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Tian M, Ma X, Lu Q, Xue G, Li L, Wu A, Zang H, Nie L. Study on the mechanism of ischemic stroke treatment based on network pharmacology and Raman spectroscopy in the larval zebrafish model, Calculus Bovis as a case. Int Immunopharmacol 2024; 141:112914. [PMID: 39181017 DOI: 10.1016/j.intimp.2024.112914] [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: 06/25/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024]
Abstract
Calculus Bovis (C. bovis) is a precious traditional Chinese medicine of animal origin, and it is one of the traditional medicines for treating cerebral inflammatory diseases such as stroke. However, the pharmacological action of C. bovis on ischemic stroke (IS) and its mechanism are still unclear. The purpose of this study was to investigate the potential mechanism to treat IS. Chemical constituents of different varieties of C. bovis were analyzed and confirmed by HPLC-MS/MS technique. We constructed a component and corresponding target network and drug-disease target protein-protein interaction (PPI) network. GO and KEGG enrichment analysis were performed. The molecular docking of the main compound with the target protein. Subsequently, the potential mechanism of therapy for IS was verified in vivo by zebrafish model. We introduced Raman spectroscopy to detect changes in the biochemical composition of zebrafish. 13 active chemical constituents and 129 potential targets were selected. 122 KEGG signaling pathways were obtained. The binding energy of the main compounds is less than -4.5. The results of animal experiments showed that C. bovis could significantly improve Ponatinib-induced IS, decrease the aggregation degree of brain macrophages, reduce the number of macrophage migrations, and significantly increase the expression level of NR3C1. Raman information indicated that the biochemical composition in the brain of the Ponatinib-induced group shifted to the control group. The mechanism may be related to anti-inflammatory process and regulation of lipid metabolism. This study demonstrates that Raman spectroscopy has great potential as a drug evaluation tool in living larval zebrafish.
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Affiliation(s)
- Mengyin Tian
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Xiaobo Ma
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Qingqing Lu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Gao Xue
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Lian Li
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Aoli Wu
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
| | - Hengchang Zang
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China.
| | - Lei Nie
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Chemical Biology (Ministry of Education), Shandong University, Jinan, Shandong 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China
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Erdoğan M, Comert Onder F. Synthesis, anticancer activity and molecular modeling study of novel substituted triazole linked tetrafluoronaphthalene hybrid derivatives. J Biomol Struct Dyn 2024; 42:9767-9786. [PMID: 37676264 DOI: 10.1080/07391102.2023.2252914] [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: 06/13/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023]
Abstract
To create some novel anticancer molecules, a library of novel series of various triazoles linked to the hydroxyl group of 5,6,7,8-tetrafluoronaphthalen-1-ol (3) was designed and synthesized via CuAAC reaction 'Click Chemistry' of tetrafluoronaphthalene based terminal alkyne with substituted organic azides. The structural characterizations of the targeted Click products 9-18 were confirmed by FTIR, 1H NMR, 19F NMR, 13C NMR and HRMS spectroscopy. Synthesized compounds were tested in two triple negative breast cancer (TNBC) cell lines to understand their anticancer potentials. According to our findings, compounds 14 and 13 showed high cytotoxicity in BT549 cells at 20 μM and 30 μM, respectively. Moreover, these compounds blocked the migration of BT549 cells. In the MDA-MB-231 cell line, compound 18 exhibited high cytotoxicity and can block cell migration for 24 h. Molecular docking study with synthesized novel compounds was performed by Glide/SP method against SphK1 drug target. Furthermore, molecular dynamics (MD) simulation was carried out for the compounds 12-14 and 18. The compounds 13 and 14 may be potential inhibitor candidates in place of a reference inhibitor. A pharmacophore model was generated with the most potent compound 14, and the approved drugs were screened using the modules of Discovery Studio to find similar drugs. Consequently, this comprehensive study encompassing design, synthesis, in vitro and in silico analyses were correlated with the structure-activity relationship between compounds. The findings have the potential to unveil promising drug candidates for future studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Musa Erdoğan
- Department of Food Engineering, Faculty of Engineering and Architecture, Kafkas University, Kars, Türkiye
| | - Ferah Comert Onder
- Department of Medical Biology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
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3
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Teotia V, Jha P, Chopra M. Discovery of Potential Inhibitors of CDK1 by Integrating Pharmacophore-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation Studies, and Evaluation of Their Inhibitory Activity. ACS OMEGA 2024; 9:39873-39892. [PMID: 39346877 PMCID: PMC11425824 DOI: 10.1021/acsomega.4c05414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 10/01/2024]
Abstract
The ability of CDK1 to compensate for the absence of other cell cycle CDKs poses a great challenge to treat cancers that overexpress these proteins. Despite several studies focusing on the area, there are no FDA-approved drugs selectively targeting CDK1. Here, the study aimed to develop potential CDK1 selective inhibitors through drug repurposing and leveraging the structural insights provided by the hit molecules generated. Approximately 280,000 compounds from DrugBank, Selleckchem, Otava and an in-house library were screened initially based on fit values using 3D QSAR pharmacophores built for CDK1 and subsequently through Lipinski, ADMET, and TOPKAT filters. 10,310 hits were investigated for docking into the binding site of CDK1 determined using the crystal structure of human CDK1 in complex with NU6102. The best 55 hits with better docking scores were further analyzed, and 12 hits were selected for 100 ns MD simulations followed by binding energy calculations using the MM-PBSA method. Finally, 10 hit molecules were tested in an in vitro CDK1 Kinase inhibition assay. Out of these, 3 hits showed significant CDK1 inhibitory potential with IC50 < 5 μM. These results indicate these compounds can be used to develop subtype-selective CDK1 inhibitors with better efficacy and reduced toxicities in the future.
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Affiliation(s)
- Vineeta Teotia
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Prakash Jha
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Madhu Chopra
- Laboratory
of Molecular Modeling and Anti-Cancer Drug Development, Dr. B. R.
Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
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Lin J, Lv H, Wang T, Tao H, Zhong Y, Zhou Y, Tang Y, Xie F, Zhuang G, Xu C, Chu Y, Wang X, Yang Y, Song T. The global distribution of the macrolide esterase EstX from the alpha/beta hydrolase superfamily. Commun Biol 2024; 7:781. [PMID: 38944651 PMCID: PMC11214618 DOI: 10.1038/s42003-024-06473-2] [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: 01/29/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024] Open
Abstract
Macrolide antibiotics, pivotal in clinical therapeutics, are confronting resistance challenges mediated by enzymes like macrolide esterases, which are classified into Ere-type and the less studied Est-type. In this study, we provide the biochemical confirmation of EstX, an Est-type macrolide esterase that initially identified as unknown protein in the 1980s. EstX is capable of hydrolyzing four 16-membered ring macrolides, encompassing both veterinary (tylosin, tidipirosin, and tilmicosin) and human-use (leucomycin A5) antibiotics. It uses typical catalytic triad (Asp233-His261-Ser102) from alpha/beta hydrolase superfamily for ester bond hydrolysis. Further genomic context analysis suggests that the dissemination of estX is likely facilitated by mobile genetic elements such as integrons and transposons. The global distribution study indicates that bacteria harboring the estX gene, predominantly pathogenic species like Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae, are prevalent in 74 countries across 6 continents. Additionally, the emergence timeline of the estX gene suggests its proliferation may be linked to the overuse of macrolide antibiotics. The widespread prevalence and dissemination of Est-type macrolide esterase highlight an urgent need for enhanced monitoring and in-depth research, underlining its significance as an escalating public health issue.
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Affiliation(s)
- Jiafu Lin
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Hua Lv
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Tiantian Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Hongkun Tao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yi Zhong
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yang Zhou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yibo Tang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Feng Xie
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Guoqing Zhuang
- Sichuan Academy of Forestry, 610081, Chengdu, Sichuan, China
| | - Changwen Xu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Xinrong Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China
| | - Yongqiang Yang
- Center of Infectious Diseases, Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
| | - Tao Song
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, 610106, Chengdu, China.
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Qandeel BM, Mowafy S, Abouzid K, Farag NA. Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations. BMC Chem 2024; 18:14. [PMID: 38245752 PMCID: PMC10800075 DOI: 10.1186/s13065-023-01110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.
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Affiliation(s)
- Basma M Qandeel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt
| | - Khaled Abouzid
- Department of Pharmaceutical Chemistry, College of Pharmacy, Ain-Shams University, Abbasia, 11566, Egypt
| | - Nahla A Farag
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
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Zhao TT, Hu HJ, Gao LX, Zhou YB, Zhu YL, Zhang C, Li J, Wang WL. Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. J Mol Graph Model 2023; 125:108585. [PMID: 37544021 DOI: 10.1016/j.jmgm.2023.108585] [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: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.
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Affiliation(s)
- Tian-Tian Zhao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Hao-Jie Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Li-Xin Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun-Long Zhu
- Wuxi Maternal and Child Health Hospital, Wuxi School of Medicine, Jiangnan University, Jiangsu, 214002, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
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Wang C, Zhou Q, Wu ST. Scopolin obtained from Smilax china L. against hepatocellular carcinoma by inhibiting glycolysis: A network pharmacology and experimental study. JOURNAL OF ETHNOPHARMACOLOGY 2022; 296:115469. [PMID: 35718053 DOI: 10.1016/j.jep.2022.115469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Smilax china L. is a well-known traditional medicinal plant. In China, it is a common anti-cancer drug that has been inherited for thousands of years. Some in vitro and in vivo studies have confirmed its potential lipid-lowering, anti-inflammatory and anti-ovarian cancer effects. However, there is no research on the material basis and mechanism of the rhizome of Smilax china L. against hepatocellular carcinoma. AIM OF THE STUDY To explore the material basis and mechanism of scopolin from Smilax china L. against hepatocellular carcinoma. METHODS The potential targets and active components of Smilax china L. against hepatocellular carcinoma were screened by transcriptomics, network pharmacology and molecular docking. Microscale Thermophoresis (MST) detection was used to verify the affinity of small molecule compounds with potential proteins and protein-protein interaction. The Extract from HepG2 cells was used to measure the expression of glycolysis-related proteins, glucose consumption and lactate production. The expression of apoptosis-related factors and glycolysis-related proteins in vivo was detected by immunohistochemistry. RESULTS The glycolysis-related proteins glucose-6-phosphate isomerase (GPI), glycerol-3-phosphate dehydrogenase, mitochondrial (GPD2) and phosphoglycerate kinase 2 (PGK2) screened by transcriptomics, network pharmacology showed strongly binding with scopolin by molecular docking. MST detection has also verified the affinity of scopolin with GPI and GPD2. It was the first time found that Heat shock protein HSP 90-alpha (Hsp90α) bound strongly to GPI and GPD2 in the worldwide, while scopolin was able to affect the interaction between Hsp90α and GPD2. In vitro and in vivo experiments further demonstrated that scopolin may play an anti-cancer role by affecting the stability of tumor-associated proteins. The results showed that scopolin obtained from Smilax china L. could regulate the expression of GPI, GPD2 and PGK2 and inhibit the interaction of protein-protein, reduce the energy metabolism of tumor tissue, thereby inhibit tumor growth. CONCLUSION Scopolin obtained from Smilax china L. plays the role of anti-hepatocellular carcinoma by regulating the expression of glycolysis proteins GPI, GPD2 and PGK2. Scopolin could affect the interaction between Hsp90α and GPD2 may provide a novel potential treatment direction for hepatocellular carcinoma.
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Affiliation(s)
- Chen Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, 430065, China.
| | - Qin Zhou
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Song-Tao Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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Stereoselective Synthesis and Application of Gibberellic Acid-Derived Aminodiols. Int J Mol Sci 2022; 23:ijms231810366. [PMID: 36142293 PMCID: PMC9499365 DOI: 10.3390/ijms231810366] [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: 08/10/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
A series of gibberellic acid-based aminodiols was designed and synthesized from commercially available gibberellic acid. Exposure of gibberellic acid to hydrochloric acid under reflux conditions resulted in aromatization followed by rearrangement to form allo-gibberic acid. The key intermediate, ethyl allo-gibberate, was prepared according to literature methods. Epoxidation of key intermediate and subsequent ring-opening of the corresponding epoxide with different nucleophiles resulted in N-substituted aminodiols. The regioselective ring closure of N-benzyl-substituted aminodiol with formaldehyde was also investigated. All aminodiol derivatives were well characterized using modern spectroscopic techniques and evaluated for their antiproliferative activity against a panel of human cancer cell lines. In addition, structure–activity relationships were examined by assessing substituent effects on the aminodiol systems. The results indicated that aminodiols containing aromatic rings on their nitrogen substituents displayed significant cytotoxic effects. Among these agents, N-naphthylmethyl-substituted aminodiols were found to be the most potent candidates in this series. One of these molecules exhibited a modest cancer selectivity determined by non-cancerous fibroblast cells. A docking study was also made to exploit the observed results.
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Network analysis and ligand-based pharmacophore modeling for discovery of small molecule against glioblastoma multiforme. Future Med Chem 2022; 14:1203-1218. [PMID: 35912955 DOI: 10.4155/fmc-2022-0100] [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: 11/17/2022] Open
Abstract
Aim: This study uses network pharmacology to design a c-Src inhibitor followed by pharmacophore modeling to combat glioblastoma multiforme. These in silico approaches are suitable for designing and developing new molecules of interest. Materials & methods: The authors performed virtual screening, pharmacophore analysis and validation of results using various in silico tools and reliable data from different types of literature and databases. Results: The in silico pipeline the authors followed produced reliable chemical information to combat glioblastoma. The authors identified a chemical template against the c-Src protein, which was validated statistically and computationally. Conclusion: The authors have successfully identified a chemical template against c-Src, which will be developed into a promising inhibitor in future studies.
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Li RY, Xie JL, Meng D, Deng P. Virtual screening of lead compounds for the treatment of Alzheimer’s disease based on multi-target strategy. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2104453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Ruo-yu Li
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Jia-li Xie
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Dan Meng
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
| | - Ping Deng
- College of Pharmacy, Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, People’s Republic of China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, People’s Republic of China
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Lead generation of cysteine based mesenchymal epithelial transition (c-Met) kinase inhibitors: Using structure-based scaffold hopping, 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics simulation. Comput Biol Med 2022; 146:105526. [PMID: 35487125 DOI: 10.1016/j.compbiomed.2022.105526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022]
Abstract
Cysteine-based mesenchymal-epithelial transition (c-Met) is a receptor tyrosine kinase that plays a definitive role during cancer progression and was identified as a possible target for anti-angiogenesis drugs. In the present study, different protocols of computer-based drug design were performed. Construction of predictive pharmacophore model using HypoGen algorithm resulted in a validated model of four features of positive ionizable, hydrogen bond acceptor, hydrophobic, and ring aromatic features with a correlation coefficient of 0.87, a configuration cost of 14.95, and a cost difference of 357.92. The model revealed a promising predictive power and had >90% probability of representing true correlation with the activity data. The model was established using Fisher's validation test at the 95% confidence level and test set prediction (r = 0.96), furthermore, the model was validated by mapping of set of compounds undergoing clinical trials as class Ⅱ c-met inhibitors. The generated valid pharmacophore model was then anticipated for virtual screening of three data bases. Moreover, scaffold hopping using replace fragments protocol was implemented. Hits generated were filtered according to Lipinski's rule; 510 selected hits were anatomized and subjected to molecular docking studies into the crystal structure of c-Met kinase. The good correlation between docking scores and ligand pharmacophore mapping fit values provided a reliable foundation for designing new potentially active candidates that may target c-Met kinase. Eventually, eight hits were selected as potential leads. Subsequently, seven (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation. Therefore, these c-Met kinase inhibitors may further serve as new chemical spaces in designing new compounds.
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Qin L, Kuai J, Yang F, Yang L, Sun P, Zhang L, Li G. Selected by bioinformatics and molecular docking analysis, Dhea and 2-14,15-Eg are effective against cholangiocarcinoma. PLoS One 2022; 17:e0260180. [PMID: 35113866 PMCID: PMC8812988 DOI: 10.1371/journal.pone.0260180] [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: 08/11/2021] [Accepted: 11/03/2021] [Indexed: 12/04/2022] Open
Abstract
OBJECT To identify novel targets for the diagnosis, treatment and prognosis of cholangiocarcinoma, we screen ideal lead compounds and preclinical drug candidates with MYC inhibitory effect from the ZINC database, and verify the therapeutic effect of Dhea and 2-14,15-Eg on cholangiocarcinoma. METHODS The gene expression profiles of GSE132305, GSE89749, and GSE45001 were obtained respectively from the Gene Expression Omnibus database. The DEGs were identified by comparing the gene expression profiles of cholangiocarcinoma and normal tissues. GO, KEGG analysis and PPI network analyses were performed. LibDock, ADME and toxicity prediction, molecular docking and molecular dynamics simulations were used to identify potential inhibitors of MYC. Moreover, in vitro, MTT assay, colony-forming assay, the scratch assay and Western blotting were performed to verify the therapeutic effect of Dhea and 2-14,15-Eg. RESULTS PPI network analysis showed that ALB, MYC, APOB, IGF1 and KNG1 were hub genes, of which MYC was mainly studied in this study. A battery of computer-aided virtual techniques showed that Dhea and 2-14,15-Eg have lower rodent carcinogenicity, Ames mutagenicity, developmental toxicity potential, and high tolerance to cytochrome P4502D6, as well as could exist stably in natural circumstances. In vitro assays showed that Dhea and 2-14,15-Eg inhibited cholangiocarcinoma cellular viability, proliferation, and migration inhibiting expression of MYC. CONCLUSION This study suggested that Dhea and 2-14,15-Eg were novel potential inhibitors of MYC targeting, as well as are a promising drug in dealing with cholangiocarcinoma and have a perspective application.
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Affiliation(s)
- Lei Qin
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Jun Kuai
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Fang Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Lu Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Peisheng Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Lanfang Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Guangpeng Li
- Department of Emergency, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
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13
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Xu F, Chen J, Lu C, Cao H, Gu W, Gu W, Zeng L. New insights into the anti-hepatoma mechanism of Alisol G-metal ions complexes based on c-myc DNA. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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14
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Shao M, Wang M, Ma L, Wang Q, Gao P, Tian X, Li C, Lu L, Li C, Wang W, Wang Y. β-elemene blocks lipid-induced inflammatory pathways via PPARβ activation in heart failure. Eur J Pharmacol 2021; 910:174450. [PMID: 34454927 DOI: 10.1016/j.ejphar.2021.174450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/26/2022]
Abstract
This study aims to investigate the effects of β-elemene on a mouse model of heart failure (HF) and to elucidate the underlying mechanisms in vitro approaches. In this study, left anterior descending (LAD)-induced HF mouse model and oxygen-glucose deprivation/recovery (OGD/R)-induced H9C2 model were leveraged to assess the therapeutic effects of β-elemene. Histological examination, western blot and quantitative real-time PCR analysis (RT-qPCR) and immunofluorescence staining was utilized to elucidate mechanism of β-elemene in lipid-induced inflammation. Results showed that β-elemene improved heart function in HF mice evidenced by the increase of cardiac ejection fraction (EF) and fractional shortening (FS) values. Furthermore, β-elemene administration rescued ventricular dilation, lipid accumulation, and inflammatory infiltration in arginal areas of mice myocardial infarction. At transcription level, β-elemene augmented the mRNA expression of fatty acid oxidation-associated genes, such as peroxisome proliferator-activated receptor-β (PPARβ). In vitro, treatment of β-elemene increased carnitine palmitoyltransferase 1A (CPT1A) and sirtuin 3 (SIRT3). Hallmarks of inflammation including the nuclear translocation of nuclear factor κB (NF-κB) and the degradation of inhibitory κBα (IκBα) were significantly suppressed. Consistently, we observed down-regulation of interleukin-6 (IL-6) and pro-inflammatory cytokines (such as TNFα) in β-elemene treated H9C2 cells. Finally, molecular docking model predicted an interaction between β-elemene and PPARβ protein. Furthermore, β-elemene increased the expression of PPARβ, which was validated by antagonist of PPARβ and siRNA for PPARβ.
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Affiliation(s)
- Mingyan Shao
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mingmin Wang
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China
| | - Lin Ma
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Pengrong Gao
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xue Tian
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Changxiang Li
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, College of Traditional Chinese Medicine, University of Chinese Medicine, Beijing 100029, China
| | - Linghui Lu
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, College of Traditional Chinese Medicine, University of Chinese Medicine, Beijing 100029, China
| | - Chun Li
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, Modern Research Center of Traditional Chinese Medicine, School of Traditional Chinese Material Medica, Beijing University of Chinese Medicine, Beijing 100029, China.
| | - Wei Wang
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, College of Traditional Chinese Medicine, University of Chinese Medicine, Beijing 100029, China.
| | - Yong Wang
- Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, School of Life Science, Beijing University of Chinese Medicine, Beijing 100029, China; Beijing Key Laboratory of Traditional Chinese Medicine Syndrome and Formula, College of Traditional Chinese Medicine, University of Chinese Medicine, Beijing 100029, China.
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15
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Cheng JX, Li YQ, Cai J, Zhang CF, Akihisa T, Li W, Kikuchi T, Liu WY, Feng F, Zhang J. Phenolic compounds from Ficus hispida L.f. as tyrosinase and melanin inhibitors: Biological evaluation, molecular docking, and molecular dynamics. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Rampogu S, Gajula RG, Lee G, Kim MO, Lee KW. Unravelling the therapeutic potential of marine drugs as SARS-CoV-2 inhibitors: An insight from essential dynamics and free energy landscape. Comput Biol Med 2021; 135:104525. [PMID: 34252682 PMCID: PMC8164349 DOI: 10.1016/j.compbiomed.2021.104525] [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: 03/04/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an ongoing pandemic. The virus that causes the disease, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), predominantly infects the respiratory tract, which may lead to pneumonia and death in severe cases. Many marine compounds have been found to have immense medicinal value and have gained approval from the Food and Drug Administration (FDA), and some are being tested in clinical trials. In the current investigation, we redirected a number of marine compounds toward SARS-CoV-2 by targeting the main protease (Mpro, PDB ID: 6Y2F), subjecting them to several advanced computational techniques using co-crystallised ligand as the reference compound. The results of the binding affinity studies showed that two compounds, eribulin mesylate (eri) and soblidotin (sob), displayed higher docking scores than did the reference compound. When these compounds were assessed using molecular dynamics simulation, it was evident that they demonstrated stable binding at the binding pocket of the target protein. The systems demonstrated stable root mean square deviation and radius of gyration values, while occupying the binding pocket during the simulation run. Furthermore, the essential dynamics and free energy landscape exploration revealed that the protein had navigated through a minimal energy basin and demonstrated favourable conformation while binding to the proposed inhibitors. Collectively, our findings suggest that two marine compounds, namely eri and sob, show potential as SARS-CoV-2 main protease inhibitors.
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Affiliation(s)
- Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea; Division of Life Science and Applied Life Science (BK 21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea.
| | - Rajesh Goud Gajula
- Primer Biotech Research Center, Jaipuri Colony, Nagole, Hyderabad, Telangana, 500068, India
| | - Gihwan Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea
| | - Myeong Ok Kim
- Division of Life Science and Applied Life Science (BK 21 Plus), College of Natural Sciences, Gyeongsang National University, Jinju, South Korea.
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea.
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17
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Huang TT, Wang X, Qiang SJ, Zhao ZN, Wu ZX, Ashby CR, Li JZ, Chen ZS. The Discovery of Novel BCR-ABL Tyrosine Kinase Inhibitors Using a Pharmacophore Modeling and Virtual Screening Approach. Front Cell Dev Biol 2021; 9:649434. [PMID: 33748144 PMCID: PMC7969810 DOI: 10.3389/fcell.2021.649434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022] Open
Abstract
Chronic myelogenous leukemia (CML) typically results from a reciprocal translocation between chromosomes 9 and 22 to produce the bcr-abl oncogene that when translated, yields the p210 BCR-ABL protein in more than 90% of all CML patients. This protein has constitutive tyrosine kinase activity that activates numerous downstream pathways that ultimately produces uncontrolled myeloid proliferation. Although the use of the BCR-ABL tyrosine kinase inhibitors (TKIs), such as imatinib, nilotinib, dasatinib, bosutinib, and ponatinib have increased the overall survival of CML patients, their use is limited by drug resistance and severe adverse effects. Therefore, there is the need to develop novel compounds that can overcome these problems that limit the use of these drugs. Therefore, in this study, we sought to find novel compounds using Hypogen and Hiphip pharmacophore models based on the structures of clinically approved BCR-ABL TKIs. We also used optimal pharmacophore models such as three-dimensional queries to screen the ZINC database to search for potential BCR-ABL inhibitors. The hit compounds were further screened using Lipinski’s rule of five, ADMET and molecular docking, and the efficacy of the hit compounds was evaluated. Our in vitro results indicated that compound ZINC21710815 significantly inhibited the proliferation of K562, BaF3/WT, and BaF3/T315I leukemia cells by inducing cell cycle arrest. The compound ZINC21710815 decreased the expression of p-BCR-ABL, STAT5, and Crkl and produced apoptosis and autophagy. Our results suggest that ZINC21710815 may be a potential BCR-ABL inhibitor that should undergo in vivo evaluation.
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Affiliation(s)
| | - Xin Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | | | - Zhen-Nan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Zhuo-Xun Wu
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Charles R Ashby
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
| | - Jia-Zhong Li
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, NY, United States
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Abstract
Lonafarnib (Zokinvy™) is an orally active farnesyltransferase inhibitor developed by Eiger BioPharmaceuticals under license from Merck & Co. for the treatment of hepatitis D virus (HDV) infections, and progeria and progeroid laminopathies. The drug was originally discovered by Merck & Co as an investigational drug in oncology. In progeria, lonafarnib inhibits farnesyltransferase to prevent farnesylation and subsequent accumulation of progerin and progerin-like proteins in the nucleus and cellular cytoskeleton. In November 2020, lonafarnib received its first approval in the USA to reduce the risk of mortality in Hutchinson-Gilford Progeria Syndrome (HGPS) and for the treatment of processing-deficient progeroid laminopathies (with either heterozygous LMNA mutation with progerin-like protein accumulation, or homozygous or compound heterozygous ZMPSTE24 mutations) in patients ≥ 12 months of age with a body surface area (BSA) of ≥ 0.39 m2. Lonafarnib is under regulatory review in the European Union. Clinical development for the treatment of HDV infections is underway in multiple countries. This article summarizes the milestones in the development of lonafarnib leading to this first approval.
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Affiliation(s)
- Sohita Dhillon
- Springer Nature, Private Bag 65901, Mairangi Bay, Auckland, 0754, New Zealand.
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19
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Rampogu S, Lee KW. Old Drugs for New Purpose—Fast Pace Therapeutic Identification for
SARS‐CoV
‐2 Infections by Pharmacophore Guided Drug Repositioning Approach. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12171] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shailima Rampogu
- Department of Bio & Medical Big Data (BK21 Four Program) Research Institute of Natural Science (RINS), Gyeongsang National University (GNU) 501 Jinju‐daero, Jinju 52828 South Korea
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK21 Four Program) Research Institute of Natural Science (RINS), Gyeongsang National University (GNU) 501 Jinju‐daero, Jinju 52828 South Korea
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