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Ding H, Xing F, Zou L, Zhao L. QSAR analysis of VEGFR-2 inhibitors based on machine learning, Topomer CoMFA and molecule docking. BMC Chem 2024; 18:59. [PMID: 38555462 PMCID: PMC10981835 DOI: 10.1186/s13065-024-01165-8] [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: 05/22/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
VEGFR-2 kinase inhibitors are clinically approved drugs that can effectively target cancer angiogenesis. However, such inhibitors have adverse effects such as skin toxicity, gastrointestinal reactions and hepatic impairment. In this study, machine learning and Topomer CoMFA, which is an alignment-dependent, descriptor-based method, were employed to build structural activity relationship models of potentially new VEGFR-2 inhibitors. The prediction ac-curacy of the training and test sets of the 2D-SAR model were 82.4 and 80.1%, respectively, with KNN. Topomer CoMFA approach was then used for 3D-QSAR modeling of VEGFR-2 inhibitors. The coefficient of q2 for cross-validation of the model 1 was greater than 0.5, suggesting that a stable drug activity-prediction model was obtained. Molecular docking was further performed to simulate the interactions between the five most promising compounds and VEGFR-2 target protein and the Total Scores were all greater than 6, indicating that they had a strong hydrogen bond interactions were present. This study successfully used machine learning to obtain five potentially novel VEGFR-2 inhibitors to increase our arsenal of drugs to combat cancer.
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Affiliation(s)
- Hao Ding
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Fei Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Lin Zou
- Medical College of Guangxi University, Nanning, 530004, Guangxi, China
| | - Liang Zhao
- Hepatobiliary and Splenic Surgery Ward, Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.
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Recent advances of dual FGFR inhibitors as a novel therapy for cancer. Eur J Med Chem 2021; 214:113205. [PMID: 33556787 DOI: 10.1016/j.ejmech.2021.113205] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Fibroblast growth factor receptor (FGFR) includes four highly conserved transmembrane receptor tyrosine kinases (FGFR1-4). FGF and FGFR regulate many biological processes, such as angiogenesis, wound healing and tissue regeneration. The abnormal expression of FGFR is related to the tumorigenesis, tumor progression and drug resistance of anti-tumor treatments in many types of tumors. Nowadays there are many anti-cancer drugs targeting FGFR. However, traditional single-target anti-tumor drugs are easy to acquire drug resistance. The therapeutic effect can be enhanced by simultaneously inhibiting FGFR and another target (such as VEGFR, EGFR, PI3K, CSF-1R, etc.). We know drug combination can bring problems such as drug interactions. Therefore, the development of FGFR dual target inhibitors is an important direction. In this paper, we reviewed the research on dual FGFR inhibitors in recent years and made brief comments on them.
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Abstract
Scientists have identified the impact of angiogenesis on tumor growth and survival. Among other efficient drugs, several small-molecule tyrosine kinase inhibitors (TKIs) targeting the vascular endothelial growth factor receptor (VEGFR) have been developed and have already been integrated into the treatment of various advanced malignancies. This review provides a compilation of current knowledge on the pharmacokinetic aspects of all VEGFR-TKIs already approved by the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) and of those still under investigation. Additional information on substance metabolism, potential for drug-drug interactions (DDIs), and the need for dose adaptation in patients with predominant renal and/or hepatic impairment has been included. All TKIs introduced in this review were administered orally, allowing for easy drug handling for healthcare professionals and patients. For almost all substances, the maximum plasma concentrations were reached within a short period of time. The majority of the substances showed a high plasma protein binding and their excretion occurred via the feces and, to a lesser extent, via the urine. In most cases, dose adaptation in patients with mild to moderate renal or hepatic impairment is not recommended. Cytochrome P450 (CYP) 3A4 was found to play a crucial role in the drug metabolic processes of many compounds. In order to prevent unwanted DDIs, co-administration of VEGFR TKIs together with CYP3A4 inhibitors or inducers should be avoided. Throughout all TKIs, the data indicate high inter-individual variability. The causes of this are still unclear and require further research to allow for individualization of treatment regimens.
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Zhou T, Zeng J, Liu S, Zhao T, Wu J, Lai W, He M, Xu B, Qu S, Xu L, Tan W. Study on the determination and chiral inversion of R-salbutamol in human plasma and urine by liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:218-27. [PMID: 26342164 DOI: 10.1016/j.jchromb.2015.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 11/30/2022]
Abstract
The chiral inversion has been a concerned issue during the research and development of a chiral drug. In this study, a sensitive chiral liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for determination of salbutamol enantiomers in human plasma and urine. The chiral inversion mechanism of R-salbutamol was fully investigated for the first time by studying the effects of physicochemical factors, including pH, temperature and time. A fitted model to predict the chiral inversion ratio of R-salbutamol was proposed using a Box-Behnken design. All the samples were separated on an Astec Chirobiotic T column and detected by a tandem mass spectrometer in multiple reaction monitoring mode. Lower limit of quantification of 0.100ng/mL was achieved under the optimized conditions. The method was fully validated and successfully applied to the clinical pharmacokinetic study of R-salbutamol in healthy volunteers. Chiral inversion of R-salbutamol to S-salbutamol has been detected in urine samples. The results indicated that pH and temperature were two dominant factors that caused the chiral inversion of R-salbutamol, which should be taken into consideration during the analysis of chiral drugs. The chiral inversion of R-salbutamol determined in this study was confirmed resulted from the gastric acid in stomach rather than caused by the analysis conditions. Moreover, the calculated results of the fitted model matched very well with the enantioselective pharmacokinetic study of R-salbutamol, and the individual difference of the chiral inversion ratio of R-salbutamol was related to the individual gastric environment. On the basis of the results, this study provides important and concrete information not only for the chiral analysis but also for the metabolism research of chiral drugs.
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Affiliation(s)
- Ting Zhou
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jing Zeng
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shan Liu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ting Zhao
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jie Wu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wenshi Lai
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Mingzhi He
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Beining Xu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Shanshan Qu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Ling Xu
- Keypharma Biomedical Inc., Songshan Lake Science & Technology Industry Park, Dongguan 523808, China
| | - Wen Tan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China; Pre-incubator for Innovative Drugs and Medicine, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China.
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