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Vlachodimou A, Bouma J, De Cleyn M, Berthelot D, Pype S, Bosmans JP, van Vlijmen H, Wroblowski B, Heitman LH, IJzerman AP. Kinetic profiling of novel spirobenzo-oxazinepiperidinone derivatives as equilibrative nucleoside transporter 1 inhibitors. Purinergic Signal 2024; 20:193-205. [PMID: 37423967 PMCID: PMC10997566 DOI: 10.1007/s11302-023-09948-9] [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: 01/31/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Evaluation of kinetic parameters of drug-target binding, kon, koff, and residence time (RT), in addition to the traditional in vitro parameter of affinity is receiving increasing attention in the early stages of drug discovery. Target binding kinetics emerges as a meaningful concept for the evaluation of a ligand's duration of action and more generally drug efficacy and safety. We report the biological evaluation of a novel series of spirobenzo-oxazinepiperidinone derivatives as inhibitors of the human equilibrative nucleoside transporter 1 (hENT1, SLC29A1). The compounds were evaluated in radioligand binding experiments, i.e., displacement, competition association, and washout assays, to evaluate their affinity and binding kinetic parameters. We also linked these pharmacological parameters to the compounds' chemical characteristics, and learned that separate moieties of the molecules governed target affinity and binding kinetics. Among the 29 compounds tested, 28 stood out with high affinity and a long residence time of 87 min. These findings reveal the importance of supplementing affinity data with binding kinetics at transport proteins such as hENT1.
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Affiliation(s)
- Anna Vlachodimou
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jara Bouma
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Michel De Cleyn
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Didier Berthelot
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Stefan Pype
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Jean-Paul Bosmans
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Herman van Vlijmen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | | | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Chitosan/guar gum-based thermoreversible hydrogels loaded with pullulan nanoparticles for enhanced nose-to-brain drug delivery. Int J Biol Macromol 2022; 215:579-595. [PMID: 35779651 DOI: 10.1016/j.ijbiomac.2022.06.161] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Accepted: 06/25/2022] [Indexed: 11/21/2022]
Abstract
The biopolymers-based two-fold system could provide a sustained release platform for drug delivery to the brain resisting the mucociliary clearance, enzymatic degradation, bypassing the first-pass hepatic metabolism, and BBB thus providing superior bioavailability through intranasal administration. In this study, poloxamers PF-127/PF-68 grafted chitosan HCl-co-guar gum-based thermoresponsive hydrogel loaded with eletriptan hydrobromide laden pullulan nanoparticles was synthesized and subjected to dynamic light scattering, Fourier transform infrared spectroscopy, thermal analysis, x-ray diffraction, scanning electron microscopy, stability studies, mucoadhesive strength and time, gel strength, cloud point assessment, rheological assessment, ex-vivo permeation, cell viability assay, histology studies, and in-vivo Pharmacokinetics studies, etc. It is quite evident that CSG-EH-NPs T-Hgel has an enhanced sustained release drug profile where approximately 86 % and 84 % of drug released in phosphate buffer saline and simulated nasal fluid respectively throughout 48 h compared to EH-NPs where 99.44 % and 97.53 % of the drug was released in PBS and SNF for 8 h. In-vivo PKa parameters i.e., mean residence time (MRT) of 11.9 ± 0.83 compared to EH-NPs MRT of 10.2 ± 0.92 and area under the curve (AUCtot) of 42,540.5 ± 5314.14 comparing to AUCtot of EH-NPs 38,026 ± 6343.1 also establish the superiority of CSG-EH-NPs T-Hgel.
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Rationally designed drug delivery systems for the local treatment of resected glioblastoma. Adv Drug Deliv Rev 2021; 177:113951. [PMID: 34461201 DOI: 10.1016/j.addr.2021.113951] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/26/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023]
Abstract
Glioblastoma (GBM) is a particularly aggressive brain cancer associated with high recurrence and poor prognosis. The standard of care, surgical resection followed by concomitant radio- and chemotherapy, leads to low survival rates. The local delivery of active agents within the tumor resection cavity has emerged as an attractive means to initiate oncological treatment immediately post-surgery. This complementary approach bypasses the blood-brain barrier, increases the local concentration at the tumor site while reducing or avoiding systemic side effects. This review will provide a global overview on the local treatment for GBM with an emphasis on the lessons learned from past clinical trials. The main parameters to be considered to rationally design fit-of-purpose biomaterials and develop drug delivery systems for local administration in the GBM resection cavity to prevent the tumor recurrence will be described. The intracavitary local treatment of GBM should i) use materials that facilitate translation to the clinic; ii) be characterized by easy GMP effective scaling up and easy-handling application by the neurosurgeons; iii) be adaptable to fill the tumor-resected niche, mold to the resection cavity or adhere to the exposed brain parenchyma; iv) be biocompatible and possess mechanical properties compatible with the brain; v) deliver a therapeutic dose of rationally-designed or repurposed drug compound(s) into the GBM infiltrative margin. Proof of concept with high translational potential will be provided. Finally, future perspectives to facilitate the clinical translation of the local perisurgical treatment of GBM will be discussed.
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Modeling the Effect of Binding Kinetics in Spatial Drug Distribution in the Brain. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5533886. [PMID: 34285707 PMCID: PMC8275424 DOI: 10.1155/2021/5533886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
A 3-dimensional mathematical model is developed to determine the effect of drug binding kinetics on the spatial distribution of a drug within the brain. The key components, namely, transport across the blood-brain barrier (BBB), drug distribution in the brain extracellular fluid (ECF), and drug binding kinetics are coupled with the bidirectional bulk flow of the brain ECF to enhance the visualization of drug concentration in the brain. The model is developed based on the cubical volume of a brain unit, which is a union of three subdomains: the brain ECF, the BBB, and the blood plasma. The model is a set of partial differential equations and the associated initial and boundary conditions through which the drug distribution process in the mentioned subdomains is described. Effects of drug binding kinetics are investigated by varying the binding parameter values for both nonspecific and specific binding sites. All variations of binding parameter values are discussed, and the results show the improved visualization of the effect of binding kinetics in the drug distribution within the brain. For more realistic visualization, we suggest incorporating more brain components that make up the large volume of the brain tissue.
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Shah SA, Sohail M, Minhas MU, Khan S, Hussain Z, Mahmood A, Kousar M, Thu HE, Abbasi M, Kashif MUR. Curcumin-laden hyaluronic acid-co-Pullulan-based biomaterials as a potential platform to synergistically enhance the diabetic wound repair. Int J Biol Macromol 2021; 185:350-368. [PMID: 34171251 DOI: 10.1016/j.ijbiomac.2021.06.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/13/2023]
Abstract
Injectable hydrogel with multifunctional tunable properties comprising biocompatibility, anti-oxidative, anti-bacterial, and/or anti-infection are highly preferred to efficiently promote diabetic wound repair and its development remains a challenge. In this study, we report hyaluronic acid and Pullulan-based injectable hydrogel loaded with curcumin that could potentiate reepithelization, increase angiogenesis, and collagen deposition at wound microenvironment to endorse healing cascade compared to other treatment groups. The physical interaction and self-assembly of hyaluronic acid-Pullulan-grafted-pluronic F127 injectable hydrogel were confirmed using nuclear magnetic resonance (1H NMR) and Fourier transformed infrared spectroscopy (FT-IR), and cytocompatibility was confirmed by fibroblast viability assay. The CUR-laden hyaluronic acid-Pullulan-g-F127 injectable hydrogel promptly undergoes a sol-gel transition and has proved to potentiate wound healing in a streptozotocin-induced diabetic rat model by promoting 93% of wound closure compared to other groups having 35%, 38%, and 62%. The comparative in vivo study and histological examination was conducted which demonstrated an expeditious recovery rate by significantly reducing the wound healing days i.e. 35 days in a control group, 33 days in the CUR suspension group, 21 days in unloaded injectable, and 13 days was observed in CUR loaded hydrogel group. Furthermore, we suggest that the injectable hydrogel laden with CUR showed a prompt wound healing potential by increasing the cell proliferation and serves as a drug delivery platform for sustained and targeted delivery of hydrophobic moieties.
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Affiliation(s)
- Syed Ahmed Shah
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Muhammad Sohail
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan.
| | | | - Shahzeb Khan
- Department of Pharmacy, University of Malakand, Lower Dir, KPK, Pakistan; Discipline of Pharmaceutical Sciences, School of Health Sciences, UKZN, Durban, South Africa
| | - Zahid Hussain
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Arshad Mahmood
- Collage of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mubeen Kousar
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Hnin Ei Thu
- Innoscience Research Sdn. Bhd., Suites B-5-7, Level 5, Skypark@ One City, Jalan Ust 25/1, Subang Jaya 47650, Selangor, Malaysia; Department of Pharmacology, Faculty of Medicine, Lincoln University College, Petaling Jaya 47301, Selangor, Malaysia
| | - Mudassir Abbasi
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
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Shah SA, Sohail M, Khan SA, Kousar M. Improved drug delivery and accelerated diabetic wound healing by chondroitin sulfate grafted alginate-based thermoreversible hydrogels. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 126:112169. [PMID: 34082970 DOI: 10.1016/j.msec.2021.112169] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022]
Abstract
Injectable hydrogels with multifunctional tunable properties comprising biocompatibility, anti-oxidative, anti-bacterial, and/or anti-infection are highly preferred to efficiently promote diabetic wound repair and its development remains a challenge. In this study, we report chondroitin sulphate (CS) and sodium alginate (SA)-based injectable hydrogel using solvent casting method loaded with curcumin that could potentiate reepithelization, increase angiogenesis, and collagen deposition at wound microenvironment to endorse healing cascade. The physical interaction and self-assembly of chondroitin sulfate grafted alginate (CS-Alg-g-PF127) hydrogel were confirmed using nuclear magnetic resonance (1H NMR) and Fourier transformed infrared spectroscopy (FT-IR), and cytocompatibility was confirmed by fibroblast viability assay. The Masson's trichrome (MT) and hematoxylin and eosin (H&E) results revealed that blank chondroitin sulfate grafted alginate (CS-Alg-g-PF127) and CUR loaded CS-Alg-g-PF127 hydrogel had promising tissue regenerative ability, and showing enhanced wound healing compared to other treatment groups. The controlled release of CUR from injectable hydrogel was evaluated by drug release studies and pharmacokinetic profile (PK) using high-performance liquid chromatography (HPLC) that exhibited the mean residence time (MRT) and area under the curve (AUC) was increased up to 16.18 h and 203.64 ± 30.1 μg/mL*h, respectively. Cytotoxicity analysis of the injectable hydrogels using 3 T3-L1 fibroblasts cells and in vivo toxicity evaluated by subcutaneous injection for 24 h followed by histological examination, confirmed good biocompatibility of CUR loaded CS-Alg-g-PF127 hydrogel. Interestingly, the results of in vivo wound healing by injectable hydrogel showed the upregulation of fibroblasts-like cells, collagen deposition, and differentiated keratinocytes stimulating dermo-epidermal junction, which might endorse that they are potential candidates for excisional wound healing models.
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Affiliation(s)
- Syed Ahmed Shah
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Muhammad Sohail
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan.
| | - Shujaat Ali Khan
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Mubeen Kousar
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
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Ying Y, Wan H, Zhao X, Yu L, He Y, Jin W. Pharmacokinetic-Pharmacodynamic Modeling of the Antioxidant Activity of Quzhou Fructus Aurantii Decoction in a Rat Model of Hyperlipidemia. Biomed Pharmacother 2020; 131:110646. [PMID: 32942150 DOI: 10.1016/j.biopha.2020.110646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Quzhou Fructus Aurantii (QFA) is an herb that is commonly used to alleviate inflammation in individuals dealing with obesity.To date, however, no systematic pharmacokinetic (PK) or pharmacodynamic (PD) analyses of the clinical efficacy of QFA under hyperlipemia-associated oxidative stress conditions have been conducted. The present study, was therefore designed to construct a PK-PD model for this herb, with the goal of linking QFA PK profiles to key therapeutic outlines to guide the therapeutic use of this herb in clinical settings. METHODS Rats were fed a high-fat diet in order to establish a model of hyperlipidemia, after which they were randomized into a normal control group (NCG), a normal treatment group (NTG), a model control group (MCG), and a model treated group (MTG) (n = 6 each). QAF decoction was used to treat rats in the NTG and MTG groups (25 g/kg), while equivalent volumes of physiological saline were administered to rats in the NCG and MCG groups. Plasma samples were collected from the mandibular vein for animals at appropriate time points and analyzed via high-performance liquid chromatography (HPLC). We evaluated PK properties for three QAF components and compared these dynamics between the NTG and MTG groups, while also measuring levels of lipid peroxidation (LPO) in the plasma of rats in all four treatment groups. We then constructed a PK-PD model based upon plasma neohesperidin, luteolin, and nobiletin concentrations and LPO levels using a three-compartment PK model together with a Sigmoid Emax PD model. This model thereby enabled us to assess the antioxidative impact of neohesperidin, luteolin, and nobiletin on hyperlipidemia in rats. RESULTS When comparing the NTG and MTG groups, we detected significant differences in the following parameters pertaining to neohesperidin, luteolin, and nobiletin:t1/2β, V1, t1/2γ, CL1 (p < 0.01) and AUC0-t, Tmax, Cmax (p < 0.05). Relative to NTG group rats, AUC0-t, TmaxandCmaxvalues significantly higher for MTG group rats (p < 0.01), while t1/2β, V1, and t1/2γ values were significantly lower in MTG group rats (p < 0.01) in MTG rats. QAF decoction also exhibited excellent PD efficacy in MTG rats, with significant reductions in plasma LPO levels relative to NTG rats (p < 0.01) following treatment. This therapeutic efficacy may be attributable to the activity of neohesperidin, luteolin, and nobiletin, as LPO levels and plasma concentrations of these compounds were negatively correlated in treated rats. Based upon Akaike Information Criterion (AIC) values, we determined that neohesperidin, luteolin, and nobiletin PK processes were consistent with a three-compartment model. Together, these findings indicated that three active components in QAF decoction (neohesperidin, luteolin, and nobiletin) may exhibit antioxidant activity in vivo. CONCLUSION Our in vivo data indicated that neohesperidin, luteolin and nobiletin components of QAF decoctions exhibit distinct PK and PD properties. Together, these findings suggest that hyperlipidemia-related oxidative stress can significantly impact QFA decoction PK and PD parameters. Our data additionally offer fundamental insights that can be used to design appropriate dosing regimens for individualized clinical QAF decoction treatment.
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Affiliation(s)
- Yuqi Ying
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
| | - Haoyu Wan
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
| | - Xixi Zhao
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
| | - Li Yu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
| | - Yu He
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
| | - Weifeng Jin
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, China.
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Liu H, Zhou Q, Wei W, Qi B, Zeng F, Bao N, Li Q, Guo F, Xia S. The potential drug for treatment in pancreatic adenocarcinoma: a bioinformatical study based on distinct drug databases. Chin Med 2020; 15:26. [PMID: 32206083 PMCID: PMC7079489 DOI: 10.1186/s13020-020-00309-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/13/2020] [Indexed: 01/05/2023] Open
Abstract
Background The prediction of drug-target interaction from chemical and biological data can advance our search for potential drug, contributing to a therapeutic strategy for pancreatic adenocarcinoma (PAAD). We aim to identify hub genes of PAAD and search for potential drugs from distinct databases. The docking simulation is adopted to validate our findings from computable perspective. Methods Differently expressed genes (DEGs) of PAAD were performed based on TCGA. With two Cytoscape plugins of CentiScaPe and MCODE, hub genes were analyzed and visualized by STRING analysis of Protein–protein Interaction (PPI). The hub genes were further selected with significant prognostic values. In addition, we examined the correlation between hub genes and immune infiltration in PAAD. Subsequently, we searched for the hub gene-targeted drugs in Connectivity map (Cmap) and cBioportal, which provided a large body of candidate drugs. The hub gene, which was covered in the above two databases, was estimated in Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Herbal Ingredients’ Targets (HIT) database, which collected natural herbs and related ingredients. After obtaining molecular structures, the potential ingredient from TCMSP was applied for a docking simulation. We finalized a network connectivity of ingredient and its targets. Results A total of 2616 DEGs of PAAD were identified, then we further determined and visualized 24 hub genes by a connectivity analysis of PPI. Based on prognostic value, we identified 5 hub genes including AURKA (p = 0.0059), CCNA2 (p = 0.0047), CXCL10 (p = 0.0044), ADAM10 (p = 0.00043), and BUB1 (p = 0.0033). We then estimated tumor immune correlation of these 5 hub genes, because the immune effector process was one major result of GO analysis. Subsequently, we continued to search for candidate drugs from Cmap and cBioportal database. BUB1, not covered in the above two databases, was estimated in TCMSP and HIT databases. Our results revealed that genistein was a potential drug of BUB1. Next, we generated two docking modes to validate drug-target interaction based on their 3D structures. We eventually constructed a network connectivity of BUB1 and its targets. Conclusions All 5 hub genes that predicted poor prognosis had their potential drugs, especially our findings showed that genistein was predicted to target BUB1 based on TCMSP and docking simulation. This study provided a reasonable approach to extensively retrieve and initially validate putative therapeutic agents for PAAD. In future, these drug-target results should be investigated with solid data from practical experiments.
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Affiliation(s)
- Han Liu
- 1College of Stomatology, Dalian Medical University, Dalian, China
| | - Qi Zhou
- 2Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Wenjuan Wei
- 3Stem Cell Clinical Research Center, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning China.,4National Joint Engineering Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning China
| | - Bing Qi
- 5Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Fen Zeng
- 2Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Nabuqi Bao
- 2Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Qian Li
- 2Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Fangyue Guo
- 2Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Shilin Xia
- 6Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China.,7Department of Palliative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
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Bosma R, Wang Z, Kooistra AJ, Bushby N, Kuhne S, van den Bor J, Waring MJ, de Graaf C, de Esch IJ, Vischer HF, Sheppard RJ, Wijtmans M, Leurs R. Route to Prolonged Residence Time at the Histamine H 1 Receptor: Growing from Desloratadine to Rupatadine. J Med Chem 2019; 62:6630-6644. [PMID: 31274307 PMCID: PMC6750840 DOI: 10.1021/acs.jmedchem.9b00447] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Drug–target
binding kinetics are an important predictor of in vivo drug efficacy,
yet the relationship
between ligand structures and their binding kinetics is often poorly
understood. We show that both rupatadine (1) and desloratadine
(2) have a long residence time at the histamine H1 receptor (H1R). Through development of a [3H]levocetirizine radiolabel, we find that the residence time
of 1 exceeds that of 2 more than 10-fold.
This was further explored with 22 synthesized rupatadine and desloratadine
analogues. Methylene-linked cycloaliphatic or β-branched substitutions
of desloratadine increase the residence time at the H1R,
conveying a longer duration of receptor antagonism. However, cycloaliphatic
substituents directly attached to the piperidine amine (i.e., lacking
the spacer) have decreased binding affinity and residence time compared
to their methylene-linked structural analogues. Guided by docking
studies, steric constraints within the binding pocket are hypothesized
to explain the observed differences in affinity and binding kinetics
between analogues.
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Affiliation(s)
- Reggie Bosma
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Zhiyong Wang
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Albert J Kooistra
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Nick Bushby
- Operations, BioPharmaceuticals R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Sebastiaan Kuhne
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Jelle van den Bor
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Michael J Waring
- Medicinal Chemistry, Research and Early Development, Oncology R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Chris de Graaf
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Iwan J de Esch
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Robert J Sheppard
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D , AstraZeneca , Gothenburg 431 50 , Sweden
| | - Maikel Wijtmans
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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12
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Sykes DA, Stoddart LA, Kilpatrick LE, Hill SJ. Binding kinetics of ligands acting at GPCRs. Mol Cell Endocrinol 2019; 485:9-19. [PMID: 30738950 PMCID: PMC6406023 DOI: 10.1016/j.mce.2019.01.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 12/31/2022]
Abstract
The influence of drug-receptor binding kinetics has often been overlooked during the development of new therapeutics that target G protein-coupled receptors (GPCRs). Over the last decade there has been a growing understanding that an in-depth knowledge of binding kinetics at GPCRs is required to successfully target this class of proteins. Ligand binding to a GPCR is often not a simple single step process with ligand freely diffusing in solution. This review will discuss the experiments and equations that are commonly used to measure binding kinetics and how factors such as allosteric regulation, rebinding and ligand interaction with the plasma membrane may influence these measurements. We will then consider the molecular characteristics of a ligand and if these can be linked to association and dissociation rates.
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Affiliation(s)
- David A Sykes
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Leigh A Stoddart
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Laura E Kilpatrick
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Stephen J Hill
- Cell Signalling and Pharmacology Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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13
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Li S, Qin C, Cui S, Xu H, Wu F, Wang J, Su M, Fang X, Li D, Jiao Q, Zhang M, Xia C, Zhu L, Wang R, Li J, Jiang H, Zhao Z, Li J, Li H. Discovery of a Natural-Product-Derived Preclinical Candidate for Once-Weekly Treatment of Type 2 Diabetes. J Med Chem 2019; 62:2348-2361. [PMID: 30694668 DOI: 10.1021/acs.jmedchem.8b01491] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Poor medication adherence is one of the leading causes of suboptimal glycaemic control in approximately half of the patients with type 2 diabetes mellitus (T2DM). Long-acting antidiabetic drugs are clinically needed for improving patients' compliance. Dipeptidyl peptidase-4 (DPP-4) inhibitors play an increasingly important role in the treatment of T2DM because of their favorable properties of weight neutrality and hypoglycemia avoidance. Herein, we report the successful discovery and scale-up synthesis of compound 5, a structurally novel, potent, and long-acting DPP-4 inhibitor for the once-weekly treatment of T2DM. Inhibitor 5 has fast-associating and slow-dissociating binding kinetics profiles as well as slow clearance rate and long terminal half-life pharmacokinetic properties. A single-dose oral administration of 5 (3 mg/kg) inhibited >80% of DPP-4 activity for more than 7 days in diabetic mice. The long-term antidiabetic efficacies of 5 (10 mg/kg, qw) were better than those of the once-weekly trelagliptin and omarigliptin, especially in decreasing the hemoglobin A1c level.
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Affiliation(s)
- Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Chun Qin
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Shichao Cui
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , P. R. China
| | - Hongling Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Fangshu Wu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jiawei Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Mingbo Su
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Xiaoyu Fang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Dan Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Jiao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Ming Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Chunmei Xia
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jia Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jingya Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , P. R. China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
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14
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Yuan X, Raniolo S, Limongelli V, Xu Y. The Molecular Mechanism Underlying Ligand Binding to the Membrane-Embedded Site of a G-Protein-Coupled Receptor. J Chem Theory Comput 2018; 14:2761-2770. [PMID: 29660291 DOI: 10.1021/acs.jctc.8b00046] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of P2Y1 receptor (P2Y1R), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in-between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents, and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ∼7.5 μs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2Y1R. Our simulations revealed that BPTU prefers partitioning into the interface of polar/lipophilic region of the lipid bilayer before associating with the receptor. Then, it interacts with the second extracellular loop of the receptor and reaches the binding site through the lipid-receptor interface. In addition, by use of funnel-metadynamics simulations which efficiently enhance the sampling of bound and unbound states, we provide a statistically accurate description of the underlying binding free energy landscape. The calculated absolute ligand-receptor binding affinity is in excellent agreement with the experimental data (Δ Gb0_theo = -11.5 kcal mol-1, Δ Gb0_exp= -11.7 kcal mol-1). Our study broadens the view of the current experimental/theoretical models and our understanding of the protein-ligand recognition mechanism in the lipid environment. The strategy used in this work is potentially applicable to investigate ligands association/dissociation with other membrane-embedded sites, allowing identification of compounds targeting membrane receptors of pharmacological interest.
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Affiliation(s)
- Xiaojing Yuan
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica , Chinese Academy of Sciences (CAS) , Shanghai 201203 , China.,School of Pharmacy , University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Stefano Raniolo
- Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , Università della Svizzera Italiana (USI) , CH-6900 Lugano , Switzerland
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , Università della Svizzera Italiana (USI) , CH-6900 Lugano , Switzerland.,Department of Pharmacy , University of Naples "Federico II" , I-80131 Naples , Italy
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica , Chinese Academy of Sciences (CAS) , Shanghai 201203 , China.,School of Pharmacy , University of Chinese Academy of Sciences , Beijing 100049 , China
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15
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Pre-equilibrium competitive library screening for tuning inhibitor association rate and specificity toward serine proteases. Biochem J 2018. [PMID: 29535275 DOI: 10.1042/bcj20180070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High structural and sequence similarity within protein families can pose significant challenges to the development of selective inhibitors, especially toward proteolytic enzymes. Such enzymes usually belong to large families of closely similar proteases and may also hydrolyze, with different rates, protein- or peptide-based inhibitors. To address this challenge, we employed a combinatorial yeast surface display library approach complemented with a novel pre-equilibrium, competitive screening strategy for facile assessment of the effects of multiple mutations on inhibitor association rates and binding specificity. As a proof of principle for this combined approach, we utilized this strategy to alter inhibitor/protease association rates and to tailor the selectivity of the amyloid β-protein precursor Kunitz protease inhibitor domain (APPI) for inhibition of the oncogenic protease mesotrypsin, in the presence of three competing serine proteases, anionic trypsin, cationic trypsin and kallikrein-6. We generated a variant, designated APPIP13W/M17G/I18F/F34V, with up to 30-fold greater specificity relative to the parental APPIM17G/I18F/F34V protein, and 6500- to 230 000-fold improved specificity relative to the wild-type APPI protein in the presence of the other proteases tested. A series of molecular docking simulations suggested a mechanism of interaction that supported the biochemical results. These simulations predicted that the selectivity and specificity are affected by the interaction of the mutated APPI residues with nonconserved enzyme residues located in or near the binding site. Our strategy will facilitate a better understanding of the binding landscape of multispecific proteins and will pave the way for design of new drugs and diagnostic tools targeting proteases and other proteins.
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van den Brink WJ, Hankemeier T, van der Graaf PH, de Lange ECM. Bundling arrows: improving translational CNS drug development by integrated PK/PD-metabolomics. Expert Opin Drug Discov 2018. [DOI: 10.1080/17460441.2018.1446935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- W. J. van den Brink
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - T. Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - P. H. van der Graaf
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Certara QSP, Canterbury Innovation House, Canterbury, United Kingdom
| | - E. C. M. de Lange
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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