1
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Yucel MA, Adal E, Aktekin MB, Hepokur C, Gambacorta N, Nicolotti O, Algul O. From Deep Learning to the Discovery of Promising VEGFR-2 Inhibitors. ChemMedChem 2024:e202400108. [PMID: 38726553 DOI: 10.1002/cmdc.202400108] [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: 02/05/2024] [Revised: 04/24/2024] [Indexed: 07/21/2024]
Abstract
Vascular endothelial growth factor receptor 2 (VEGFR-2) stands as a prominent therapeutic target in oncology, playing a critical role in angiogenesis, tumor growth, and metastasis. FDA-approved VEGFR-2 inhibitors are associated with diverse side effects. Thus, finding novel and more effective inhibitors is of utmost importance. In this study, a deep learning (DL) classification model was first developed and then employed to select putative active VEGFR-2 inhibitors from an in-house chemical library including 187 druglike compounds. A pool of 18 promising candidates was shortlisted and screened against VEGFR-2 by using molecular docking. Finally, two compounds, RHE-334 and EA-11, were prioritized as promising VEGFR-2 inhibitors by employing PLATO, our target fishing and bioactivity prediction platform. Based on this rationale, we prepared RHE-334 and EA-11 and successfully tested their anti-proliferative potential against MCF-7 human breast cancer cells with IC50 values of 26.78±4.02 and 38.73±3.84 μM, respectively. Their toxicities were instead challenged against the WI-38. Interestingly, expression studies indicated that, in the presence of RHE-334, VEGFR-2 was equal to 0.52±0.03, thus comparable to imatinib equal to 0.63±0.03. In conclusion, this workflow based on theoretical and experimental approaches demonstrates effective in identifying VEGFR-2 inhibitors and can be easily adapted to other medicinal chemistry goals.
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Affiliation(s)
- Mehmet Ali Yucel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yildirim University, 24002, Erzincan, Türkiye
| | - Ercan Adal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, 33160, Mersin, Türkiye
| | - Mine Buga Aktekin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, 33160, Mersin, Türkiye
| | - Ceylan Hepokur
- Department of Biochemistry, Faculty of Pharmacy, Sivas Cumhuriyet University, 58140, Sivas, Türkiye
| | - Nicola Gambacorta
- Dipartimento di Farmacia-Scienze del Farmaco, Universita 'degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, Bari I, 70125, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Universita 'degli Studi di Bari "Aldo Moro", Via E. Orabona, 4, Bari I, 70125, Italy
| | - Oztekin Algul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yildirim University, 24002, Erzincan, Türkiye
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, 33160, Mersin, Türkiye
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2
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Priyankha S, Rajapandian V, Palanisamy K, Esther Rubavathy SM, Thilagavathi R, Selvam C, Prakash M. Identification of indole-based natural compounds as inhibitors of PARP-1 against triple-negative breast cancer: a computational study. J Biomol Struct Dyn 2024; 42:2667-2680. [PMID: 37154583 DOI: 10.1080/07391102.2023.2208215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive kind of breast cancer known to mankind. It is a heterogeneous disease that is formed due to the missing estrogen, progesterone and human epidermal growth factor 2 receptors. Poly(ADP-ribose) polymerase-1 (PARP-1) protein helps in the development of TNBC by repairing the cancer cells, which proliferate and spread metastatically. To determine the potential PARP-1 inhibitors (PARPi), 0.2 million natural products from Universal Natural Product Database were screened using molecular docking and six hit compounds were selected based on their binding affinity towards PARP-1. The bio-availability and drug-like properties of these natural products were evaluated using ADMET analysis. Molecular dynamics simulations were conducted for these complexes for 200 ns to examine their structural stability and dynamic behaviour and further compared with the complex of talazoparib (TALA), an FDA-approved PARPi. Using MM/PBSA calculations, we conclude that the complexes HIT-3 and HIT-5 (-25.64 and -23.14 kcal/mol, respectively) show stronger binding energies with PARP-1 than TALA with PARP-1 (-10.74 kcal/mol). Strong interactions were observed between the compounds and hotspot residues, Asp770, Ala880, Tyr889, Tyr896, Ala898, Asp899 and Tyr907, of PARP-1 due to the existence of various types of non-covalent interactions between the compounds and PARP-1. This research offers critical information about PARPi, which could potentially be incorporated into the treatment of TNBC. Moreover, these findings were validated by comparing them with an FDA-approved PARPi.
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Affiliation(s)
- Sridhar Priyankha
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science, Coimbatore, Tamil Nadu, India
| | - Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - S M Esther Rubavathy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education, Coimbatore, India
| | - Chelliah Selvam
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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3
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Șandor A, Fizeșan I, Ionuț I, Marc G, Moldovan C, Oniga I, Pîrnău A, Vlase L, Petru AE, Macasoi I, Oniga O. Discovery of A Novel Series of Quinazoline-Thiazole Hybrids as Potential Antiproliferative and Anti-Angiogenic Agents. Biomolecules 2024; 14:218. [PMID: 38397456 PMCID: PMC10886515 DOI: 10.3390/biom14020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Considering the pivotal role of angiogenesis in solid tumor progression, we developed a novel series of quinazoline-thiazole hybrids (SA01-SA07) as antiproliferative and anti-angiogenic agents. Four out of the seven compounds displayed superior antiproliferative activity (IC50 =1.83-4.24 µM) on HepG2 cells compared to sorafenib (IC50 = 6.28 µM). The affinity towards the VEGFR2 kinase domain was assessed through in silico prediction by molecular docking, molecular dynamics studies, and MM-PBSA. The series displayed a high degree of similarity to sorafenib regarding the binding pose within the active site of VEGFR2, with a different orientation of the 4-substituted-thiazole moieties in the allosteric pocket. Molecular dynamics and MM-PBSA evaluations identified SA05 as the hybrid forming the most stable complex with VEGFR2 compared to sorafenib. The impact of the compounds on vascular cell proliferation was assessed on EA.hy926 cells. Six compounds (SA01-SA05, SA07) displayed superior anti-proliferative activity (IC50 = 0.79-5.85 µM) compared to sorafenib (IC50 = 6.62 µM). The toxicity was evaluated on BJ cells. Further studies of the anti-angiogenic effect of the most promising compounds, SA04 and SA05, through the assessment of impact on EA.hy296 motility using a wound healing assay and in ovo potential in a CAM assay compared to sorafenib, led to the confirmation of the anti-angiogenic potential.
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Affiliation(s)
- Alexandru Șandor
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Ionel Fizeșan
- Department of Toxicology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Ioana Ionuț
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Gabriel Marc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Cristina Moldovan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Ilioara Oniga
- Department of Pharmacognosy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 12 Ion Creangă Street, 400010 Cluj-Napoca, Romania;
| | - Adrian Pîrnău
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donath Street, 400293 Cluj-Napoca, Romania;
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș, Street, 400012 Cluj-Napoca, Romania;
| | - Andreea-Elena Petru
- Department of Toxicology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Ioana Macasoi
- Department of Toxicology, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
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4
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Al-Sanea MM, Hamdi A, Mohamed AAB, El-Shafey HW, Moustafa M, Elgazar AA, Eldehna WM, Ur Rahman H, Parambi DGT, Elbargisy RM, Selim S, Bukhari SNA, Magdy Hendawy O, Tawfik SS. New benzothiazole hybrids as potential VEGFR-2 inhibitors: design, synthesis, anticancer evaluation, and in silico study. J Enzyme Inhib Med Chem 2023; 38:2166036. [PMID: 36691927 PMCID: PMC9879182 DOI: 10.1080/14756366.2023.2166036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A new series of 2-aminobenzothiazole hybrids linked to thiazolidine-2,4-dione 4a-e, 1,3,4-thiadiazole aryl urea 6a-d, and cyanothiouracil moieties 8a-d was synthesised. The in vitro antitumor effect of the new hybrids was assessed against three cancer cell lines, namely, HCT-116, HEPG-2, and MCF-7 using Sorafenib (SOR) as a standard drug. Among the tested compounds, 4a was the most potent showing IC50 of 5.61, 7.92, and 3.84 µM, respectively. Furthermore, compounds 4e and 8a proved to have strong impact on breast cancer cell line with IC50 of 6.11 and 10.86 µM, respectively. The three compounds showed a good safety profile towards normal WI-38 cells. Flow cytometric analysis of the three compounds in MCF-7 cells revealed that compounds 4a and 4c inhibited cell population in the S phase, whereas 8a inhibited the population in the G1/S phase. The most promising compounds were subjected to a VEGFR-2 inhibitory assay where 4a emerged as the best active inhibitor of VEGFR-2 with IC50 91 nM, compared to 53 nM for SOR. In silico analysis showed that the three new hybrids succeeded to link to the active site like the co-crystallized inhibitor SOR.
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Affiliation(s)
- Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia,CONTACT Mohammad M. Al-Sanea Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf72341, Saudi Arabia
| | - Abdelrahman Hamdi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Ahmed A. B. Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Ahmed A. B. Mohamed Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura35516, Egypt
| | - Hamed W. El-Shafey
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mahmoud Moustafa
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abdullah A. Elgazar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Hidayat Ur Rahman
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Della G. T. Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Rehab M. Elbargisy
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Syed Nasir Abbas Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Omnia Magdy Hendawy
- Department of Pharmacology, College of Pharmacy, Jouf University, Aljouf, Saudi Arabia
| | - Samar S. Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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5
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Abdel Rahman DE, Fouad MA, Mohammed ER, El-Zoheiry HH, Abdelrasheed Allam H. Novel VEGFR-2 inhibitors as antiangiogenic and apoptotic agents via paracrine and autocrine cascades: Design, synthesis, and biological evaluation. Bioorg Chem 2023; 139:106678. [PMID: 37354661 DOI: 10.1016/j.bioorg.2023.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Appertaining to its paracrine and autocrine signaling loops, VEGFR-2 succeeded in grabbing attention as one of the leading targets in cancer treatment. Based on the foregoing and our comprehensive studies regarding pharmacophoric features and activity of sorafenib, novel phenylpyridazinone based VEGFR-2 inhibitors 4, 6a-e, 7a,b, 9a,b, 12a-c, 13a,b, 14a,b, 15a,b, and 17a-d were optimized. An assortment of biological assays was conducted to assess the antiangiogenic and apoptotic activities of the synthesized derivatives. In vitro VEGFR-2 kinase assay verified the inhibitory activity of the synthesized derivatives with IC50 values from 49.1 to 418.0 nM relative to the reference drug sorafenib (IC50 = 81.8 nM). Antiproliferative activity against HUVECs revealed that compounds 2-{2-[2-(6-oxo-3-phenylpyridazin-1(6H)-yl)acetyl]hydrazineyl}-N-(p-tolyl)acetamide (12c) and 2-[(5-mercapto-4-methyl-4H-1,2,4-triazol-3-yl)methyl]-6-phenylpyridazin-3(2H)-one (13a) possessed superior activity (IC50 values = 11.5 and 12.3 nM, respectively) in comparison to sorafenib (IC50 = 23.2 nM). For the purpose of appraising their antiproliferative effect, derivatives 12c and 13a were exposed to cell cycle analysis, apoptotic, cell invasion and migration assays in addition to determination of VEGFR-2 in protein level. Moreover, cytotoxicity as well as selectivity index against WI-38 cell line was measured to examine safety of derivatives 12c and 13a. After that, molecular docking study was executed on the top five compounds in the in vitro VEGFR-2 kinase assay 6d, 12c, 13a, 14a and 17c to get a deep perception on binding mode of the synthesized compounds and correlate the design strategy with biological results. Finally, physicochemical, pharmacokinetic properties, and drug-likeness studies were performed on the top five derivative in in vitro VEGFR-2 kinase assay.
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Affiliation(s)
- Doaa E Abdel Rahman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Pharmaceutical Chemistry Department, School of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Eman R Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Haidy H El-Zoheiry
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt.
| | - Heba Abdelrasheed Allam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
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6
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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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7
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Zhou Z, Dong Y, Li N, Niu M, Wang S, Zhou Y, Sun Z, Chu P, Tang Z. An oleanolic acid derivative, K73-03, inhibits pancreatic cancer cells proliferation in vitro and in vivo via blocking EGFR/Akt pathway. Cell Biol Int 2022; 46:1801-1813. [PMID: 35925004 DOI: 10.1002/cbin.11866] [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: 12/02/2021] [Revised: 04/01/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022]
Abstract
Oleanolic acid (OA) and its derivatives show potent anticancer function. Pancreatic cancer (PC) is the fourth core motive of cancer-related deaths worldwide. Epidermal growth factor receptor (EGFR) has been implicated in PC and has been validated as a therapeutic target. Our study demonstrated that K73-03, an OA derivative, was identified as a potent inhibitor of EGFR by using reverse pharmacophore screening and molecular dynamics simulation assays. Moreover, Western blot analysis showed that K73-03 markedly suppressed the levels of phosphorylated-EGFR (p-EGFR) and phosphorylated-Akt (p-Akt). The inhibitory effect of K73-03 on PC cells was assessed in vitro and in vivo. Mechanistically, K73-03 effectively inhibited the cell proliferation of PC cells, and induced apoptosis and autophagy of ASPC-1 cells in a dose-dependent manner. Additionally, pretreatment with chloroquine, an autophagy inhibitor, significantly inhibited K73-03-induced autophagy and enhanced K73-03-induced apoptotic cell death. K73-03 also strongly repressed ASPC-1 cells xenograft growth in vivo. Thus, all these findings provided new clues about OA analog K73-03 as an effective anticancer agent targeted EGFR against ASPC-1 cells, it is worth further evaluation in the future.
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Affiliation(s)
- Zheng Zhou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Yaokun Dong
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Na Li
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Mengyue Niu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Shisheng Wang
- Department of pharmacy, School of chemical engineering, Dalian University of Technology, Dalian, China
| | - Yuanzhang Zhou
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zhaolin Sun
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Peng Chu
- Department of Pharmacology, Dalian Medical University, Dalian, China
| | - Zeyao Tang
- Department of Pharmacology, Dalian Medical University, Dalian, China
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8
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Schöller A, Kearns F, Woodcock HL, Boresch S. Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations. J Phys Chem B 2022; 126:2798-2811. [PMID: 35404610 PMCID: PMC9036525 DOI: 10.1021/acs.jpcb.2c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/24/2022] [Indexed: 11/27/2022]
Abstract
A key step during indirect alchemical free energy simulations using quantum mechanical/molecular mechanical (QM/MM) hybrid potential energy functions is the calculation of the free energy difference ΔAlow→high between the low level (e.g., pure MM) and the high level of theory (QM/MM). A reliable approach uses nonequilibrium work (NEW) switching simulations in combination with Jarzynski's equation; however, it is computationally expensive. In this study, we investigate whether it is more efficient to use more shorter switches or fewer but longer switches. We compare results obtained with various protocols to reference free energy differences calculated with Crooks' equation. The central finding is that fewer longer switches give better converged results. As few as 200 sufficiently long switches lead to ΔAlow→high values in good agreement with the reference results. This optimized protocol reduces the computational cost by a factor of 40 compared to earlier work. We also describe two tools/ways of analyzing the raw data to detect sources of poor convergence. Specifically, we find it helpful to analyze the raw data (work values from the NEW switching simulations) in a quasi-time series-like manner. Principal component analysis helps to detect cases where one or more conformational degrees of freedom are different at the low and high level of theory.
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Affiliation(s)
- Andreas Schöller
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria
| | - Fiona Kearns
- Department
of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - H. Lee Woodcock
- Department
of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Stefan Boresch
- Faculty
of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
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9
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Capability of MXene 2D material as an amoxicillin, ampicillin, and cloxacillin adsorbent in wastewater. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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10
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Xu D, Zheng QC. Theoretical investigations on the effects of mutations in important residues of NS1B on its RNA-binding using molecular dynamics simulations. Comput Biol Med 2022; 145:105412. [PMID: 35344866 DOI: 10.1016/j.compbiomed.2022.105412] [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: 02/21/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022]
Abstract
NS1B protein plays an important role in countering host antiviral defense and virulence of influenza virus B, considered as the promising target. The first experimental structure of the NS1B protein has recently been determined, was able to bind to double-stranded RNA (dsRNA). However, few studies attempt to investigate the RNA-binding mechanism of the NS1B. In this study, we provide our understanding of the structure-function relationship, dynamics and RNA-binding mechanism of the NS1B protein by performing molecular dynamics simulations combined and MM-GBSA calculations on the NS1B-dsRNA complex. 12 key residues are identified for RNA-binding by forming hydrogen bonds with the. Our results also demonstrate that mutations (R156A, K160A, R208A and K221A) can cause the local structure changes of NS1B CTD and the hydrogen bonds between NS1B CTD and RNA disappearance, which may be the main reasons for the decrease in RNA-binding affinity. These results mentioned will help us understanding the RNA-binding mechanism and could provide some medicinal chemistry insights chances for rational drug design targeting NS1B protein.
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Affiliation(s)
- Dan Xu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, China.
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11
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Synthesis and Characterization of Novel Copper(II)-Sunitinib Complex: Molecular Docking, DFT Studies, Hirshfeld Analysis and Cytotoxicity Studies. INORGANICS 2021. [DOI: 10.3390/inorganics10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The main goal of this work was to report the synthesis, characterization, and cytotoxicity study of a novel copper(II)-sunitinib complex, CuSun. It has been synthesized and characterized in solid state and in solution by different methods (such as DFT, FTIR, Raman, UV-vis, EPR, NMR, etc.). The solid-state molecular structure of trichlorosunitinibcopper(II), where sunitinib: N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carboxamide, for short Cu(Sun)Cl3, was determined by X-ray diffraction. It crystallizes in the triclinic space group P-1 with a = 7.9061(5) Å, b = 12.412(1) Å, c = 13.7005(8) Å, α = 105.021(6)°, β = 106.744(5)°, γ = 91.749(5)°, and Z = 2 molecules per unit cell. Also, we have found π-π interactions and classic and non-classic H-bonds in the crystal structure by using Hirshfeld surface analysis. In the speciation studies, the complex has dissociated in protonated sunitinib and chlorocomplex of copper(II), according to 1HNMR, EPR, UV-vis and conductimetric analysis. Molecular docking of the complex in both, ATP binding site and allosteric site of VEGFR2 have shown no improvement in comparison to the free ligand. Besides, cytotoxicity assay on HepG2 cell line shows similar activity for complex and ligand in the range between 1–25 μM supporting the data obtained from studies in solution.
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Synthesis, in vitro anticancer activity and in silico studies of certain isoxazole-based carboxamides, ureates, and hydrazones as potential inhibitors of VEGFR2. Bioorg Chem 2021; 116:105334. [PMID: 34534755 DOI: 10.1016/j.bioorg.2021.105334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/29/2021] [Accepted: 09/03/2021] [Indexed: 11/23/2022]
Abstract
The ensuing research presents the results of in vitro anticancer activity of novel 28 compounds of isoxazole-based carboxamides 3(a-d); ureates 4(a-g), 5, 6, 7a,b, 8; and hydrazones 9(a-f), 10(a-d), 11a,b as potential inhibitors of VEGFR2. The carboxamides and ureates were synthesized by converting 5-(aryl)-isoxzaole-3-carbohydrazides 1a,b to the corresponding carbonylazides 2a,b followed by treatment with the appropriate amines. The hydrazones were directly obtained through condensation of the carbohydrazide 1a,b with aldehydes and/or ketones. The structures of the target compounds were confirmed by elemental and spectral analyses. A preliminary in vitro anticancer screening of solutions (10-5M) on 60 cancer cell lines (NCI, USA) revealed that the carboxamide 3c is the most promising growth inhibitor. Explicitly, 3c showed potent anticancer activity at 10µ M against leukemia (HL-60(TB), K-562 and MOLT-4), colon cancer (KM12) and melanoma (LOX IMVI) cell lines with %GI range = 70.79-92.21. Evaluation of growth inhibitory activity of the synthesized compounds against hepatocellular carcinoma (HepG2), that overexpresses VEGFR2, showed superior activity of compounds 8, 10a and 10c with IC50 in sub micromolar concentrations of 0.84, 0.79 and 0.69 μM, respectively, which is better than that of the reference drug, Sorafenib (IC50 = 3.99 µM). Moreover, these compounds displayed high selective cytotoxicity for HepG2 cancer cells over the nontumorigenic THLE2 liver cells (SI range = 26.37-38.60) which reflect their safety. The results of VEGFR2 kinase inhibition assay demonstrate that, compounds 8 and 10a are the most active inhibitors with IC50 = 25.7 and 28.2 nM, respectively, (Sorafenib IC50 = 28.1 nM). Molecular docking of the synthesized derivatives to VEGFR2 (PDB: 3WZE) showed similar binding modes to that of the co-crystallized ligand, sorafenib. Moreover, the results of computational assessment of ADME and drug-likeness characteristics inspire further investigations of the new isoxazole-based derivatives to afford more potent, safe and orally active VEGFR2 inhibitors as potential anticancer drug candidates.
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Shaik F, Cuthbert GA, Homer-Vanniasinkam S, Muench SP, Ponnambalam S, Harrison MA. Structural Basis for Vascular Endothelial Growth Factor Receptor Activation and Implications for Disease Therapy. Biomolecules 2020; 10:biom10121673. [PMID: 33333800 PMCID: PMC7765180 DOI: 10.3390/biom10121673] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/15/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) bind to membrane receptors on a wide variety of cells to regulate diverse biological responses. The VEGF-A family member promotes vasculogenesis and angiogenesis, processes which are essential for vascular development and physiology. As angiogenesis can be subverted in many disease states, including tumour development and progression, there is much interest in understanding the mechanistic basis for how VEGF-A regulates cell and tissue function. VEGF-A binds with high affinity to two VEGF receptor tyrosine kinases (VEGFR1, VEGFR2) and with lower affinity to co-receptors called neuropilin-1 and neuropilin-2 (NRP1, NRP2). Here, we use a structural viewpoint to summarise our current knowledge of VEGF-VEGFR activation and signal transduction. As targeting VEGF-VEGFR activation holds much therapeutic promise, we examine the structural basis for anti-angiogenic therapy using small-molecule compounds such as tyrosine kinase inhibitors that block VEGFR activation and downstream signalling. This review provides a rational basis towards reconciling VEGF and VEGFR structure and function in developing new therapeutics for a diverse range of ailments.
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Affiliation(s)
- Faheem Shaik
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK;
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Correspondence: ; Tel.: +44-207-8824207
| | - Gary A. Cuthbert
- Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (G.A.C.); (S.H.-V.); (M.A.H.)
| | | | - Stephen P. Muench
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | | | - Michael A. Harrison
- Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK; (G.A.C.); (S.H.-V.); (M.A.H.)
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Sbenati RM, Zaraei SO, El-Gamal MI, Anbar HS, Tarazi H, Zoghbor MM, Mohamood NA, Khakpour MM, Zaher DM, Omar HA, Alach NN, Shehata MK, El-Gamal R. Design, synthesis, biological evaluation, and modeling studies of novel conformationally-restricted analogues of sorafenib as selective kinase-inhibitory antiproliferative agents against hepatocellular carcinoma cells. Eur J Med Chem 2020; 210:113081. [PMID: 33310290 DOI: 10.1016/j.ejmech.2020.113081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022]
Abstract
Sorafenib is one of the clinically used anticancer agents that inhibits several kinases. In this study, novel indole-based rigid analogues of sorafenib were designed and synthesized in order to enhance kinase selectivity and hence minimize the side effects associated with its use. The target compounds possess different linkers; urea, amide, sulfonamide, or thiourea, in addition to different terminal aryl moieties attached to the linker in order to investigate their impact on biological activity. They were tested against Hep3B, Huh7, and Hep-G2 hepatocellular carcinoma (HCC) cell lines to study their potency. Among all the tested target derivatives, compound 1h exerted superior antiproliferative potency against all the three tested HCC cell lines compared to sorafenib. Based on these preliminary results, compound 1h was selected for further biological and in silico investigations. Up to 30 μM, compound 1h did not inhibit 50% of the proliferation of WI-38 normal cells, which indicated promising selectivity against HCC cells than normal cells. In addition, compound 1h exerted superior kinase selectivity than sorafenib. It is selective for VEGFR2 and VEGFR3 angiogenesis-related kinases, while sorafenib is a multikinase inhibitor. Superior kinase selectivity of compound 1h to sorafenib can be attributed to its conformationally-restricted indole nucleus and the bulky N-methylpiperazinyl moiety. Western blotting was carried out and confirmed the ability of compound 1h to inhibit VEGFR2 kinase inside Hep-G2 HCC cells in a dose-dependent pattern. Compound 1h induces apoptosis and necrosis in Hep-G2 cell line, as shown by caspase-3/7 and lactate dehydrogenase (LDH) release assays, respectively. Moreover, compound 1h is rather safe against hERG. Thus, we could achieve a more selective kinase inhibitor than sorafenib with retained or even better antiproliferative potency against HCC cell lines. Furthermore, molecular docking and dynamic simulation studies were carried out to investigate its binding mode with VEGFR2 kinase. The molecule has a unique orientation upon binding with the kinase.
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Affiliation(s)
- Rawan M Sbenati
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Seyed-Omar Zaraei
- Center for Biomaterials, Korea Institute of Science and Technology, PO Box 131, Cheongryang, Seoul, 130-650, Republic of Korea; Department of Biomolecular Science, Korea University of Science and Technology, 113 Gwahangno, Yuseong-gu, Daejeon, 305-333, Republic of Korea
| | - Mohammed I El-Gamal
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, 35516, Egypt.
| | - Hanan S Anbar
- Department of Clinical Pharmacy and Pharmacotherapeutics, Dubai Pharmacy College for Girls, Dubai, 19099, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Malaka M Zoghbor
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Najma A Mohamood
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mahta M Khakpour
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Nour N Alach
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Mahmoud K Shehata
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Randa El-Gamal
- Department of Medical Biochemistry, Faculty of Medicine, University of Mansoura, Mansoura, 35516, Egypt
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Abula A, Xu Z, Zhu Z, Peng C, Chen Z, Zhu W, Aisa HA. Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations. J Chem Inf Model 2020; 60:6242-6250. [DOI: 10.1021/acs.jcim.0c00898] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amina Abula
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhengdan Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Cheng Peng
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhaoqiang Chen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Weiliang Zhu
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Haji Akber Aisa
- The Key Laboratory of Plant Resources and Chemistry in Arid Regions and Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Road 40-1, Urumqi, Xinjiang 830011, People’s Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, People’s Republic of China
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Zheng YG, Wang JA, Meng L, Pei X, Zhang L, An L, Li CL, Miao YL. Design, synthesis, biological activity evaluation of 3-(4-phenyl-1H-imidazol-2-yl)-1H-pyrazole derivatives as potent JAK 2/3 and aurora A/B kinases multi-targeted inhibitors. Eur J Med Chem 2020; 209:112934. [PMID: 33109396 DOI: 10.1016/j.ejmech.2020.112934] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 11/15/2022]
Abstract
In this study, a series of 3-(4-phenyl-1H-imidazol-2-yl)-1H-pyrazole derivatives were designed, synthesized, and evaluated for their biological activities. Upon performing kinase assays, most of the compounds exhibited potent inhibition against JAK2/3 and Aurora A/B with the IC50 values ranging from 0.008 to 2.52 μM. Among these derivatives, compound 10e expressed the most moderate inhibiting activities against all the four kinases with the IC50 values of 0.166 μM (JAK2), 0.057 μM (JAK3), 0.939 μM (Aurora A), and 0.583 μM (Aurora B), respectively. Moreover, most of the derived compounds exhibited potent cytotoxicity against human chronic myeloid leukemia cells K562 and human colon cancer cells HCT116, while compound 10e expressed antiproliferative activities against K562 (IC50=6.726 μM). According to western blot analysis, compound 10e down-regulated the phosphorylation of STAT3, STAT5, Aurora A, and Aurora B in a dose-dependent manner in K562 and HCT116 cells. Cell cycle analysis revealed that compound 10e inhibited the proliferation of cells by inducing cell cycle arrest in the G2 phase. The molecular modeling suggested that compound 10e could maintain a binding mode similar to the binding mode of AT9832, a common JAK 2/3 and Aurora A/B kinases multi-target kinase inhibitor. Therefore, compound 10e might be a potential agent for cancer therapy deserving further research.
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Affiliation(s)
- You-Guang Zheng
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China.
| | - Jin-An Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Long Meng
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Xin Pei
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Ling Zhang
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Lin An
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Cheng-Lin Li
- College of Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China; Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, PR China
| | - Ying-Long Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
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