μM respectively. Interestingly, the compounds 5a-r did not show any cytotoxicity towards the normal cell lines. The results advance the position of substituted triazoles in the area of drug design with no ambiguity.
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Affiliation(s)
- Nadipolla Naresh Reddy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Sung-Jen Hung
- Department of Dermatology, Buddhist Tzu-Chi General Hospital, Hualien 97002, Taiwan;
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97002, Taiwan
| | - Merugu Kumara Swamy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Ananthula Sanjeev
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Vankadari Srinivasa Rao
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Rondla Rohini
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Atcha Krishnam Raju
- Department of Chemistry, Nizam College, Osmania University, Hyderabad 500001, India;
| | - Kuthati Bhaskar
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
| | - Anren Hu
- Institute of Medical Sciences, Tzu-Chi University, Hualien 97002, Taiwan
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu-Chi University, Hualien 97004, Taiwan
| | - Puchakayala Muralidhar Reddy
- Department of Chemistry, Osmania University, Hyderabad, Telangana 500007, India; (N.N.R.); (M.K.S.); (A.S.); (V.S.R.); (R.R.); (K.B.)
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16
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Targeting the Autophagy Specific Lipid Kinase VPS34 for Cancer Treatment: An Integrative Repurposing Strategy. Protein J 2021; 40:41-53. [PMID: 33400087 DOI: 10.1007/s10930-020-09955-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
The impact of autophagy on cancer treatment and its corresponding responsiveness has galvanized the scientific community to develop novel inhibitors for cancer treatment. Importantly, the discovery of inhibitors that targets the early phase of autophagy was identified as a beneficial choice. Despite the number of research in recent years, screening of the DrugBank repository (9591 molecules) for the Vacuolar protein sorting 34 (VPS34) has not been reported earlier. Therefore, the present study was designed to identify potential VPS34 antagonists using integrated pharmacophore strategies. Primarily, an energy-based pharmacophore and receptor cavity-based analysis yielded five (DHRRR) and seven featured (AADDHRR) pharmacophore hypotheses respectively, which were utilized for the database screening process. The glide score, the binding free energy, pharmacokinetics and pharmacodynamics properties were examined to narrow down the screened compounds. This analysis yielded a hit molecule, DB03916 that exhibited a better docking score, higher binding affinity and better drug-like properties in contrast to the reference compound that suffers from a toxicity property. Importantly, the result was validated using a 50 ns molecular dynamics simulation study. Overall, we conclude that the identified hit molecule DB03916 is believed to serve as a prospective antagonist against VPS34 for cancer treatment.
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17
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Faraji A, Motahari R, Hasanvand Z, Oghabi Bakhshaiesh T, Toolabi M, Moghimi S, Firoozpour L, Boshagh MA, Rahmani R, Ketabforoosh SHME, Bijanzadeh HR, Esmaeili R, Foroumadi A. Quinazolin-4(3H)-one based agents bearing thiadiazole-urea: Synthesis and evaluation of anti-proliferative and antiangiogenic activity. Bioorg Chem 2020; 108:104553. [PMID: 33376012 DOI: 10.1016/j.bioorg.2020.104553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/03/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
A series of quinazolin-4(3H)-one based agents containing thiadiazole-urea were designed, synthesized, and biologically evaluated. The proliferation rate of PC3 cells was moderately reduced by compound 9f (IC50 = 17.7 μM)which was comparable with sorafenib (IC50 = 17.3 μM). There was also a significant reduction in the number of HUVEC cells, when they were exposed to compound 9y (IC50 = 6.1 μM). To test the potential of compounds in inducing apoptosis, Annexin V-FITC/propidium iodide double staining assay was used. After the treatment of HUVEC cells with 9f, they underwent apoptotic effects. A substantial effort was dedicated to gathering comprehensive data across CAM assay. These data showed that 9f moderately inhibits the growth of corresponding blood vessels. Finally, the outcomes of Western blotting proposed a mechanism of action, by which the phosphorylation of VEGFR-2 is inhibited by compounds 9f and 9y.
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Affiliation(s)
- Aram Faraji
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Motahari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zaman Hasanvand
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahsa Toolabi
- Department of Medicinal Chemistry, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Loghman Firoozpour
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Boshagh
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Roya Rahmani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Shima H M E Ketabforoosh
- Department of Medicinal Chemistry, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
| | - Hamid Reza Bijanzadeh
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
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18
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Ligand-Based Pharmacophore Modeling, Molecular Docking, and Molecular Dynamic Studies of Dual Tyrosine Kinase Inhibitor of EGFR and VEGFR2. Int J Mol Sci 2020; 21:ijms21207779. [PMID: 33096664 PMCID: PMC7590020 DOI: 10.3390/ijms21207779] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor 2 (VEGFR2) play an important role in cancer growth. Both of them have close relationships. Expression of EGFR will induce an angiogenic factor (VEGF) release for binding with VEGFR2. However, the existence of VEGF up-regulation independent of EGFR leads to cancer cell resistance to anti-EGFR. Therefore, a therapeutic approach targeting EGFR and VEGFR2 simultaneously may improve the outcome of cancer treatment. The present study was designed to identify potential compounds as a dual inhibitor of EGFR and VEGFR2 by the computational method. Firstly, the ligand-based pharmacophore model for each target was setup to screen of ZINC database of purchasable compounds. The hit compounds obtained by pharmacophore screening were then further screened by molecular docking studies. Taking erlotinib (EGFR inhibitor) and axitinib (VEGFR2 inhibitor) as reference drugs, six potential compounds (ZINC08398597, ZINC12047553, ZINC16525481, ZINC17418102, ZINC21942954, and ZINC38484632) were selected based on their docking scores and binding interaction. However, molecular dynamics simulations demonstrated that only ZINC16525481 and ZINC38484632 which have good binding free energy and stable hydrogen bonding interactions with EGFR and VEGFR2. The result represents a promising starting point for developing potent dual tyrosine kinases inhibitor of EGFR and VEGFR2.
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19
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Faraji A, Oghabi Bakhshaiesh T, Hasanvand Z, Motahari R, Nazeri E, Boshagh MA, Firoozpour L, Mehrabi H, Khalaj A, Esmaeili R, Foroumadi A. Design, synthesis and evaluation of novel thienopyrimidine-based agents bearing diaryl urea functionality as potential inhibitors of angiogenesis. Eur J Med Chem 2020; 209:112942. [PMID: 33328104 DOI: 10.1016/j.ejmech.2020.112942] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 01/22/2023]
Abstract
Inhibition of angiogenesis is a promising strategy for the treatment of cancer. Herein, we describe the design and synthesis of thieno[2,3-d]pyrimidine-1,3,4-thiadiazole-aryl urea derivatives 11a-m to evaluate their efficacy in the chick chorioallantoic membrane (CAM) assay. Among target agents, 11i had a considerable activity against prostate cancer cell line, PC3 (IC50 = 3.6 μM). Moreover, induction of apoptosis, good inhibitory activity against the growth of capillary blood vessels, and inhibition of VEGFR-2 phosphorylation were noticeable parameters which convinced us that 11i could be considered as a promising candidate for the discovery of novel drugs to treat tumors, particularly prostate cancer.
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Affiliation(s)
- Aram Faraji
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Zaman Hasanvand
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Motahari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Elahe Nazeri
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mohammad Amin Boshagh
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Loghman Firoozpour
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Mehrabi
- Department of Chemistry, Vali-e-Asr University of Rafsanjan, 77176, Rafsanjan, Iran
| | - Ali Khalaj
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
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20
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Saranyadevi S, Shanthi V. Molecular simulation strategies for the discovery of selective inhibitors of β-catenin. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tumor dissemination and relapse in lung cancer were found to be due to the existence of cancer stem cells. In particular, the [Formula: see text]-catenin pathway is found to be one of the crucial pathways in maintaining the stem-like properties of the cells. Thus, targeting the [Formula: see text]-catenin family of proteins is a significant therapeutic route in the treatment of lung cancer. Therefore, in the present study, a pharmacophore-based drug repurposing approach was accomplished to pinpoint potent [Formula: see text]-catenin inhibitors from the DrugBank database. Primarily, ligand-based pharmacophore hypothesis (AAHHR) was generated using existing [Formula: see text]-catenin inhibitors available in the literature and utilized for library screening. Subsequently, the inhibitory activity of the screened compounds was examined by the hierarchical docking process and the Prime MM-GBSA algorithm. Moreover, quantum chemical calculations and molecular dynamics simulations were executed to analyze the inhibitory effects of the screened hit molecule. The results indicate that hit molecule, DB08047 was found to possess better binding free energy, favorable ligand strain energy, satisfactory pharmacokinetic properties and superior free energy landscape profile. Eventually, the pIC[Formula: see text] values of the lead compounds were predicted by the AutoQSAR algorithm. It is noteworthy to mention that DB08047 was found to possess pyrazole scaffolds which could downregulate [Formula: see text]-catenin pathway and thus facilitate the controlled cell growth/inhibit tumor growth.
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Affiliation(s)
- S. Saranyadevi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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21
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Ekowati J, Diyah NW, Syahrani A. Synthesis and Antiplatelet Activites of Some Derivatives of p-Coumaric Acid. CHEMISTRY & CHEMICAL TECHNOLOGY 2019. [DOI: 10.23939/chcht13.03.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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8-Acetonyldihydronitidine inhibits the proliferation of human colorectal cancer cells via activation of p53. Eur J Pharmacol 2019; 854:256-264. [DOI: 10.1016/j.ejphar.2019.03.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 12/27/2022]
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In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate. Molecules 2019; 24:molecules24071445. [PMID: 30979098 PMCID: PMC6480119 DOI: 10.3390/molecules24071445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
The EGCG, an important component of polyphenol in green tea, is well known due to its numerous health benefits. We employed the reverse docking method for the identification of the putative targets of EGCG in the anti-tumor target protein database and these targets were further uploaded to public databases in order to understand the underlying pharmacological mechanisms and search for novel EGCG-associated targets. Similarly, the pharmacological linkage between tumor-related proteins and EGCG was manually constructed in order to provide greater insight into the molecular mechanisms through a systematic integration with applicable bioinformatics. The results indicated that the anti-tumor mechanisms of EGCG may involve 12 signaling transduction pathways and 33 vital target proteins. Moreover, we also discovered four novel putative target proteins of EGCG, including IKBKB, KRAS, WEE1 and NTRK1, which are significantly related to tumorigenesis. In conclusion, this work may provide a useful perspective that will improve our understanding of the pharmacological mechanism of EGCG and identify novel potential therapeutic targets.
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24
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Rampogu S, Baek A, Park C, Son M, Parate S, Parameswaran S, Park Y, Shaik B, Kim JH, Park SJ, Lee KW. Discovery of Small Molecules that Target Vascular Endothelial Growth Factor Receptor-2 Signalling Pathway Employing Molecular Modelling Studies. Cells 2019; 8:E269. [PMID: 30901950 PMCID: PMC6468367 DOI: 10.3390/cells8030269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/08/2019] [Accepted: 03/16/2019] [Indexed: 12/15/2022] Open
Abstract
Angiogenesis is defined as the formation of new blood vessels and is a key phenomenon manifested in a host of cancers during which tyrosine kinases play a crucial role. Vascular endothelial growth factor receptor-2 (VEGFR-2) is pivotal in cancer angiogenesis, which warrants the urgency of discovering new anti-angiogenic inhibitors that target the signalling pathways. To obtain this objective, a structure-based pharmacophore model was built from the drug target VEGFR-2 (PDB code: 4AG8), complexed with axitinib and was subsequently validated and employed as a 3D query to retrieve the candidate compounds with the key inhibitory features. The model was escalated to molecular docking studies resulting in seven candidate compounds. The molecular docking studies revealed that the seven compounds displayed a higher dock score than the reference-cocrystallised compound. The GROningen MAchine for Chemical Simulations (GROMACS) package guided molecular dynamics (MD) results determined their binding mode and affirmed stable root mean square deviation. Furthermore, these compounds have preserved their key interactions with the residues Glu885, Glu917, Cys919 and Asp1046. The obtained findings deem that the seven compounds could act as novel anti-angiogenic inhibitors and may further assist as the prototype in designing and developing new inhibitors.
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Affiliation(s)
- Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Ayoung Baek
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Chanin Park
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Minky Son
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Shraddha Parate
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Saravanan Parameswaran
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Yohan Park
- College of Pharmacy, Inje University, 197 Inje-ro, Gimhae, Gyeongnam 50834, Korea;
| | - Baji Shaik
- Department of Chemistry (BK 21 plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, Gyeongnam 52828, Korea; (B.S.); (J.H.K.)
| | - Ju Hyun Kim
- Department of Chemistry (BK 21 plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, Gyeongnam 52828, Korea; (B.S.); (J.H.K.)
| | - Seok Ju Park
- Department of Internal Medicine, College of Medicine, Busan Paik Hospital, Inje University, Gyeongnam 47392, Korea
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
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Nagabhishek SN, Madan Kumar A, B. S, Balakrishnan A, Katakia YT, Chatterjee S, Nagasundaram N. A marine sponge associated fungal metabolite monacolin X suppresses angiogenesis by down regulating VEGFR2 signaling. RSC Adv 2019; 9:26646-26667. [PMID: 35528587 PMCID: PMC9070443 DOI: 10.1039/c9ra05262c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the leading causes of global death and there is an urgent need for the development of cancer treatment; targeting VEGFR2 could be one of the promising therapies. In the present study, previously isolated marine fungal metabolite monacolin X, suppresses in vitro angiogenic characteristics such as proliferation, migration, adhesion, invasion and tube formation of HUVECs when stimulated by VEGF, at a non-toxic concentration. Monacolin X downregulated VEGFR2, PKCα and PKCη mRNA expression. Further, monacolin X inhibited in vivo angiogenesis in CAM assay, vascular sprouting in aortic ring, decreased ISV and SIV length and diameter in Tg (Kdr:EGFP)/ko1 zebrafish embryos. Monacolin X showed reduced protein expression of pVEGFR2, pAKT1, pMAPKAPK2, pFAK and pERK1 in breast cancer lines and in DMBA induced mammary carcinoma in SD rats showed tumor regression and anti-angiogenesis ability via decrease pVEGFR2 and pAKT1 protein expression. In silico studies also revealed monacolin X ability to bind to crucial amino acid Cys 919 in the active site of VEGFR2 suggesting it to be a potent VEGFR2 inhibitor. Cancer is one of the leading causes of global deaths and there is an urgent need for the development cancer treatment; targeting VEGFR2 could be one of the promising therapies.![]()
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Affiliation(s)
- Sirpu Natesh Nagabhishek
- Cancer Biology Lab
- Molecular and Nanomedicine Research Unit
- Sathyabama Institute of Science and Technology
- Chennai-600 119
- India
| | - Arumugam Madan Kumar
- Cancer Biology Lab
- Molecular and Nanomedicine Research Unit
- Sathyabama Institute of Science and Technology
- Chennai-600 119
- India
| | - Sambhavi B.
- Department of Genetics
- Dr ALM PGIBMS University of Madras Taramani
- Chennai
- India
| | | | - Yash T. Katakia
- Vascular Biology Lab
- AU-KBC Research Centre
- Department of Biotechnology
- Anna University
- Chennai
| | - Suvro Chatterjee
- Vascular Biology Lab
- AU-KBC Research Centre
- Department of Biotechnology
- Anna University
- Chennai
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26
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Shan Y, Wang B, Zhang J. New strategies in achieving antiangiogenic effect: Multiplex inhibitors suppressing compensatory activations of RTKs. Med Res Rev 2018; 38:1674-1705. [DOI: 10.1002/med.21517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Yuanyuan Shan
- Department of Pharmacy; The First Affiliated Hospital of Xi'an Jiaotong University; Xi'an China
| | - Binghe Wang
- Department of Chemistry; Center for Diagnostics and Therapeutics; Georgia State University; Atlanta GA USA
| | - Jie Zhang
- School of Pharmacy, Health Science Center; Xi'an Jiaotong University; Xi'an China
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Xie C, Wan X, Quan H, Zheng M, Fu L, Li Y, Lou L. Preclinical characterization of anlotinib, a highly potent and selective vascular endothelial growth factor receptor-2 inhibitor. Cancer Sci 2018; 109:1207-1219. [PMID: 29446853 PMCID: PMC5891194 DOI: 10.1111/cas.13536] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/02/2018] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
Abrogating tumor angiogenesis by inhibiting vascular endothelial growth factor receptor‐2 (VEGFR2) has been established as a therapeutic strategy for treating cancer. However, because of their low selectivity, most small molecule inhibitors of VEGFR2 tyrosine kinase show unexpected adverse effects and limited anticancer efficacy. In the present study, we detailed the pharmacological properties of anlotinib, a highly potent and selective VEGFR2 inhibitor, in preclinical models. Anlotinib occupied the ATP‐binding pocket of VEGFR2 tyrosine kinase and showed high selectivity and inhibitory potency (IC50 <1 nmol/L) for VEGFR2 relative to other tyrosine kinases. Concordant with this activity, anlotinib inhibited VEGF‐induced signaling and cell proliferation in HUVEC with picomolar IC50 values. However, micromolar concentrations of anlotinib were required to inhibit tumor cell proliferation directly in vitro. Anlotinib significantly inhibited HUVEC migration and tube formation; it also inhibited microvessel growth from explants of rat aorta in vitro and decreased vascular density in tumor tissue in vivo. Compared with the well‐known tyrosine kinase inhibitor sunitinib, once‐daily oral dose of anlotinib showed broader and stronger in vivo antitumor efficacy and, in some models, caused tumor regression in nude mice. Collectively, these results indicate that anlotinib is a well‐tolerated, orally active VEGFR2 inhibitor that targets angiogenesis in tumor growth, and support ongoing clinical evaluation of anlotinib for a variety of malignancies.
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Affiliation(s)
- Chengying Xie
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaozhe Wan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Haitian Quan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingyue Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Li Fu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yun Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liguang Lou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Rampogu S, Baek A, Zeb A, Lee KW. Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer 2018. [PMID: 29514608 PMCID: PMC5842552 DOI: 10.1186/s12885-018-4050-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression. Methods In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2. Results The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW. Conclusion The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailima Rampogu
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Ayoung Baek
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Amir Zeb
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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29
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Design and synthesis of novel bis-hydroxychalcones with consideration of their biological activities. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-018-3290-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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2-Methylpyridine-1-ium-1-sulfonate from Allium hirtifolium: An anti-angiogenic compound which inhibits growth of MCF-7 and MDA-MB-231 cells through cell cycle arrest and apoptosis induction. Biomed Pharmacother 2017. [DOI: 10.1016/j.biopha.2017.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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31
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Zhang W, Li J, Huang Z, Wang H, Luo H, Wang X, Zhou N, Wu C, Bao J. Computer-aided identification of potential TYK2 inhibitors from drug database. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Rodriguez-Merchan EC. Pathophysiology of the disturbed angiogenesis in hemophilia. Expert Rev Hematol 2016; 9:933-8. [DOI: 10.1080/17474086.2016.1234933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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33
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Herbrink M, Schellens JHM, Beijnen JH, Nuijen B. Inherent formulation issues of kinase inhibitors. J Control Release 2016; 239:118-27. [PMID: 27578098 DOI: 10.1016/j.jconrel.2016.08.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/18/2022]
Abstract
The small molecular Kinase Inhibitor (smKI) drug class is very promising and rapidly expanding. All of these drugs are administered orally. The clear relationship between structure and function has led to drugs with a general low intrinsic solubility. The majority of the commercial pharmaceutical formulations of the smKIs are physical mixtures that are limited by the low drug solubility of a salt form. This class of drugs is therefore characterized by an impaired and variable bioavailability rendering them costly and their therapies suboptimal. New formulations are sparingly being reported in literature and patents. The presented data suggests that continued research into formulation design can help to develop more efficient and cost-effective smKI formulation. Moreover, it may also be of help in the future design of the formulations of new smKIs.
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Affiliation(s)
- M Herbrink
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands.
| | - J H M Schellens
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
| | - J H Beijnen
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
| | - B Nuijen
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
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Discovery of a Potential HER2 Inhibitor from Natural Products for the Treatment of HER2-Positive Breast Cancer. Int J Mol Sci 2016; 17:ijms17071055. [PMID: 27376283 PMCID: PMC4964431 DOI: 10.3390/ijms17071055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 02/05/2023] Open
Abstract
Breast cancer is one of the most lethal types of cancer in women worldwide due to the late stage detection and resistance to traditional chemotherapy. The human epidermal growth factor receptor 2 (HER2) is considered as a validated target in breast cancer therapy. Even though a substantial effort has been made to develop HER2 inhibitors, only lapatinib has been approved by the U.S. Food and Drug Administration (FDA). Side effects were observed in a majority of the patients within one year of treatment initiation. Here, we took advantage of bioinformatics tools to identify novel effective HER2 inhibitors. The structure-based virtual screening combined with ADMET (absorption, distribution, metabolism, excretion and toxicity) prediction was explored. In total, 11,247 natural compounds were screened. The top hits were evaluated by an in vitro HER2 kinase inhibition assay. The cell proliferation inhibition effect of identified inhibitors was evaluated in HER2-overexpressing SKBR3 and BT474 cell lines. We found that ZINC15122021 showed favorable ADMET properties and attained high binding affinity against HER2. Moreover, ZINC15122021 showed high kinase inhibition activity against HER2 and presented outstanding cell proliferation inhibition activity against both SKBR3 and BT474 cell lines. Results reveal that ZINC15122021 can be a potential HER2 inhibitor.
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35
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Li J, Zhou N, Cai P, Bao J. In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment. Int J Mol Sci 2016; 17:258. [PMID: 26907257 PMCID: PMC4783987 DOI: 10.3390/ijms17020258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 11/16/2022] Open
Abstract
Synthetic lethality describes situations in which defects in two different genes or pathways together result in cell death. This concept has been applied to drug development for cancer treatment, as represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. In the current study, we performed a computational screening to discover new PARP inhibitors. Among the 11,247 compounds analyzed, one natural product, ZINC67913374, stood out by its superior performance in the simulation analyses. Compared with the FDA approved PARP1 inhibitor, olaparib, our results demonstrated that the ZINC67913374 compound achieved a better grid score (-86.8) and amber score (-51.42). Molecular dynamics simulations suggested that the PARP1-ZINC67913374 complex was more stable than olaparib. The binding free energy for ZINC67913374 was -177.28 kJ/mol while that of olaparib was -159.16 kJ/mol. These results indicated ZINC67913374 bound to PARP1 with a higher affinity, which suggest ZINC67913374 has promising potential for cancer drug development.
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Affiliation(s)
- Jian Li
- School of Medicine, Chengdu University, Chengdu 610106, China.
| | - Nan Zhou
- College of Life Sciences and Key Laboratory for Bio-Resources of Ministry of Education, Sichuan University, Chengdu 610064, China.
| | - Peiling Cai
- School of Medicine, Chengdu University, Chengdu 610106, China.
| | - Jinku Bao
- College of Life Sciences and Key Laboratory for Bio-Resources of Ministry of Education, Sichuan University, Chengdu 610064, China.
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36
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Li J, Zhou N, Liu W, Li J, Feng Y, Wang X, Wu C, Bao J. Discover natural compounds as potential phosphodiesterase-4B inhibitors via computational approaches. J Biomol Struct Dyn 2016; 34:1101-12. [PMID: 26159554 DOI: 10.1080/07391102.2015.1070749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
cAMP, intracellular cyclic adenosine monophosphate, is a ubiquitous second messenger that plays a key role in many physiological processes. PDE4B which can reduce the cAMP level by hydrolyzing cAMP to 5'-AMP has become a therapeutic target for the treatment of human diseases such as respiratory disorders, inflammation diseases, neurological and psychiatric disorders. However, the use of currently available PDE4B inhibitors is restricted due to serious side effects caused by targeting PDE4D. Hence, we are attempting to find out subfamily-selective PDE4B inhibitors from natural products, using computer-aided approaches such as virtual screening, docking, and molecular dynamics simulation. Finally, four potential PDE4B-selective inhibitors (ZINC67912770, ZINC67912780, ZINC72320169, and ZINC28882432) were found. Compared to the reference drug (roflumilast), they scored better during the virtual screening process. Binding free energy for them was -317.51, -239.44, -215.52, and -165.77 kJ/mol, better than -129.05 kJ/mol of roflumilast. The pharmacophore model of the four candidate inhibitors comprised six features, including one hydrogen bond donor, four hydrogen bond acceptors, and one aromatic ring feature. It is expected that our study will pave the way for the design of potent PDE4B-selective inhibitors of new drugs to treat a wide variety of diseases such as asthma, COPD, psoriasis, depression, etc.
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Affiliation(s)
- Jing Li
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Nan Zhou
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Wen Liu
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Jianzong Li
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Yu Feng
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Xiaoyun Wang
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Chuanfang Wu
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China
| | - Jinku Bao
- a College of Life Sciences & Key Laboratory for Bio-resources of Ministry of Education , Sichuan University , Chengdu 610064 , China.,b State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital , Sichuan University , Chengdu 610041 , China.,c State Key Laboratory of Oral Diseases , West China College of Stomatology, Sichuan University , Chengdu 610041 , China
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37
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Sneha P, Doss CGP. Molecular Dynamics: New Frontier in Personalized Medicine. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:181-224. [PMID: 26827606 DOI: 10.1016/bs.apcsb.2015.09.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.
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Affiliation(s)
- P Sneha
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- Medical Biotechnology Division, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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38
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Singh P, Bast F. Screening of multi-targeted natural compounds for receptor tyrosine kinases inhibitors and biological evaluation on cancer cell lines, in silico and in vitro. Med Oncol 2015; 32:233. [PMID: 26298529 DOI: 10.1007/s12032-015-0678-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 12/27/2022]
Abstract
Receptors for growth factors encompass within the superfamily of receptor tyrosine kinases and are known to regulate numerous biological processes including cellular growth, proliferation, metabolism, survival, cell differentiation and apoptosis. These receptors have recently caught the attention of the researchers as an attractive target to combat cancer owing to the evidence suggesting their over-expression in cancer cells. Therefore, we studied receptor-based molecular docking of IR (PDB; 3ETA), IGF1R (PDB; 1K3A), EGFR (PDB; 1M17), VEGFIR (PDB; 3HNG), and VEGFIIR (PDB; 2OH4) against natural compounds. Further, in vitro investigation of the biological effect of lead molecules in an array of cancer cell lines was done. All selected natural compounds were docked with the X-ray crystal structure of selected protein by employing GLIDE (Grid-based Ligand Docking with Energetics) Maestro 9.6. InterBioScreen natural compounds docked with each selected protein molecules by using GLIDE high throughput virtual screening. On the basis of Gscore, we select 20 compounds along with 68 anticancer compounds for GLIDE extra precision molecular docking. It was discovered in this study that compound epigallocatechin gallate (EGCG) yielded magnificent Gscore with IGF1R (PDB; 1K3A) and VEGFIIR (PDB; 2OH4), and protein-ligand interactions are chart out. Effect of EGCG on biological activity such as mRNA expression of selected protein, cell proliferation, oxidative stress, and cell migration was reported after the 48 h treatments in cancer cell lines. The RT-PCR densitometric bands analysis showed that compound EGCG reduced the mRNA expression of IGF1R, VEGFIIR, and mTOR at 80 μM concentration. Moreover, EGCG significantly reduced cell proliferation and ROS generation after 48 h treatments. Our result also indicated a reduction in the potential for cell migration that might show in vivo anti-metastasis activity of EGCG.
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Affiliation(s)
- Pushpendra Singh
- Centre for Biosciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, Punjab, India
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Su P, Wang J, Shi Y, Pan X, Shao R, Zhang J. Discovery of biphenyl-aryl ureas as novel VEGFR-2 inhibitors. Part 4: exploration of diverse hinge-binding fragments. Bioorg Med Chem 2015; 23:3228-36. [PMID: 25982075 DOI: 10.1016/j.bmc.2015.04.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 01/07/2023]
Abstract
VEGFR-2 plays an essential role in angiogenesis and is an important target for cancer therapy. A series of biphenyl-aryl ureas were synthesized and evaluated as novel VEGFR-2 inhibitors. The pyridine, methylamine carbonyl pyridine and pivaloyl amide pyridine were introduced as novel hinge binding fragment. The majority of title compounds displayed potent VEGFR-2 inhibition. In particular, L1, L9, W14 and W15 exhibited significant enzymatic inhibitory activity with IC50 values of 0.36nM, 0.22nM, 0.15nM and 0.14nM. Compounds L1, L9 and W15 displayed potent antiproliferative activity against A549 and SMMC-7721 cells. SAR study suggested that incorporation of 3-trifluoromethyl and methylamine carbonyl on terminal pyridine could improve VEGFR-2 inhibitory activity. Molecular docking illustrated that urea moiety formed two critical hydrogen bonds with the DFG residues of VEGFR-2. The results indicated that these biphenyl-aryl ureas could serve as promising lead compounds for further optimization.
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Affiliation(s)
- Ping Su
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Jinfeng Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Yaling Shi
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Ruili Shao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Road, Xi'an, Shaanxi Province 710061, PR China.
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40
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He JY, Li C, Wu G. Discovery of potential drugs for human-infecting H7N9 virus containing R294K mutation. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:2377-90. [PMID: 25489236 PMCID: PMC4257025 DOI: 10.2147/dddt.s74061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Background After the first epidemic wave from February through May 2013, the influenza A (H7N9) virus emerged and has followed a second epidemic wave since June 2013. As of June 27, 2014, the outbreak of H7N9 had caused 450 confirmed cases of human infection, with 165 deaths included. The case-fatality rate of all confirmed cases is about 36%, making the H7N9 virus a significant threat to people’s health. At present, neuraminidase inhibitors are the only licensed antiviral medications available to treat H7N9 infections in humans. Oseltamivir is the most commonly used inhibitor, and it is also a front-line drug for the threatening H7N9. Unfortunately, it has been reported that patients treated with oseltamivir can induce R294K (Arg294Lys) substitution in the H7N9 virus, which is a rare mutation and can reduce the antiviral efficacy of inhibitors. Even worse, deaths caused by such mutation after oseltamivir treatment have already been reported, indicating that the need to find substitutive neuraminidase inhibitors for currently available drugs to treat drug-resistant H7N9 is really pressing. Materials and methods First, the structure of H7N9 containing the R294K substitution was downloaded from the Protein Data Bank, and structural information of approved drugs was downloaded from the ZINC (ZINC Is Not Commercial) database. Taking oseltamivir carboxylate as a reference drug, we then filtered these molecules through virtual screening to find out potential inhibitors targeting the mutated H7N9 virus. For further evaluation, we carried out a 14 ns molecular dynamic simulation for each H7N9–drug complex and calculated the binding energy for each candidate drug. Results We found five inhibitors that could be candidate drugs for treating the mutated H7N9 virus. Docking poses showed these drugs could bind to the virus effectively, with the contribution of hydrogen bonds and hydrophobic interactions. With regard to the molecular dynamic simulations, receptor–ligand complexes formed by these candidate drugs were more stable than the one formed by oseltamivir carboxylate. The binding energy of oseltamivir carboxylate was −122.4 kJ/mol, while those for these potential inhibitors were −417.5, −404.7, −372.2, −304.3, and −289.9 kJ/mol, much better than the reference drug. Conclusion Given the current and future threat of the mutated H7N9 virus, it is urgent that potent drugs and effective antiviral therapeutics be found. Our study therefore is able to complement currently available drugs for influenza A infectors and helps to prevent the ongoing threat of H7N9 virus.
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Affiliation(s)
- Jiao-Yu He
- College of Life Sciences and Key Laboratory for Bio-resources of Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Cheng Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Guo Wu
- College of Life Sciences, Sichuan Normal University, Chengdu, People's Republic of China
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