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Article ; Online: Artificial intelligence in pharmacology research and practice.

van der Lee, Maaike / Swen, Jesse J

2022 Volume 16, Issue 1, Page(s) 31–36

Abstract: In recent years, the use of artificial intelligence (AI) in health care has risen steadily, including a wide range of applications in the field of pharmacology. AI is now used throughout the entire continuum of pharmacology research and clinical practice ...

Abstract	In recent years, the use of artificial intelligence (AI) in health care has risen steadily, including a wide range of applications in the field of pharmacology. AI is now used throughout the entire continuum of pharmacology research and clinical practice and from early drug discovery to real-world datamining. The types of AI models used range from unsupervised clustering of drugs or patients aimed at identifying potential drug compounds or suitable patient populations, to supervised machine learning approaches to improve therapeutic drug monitoring. Additionally, natural language processing is increasingly used to mine electronic health records to obtain real-world data. In this mini-review, we discuss the basics of AI followed by an outline of its application in pharmacology research and clinical practice.
MeSH term(s)	Humans ; Artificial Intelligence ; Natural Language Processing
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2433157-0
ISSN	1752-8062 ; 1752-8054
ISSN (online)	1752-8062
ISSN	1752-8054
DOI	10.1111/cts.13431
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Substrate specificity of CYP2D6 genetic variants.

van der Lee, Maaike / Guchelaar, Henk-Jan / Swen, Jesse J

Pharmacogenomics

2021 Volume 22, Issue 16, Page(s) 1081–1089

Abstract: Genetic variation in the gene encoding CYP2D6 is used to guide drug prescribing in clinical practice. However, genetic variants in CYP2D6 show substrate-specific effects that are currently not accounted for. With a systematic literature, we retrieved 22 ... ...

Abstract	Genetic variation in the gene encoding CYP2D6 is used to guide drug prescribing in clinical practice. However, genetic variants in CYP2D6 show substrate-specific effects that are currently not accounted for. With a systematic literature, we retrieved 22 original studies describing
MeSH term(s)	Alleles ; Cytochrome P-450 CYP2D6/genetics ; Cytochrome P-450 CYP2D6/metabolism ; Debrisoquin/pharmacokinetics ; Genetic Variation ; Humans ; Isoenzymes/genetics ; Substrate Specificity
Chemical Substances	Isoenzymes ; Cytochrome P-450 CYP2D6 (EC 1.14.14.1) ; Debrisoquin (X31CDK040E)
Language	English
Publishing date	2021-09-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2019513-8
ISSN	1744-8042 ; 1462-2416
ISSN (online)	1744-8042
ISSN	1462-2416
DOI	10.2217/pgs-2021-0093
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Why We Need to Take a Closer Look at Genetic Contributions to CYP3A Activity.

Zhai, Qinglian / van der Lee, Maaike / van Gelder, Teun / Swen, Jesse J

Frontiers in pharmacology

2022 Volume 13, Page(s) 912618

Abstract: Cytochrome P450 3A (CYP3A) subfamily enzymes are involved in the metabolism of 40% of drugs in clinical use. Twin studies have indicated that 66% of the variability in CYP3A4 activity is hereditary. Yet, the complexity of ... ...

Abstract	Cytochrome P450 3A (CYP3A) subfamily enzymes are involved in the metabolism of 40% of drugs in clinical use. Twin studies have indicated that 66% of the variability in CYP3A4 activity is hereditary. Yet, the complexity of the
Language	English
Publishing date	2022-06-16
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.912618
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: From gene to dose: Long-read sequencing and *-allele tools to refine phenotype predictions of

Graansma, Lonneke J / Zhai, Qinglian / Busscher, Loes / Menafra, Roberta / van den Berg, Redmar R / Kloet, Susan L / van der Lee, Maaike

Frontiers in pharmacology

2023 Volume 14, Page(s) 1076574

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2023-03-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1076574
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Study protocol of the HD-MED study aiming to personalize drug treatment in Huntington's disease: a longitudinal, observational study to assess medication use and efficacy in relation to pharmacogenetics.

Feleus, Stephanie / van der Lee, Maaike / Swen, Jesse J / Roos, Raymund A C / de Bot, Susanne T

Therapeutic advances in rare disease

2023 Volume 4, Page(s) 26330040231204643

Abstract: Background: Huntington's disease (HD) is a hereditary, neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms. Currently, HD can only be managed symptomatically, including a large variety of prescribed drugs. Many HD ... ...

Abstract	Background: Huntington's disease (HD) is a hereditary, neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms. Currently, HD can only be managed symptomatically, including a large variety of prescribed drugs. Many HD patients experience negative medication effects (e.g. side effects or non-response). Pharmacogenetic (PGx) studies show how genetic variation affects both medication efficacy and toxicity and holds the potential to improve these outcomes of drug treatment. Primary objective: To classify the effect of the PGx profile of CYP2C19 and CYP2D6 in HD gene expansion carriers on negative medication effects of HD-related medication. Design: Multicenter, observational study with 1-year follow-up. Adult HD gene expansion carriers who use one or more HD-related medications are eligible to participate. Methods and analysis: A detailed overview of medication use, medication efficacy, and side effects is retrospectively and prospectively collected Ethics: The original study protocol was approved by the medical research ethics committee Leiden Den Haag Delft on 26 November 2019. Discussion: HD-MED is a low-risk study that will generate personalized PGx results that can immediately be implemented in clinical practice, thus potentially improving pharmacovigilance and patients' quality of life. Registration: This study is registered in the International Clinical Trial Registry Platform under registration number NL8251, URL https://trialsearch.who.int/Trial2.aspx?TrialID=NL8251.
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ISSN	2633-0040
ISSN (online)	2633-0040
DOI	10.1177/26330040231204643
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The effect of genetic variants in the transcription factor TSPYL family on the CYP3A4 mediated cyclosporine metabolism in kidney transplant patients.

Zhai, Qinglian / Moes, Dirk Jan A R / van Gelder, Teun / van der Lee, Maaike / Sanders, Jan-Stephan / Bemelman, Frederike J / de Fijter, Johan W / Klein, Kathrin / Schwab, Matthias / Swen, Jesse J

Clinical and translational science

2024 Volume 17, Issue 2, Page(s) e13729

Abstract: CYP3A4 activity shows considerable interindividual variability. Although studies indicate 60%-80% is heritable, common single nucleotide variants (SNVs) in CYP3A4 together only explain ~10%. Transcriptional factors, such as the testis-specific Y-encoded- ... ...

Abstract	CYP3A4 activity shows considerable interindividual variability. Although studies indicate 60%-80% is heritable, common single nucleotide variants (SNVs) in CYP3A4 together only explain ~10%. Transcriptional factors, such as the testis-specific Y-encoded-like proteins (TSPYLs) family, have been reported to regulate the expression of CYP enzymes including CYP3A4 in vitro. Here, we investigated the effect of genetic variants in TSPYL on CYP3A4 activity using data from a clinical study and a human liver bank. Five SNVs (rs3828743, rs10223646, rs6909133, rs1204807, and rs1204811) in TSPYL were selected because of a reported effect on CYP3A4 expression in vitro or suggested clinical effect. For the clinical study, whole blood concentrations, clinical data, and DNA were available from 295 kidney transplant recipients participating in the prospective MECANO study. A multivariate pharmacokinetic model adjusted for body weight, steroid treatment, and CYP3A4 genotype was used to assess the effect of the genetic variants on cyclosporine clearance. In multivariate analysis, homozygous carriers of rs3828743 had a 18% lower cyclosporin clearance compared to the wild-type and heterozygous patients (28.72 vs. 35.03 L/h, p = 0.018) indicating a lower CYP3A4 activity and an opposite direction of effect compared to the previously reported increased CYP3A4 expression. To validate, we tested associations between rs3828743 and CYP3A4 mRNA and protein expression as well as enzyme activity with data from a liver bank (n = 150). No association with any of these end points was observed. In conclusion, the totality of evidence is not in support of a significant role for TSPYL SNV rs3828743 in explaining variability in CYP3A4 activity.
MeSH term(s)	Male ; Humans ; Cyclosporine/pharmacokinetics ; Cytochrome P-450 CYP3A/genetics ; Immunosuppressive Agents/pharmacokinetics ; Transcription Factors/genetics ; Kidney Transplantation/adverse effects ; Prospective Studies ; Genotype ; Polymorphism, Single Nucleotide
Chemical Substances	Cyclosporine (83HN0GTJ6D) ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Immunosuppressive Agents ; Transcription Factors ; CYP3A4 protein, human (EC 1.14.14.55)
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2433157-0
ISSN	1752-8062 ; 1752-8054
ISSN (online)	1752-8062
ISSN	1752-8054
DOI	10.1111/cts.13729
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Technologies for Pharmacogenomics: A Review

van der Lee, Maaike / Kriek, Marjolein / Guchelaar, Henk-Jan / Swen, Jesse J

Genes. 2020 Dec. 04, v. 11, no. 12

2020

Abstract: The continuous development of new genotyping technologies requires awareness of their potential advantages and limitations concerning utility for pharmacogenomics (PGx). In this review, we provide an overview of technologies that can be applied in PGx ... ...

Abstract	The continuous development of new genotyping technologies requires awareness of their potential advantages and limitations concerning utility for pharmacogenomics (PGx). In this review, we provide an overview of technologies that can be applied in PGx research and clinical practice. Most commonly used are single nucleotide variant (SNV) panels which contain a pre-selected panel of genetic variants. SNV panels offer a short turnaround time and straightforward interpretation, making them suitable for clinical practice. However, they are limited in their ability to assess rare and structural variants. Next-generation sequencing (NGS) and long-read sequencing are promising technologies for the field of PGx research. Both NGS and long-read sequencing often provide more data and more options with regard to deciphering structural and rare variants compared to SNV panels—in particular, in regard to the number of variants that can be identified, as well as the option for haplotype phasing. Nonetheless, while useful for research, not all sequencing data can be applied to clinical practice yet. Ultimately, selecting the right technology is not a matter of fact but a matter of choosing the right technique for the right problem.
Keywords	genotyping ; haplotypes ; pharmacogenomics
Language	English
Dates of publication	2020-1204
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11121456
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Technologies for Pharmacogenomics: A Review.

van der Lee, Maaike / Kriek, Marjolein / Guchelaar, Henk-Jan / Swen, Jesse J

Genes

2020 Volume 11, Issue 12

Abstract	The continuous development of new genotyping technologies requires awareness of their potential advantages and limitations concerning utility for pharmacogenomics (PGx). In this review, we provide an overview of technologies that can be applied in PGx research and clinical practice. Most commonly used are single nucleotide variant (SNV) panels which contain a pre-selected panel of genetic variants. SNV panels offer a short turnaround time and straightforward interpretation, making them suitable for clinical practice. However, they are limited in their ability to assess rare and structural variants. Next-generation sequencing (NGS) and long-read sequencing are promising technologies for the field of PGx research. Both NGS and long-read sequencing often provide more data and more options with regard to deciphering structural and rare variants compared to SNV panels-in particular, in regard to the number of variants that can be identified, as well as the option for haplotype phasing. Nonetheless, while useful for research, not all sequencing data can be applied to clinical practice yet. Ultimately, selecting the right technology is not a matter of fact but a matter of choosing the right technique for the right problem.
MeSH term(s)	Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Pharmacogenetics ; Polymorphism, Single Nucleotide ; Precision Medicine
Language	English
Publishing date	2020-12-04
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11121456
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Physiologically-based pharmacokinetic modeling of quinidine to establish a CYP3A4, P-gp, and CYP2D6 drug-drug-gene interaction network.

Feick, Denise / Rüdesheim, Simeon / Marok, Fatima Zahra / Selzer, Dominik / Loer, Helena Leonie Hanae / Teutonico, Donato / Frechen, Sebastian / van der Lee, Maaike / Moes, Dirk Jan A R / Swen, Jesse J / Schwab, Matthias / Lehr, Thorsten

CPT: pharmacometrics & systems pharmacology

2023 Volume 12, Issue 8, Page(s) 1143–1156

Abstract: The antiarrhythmic agent quinidine is a potent inhibitor of cytochrome P450 (CYP) 2D6 and P-glycoprotein (P-gp) and is therefore recommended for use in clinical drug-drug interaction (DDI) studies. However, as quinidine is also a substrate of CYP3A4 and ... ...

Abstract	The antiarrhythmic agent quinidine is a potent inhibitor of cytochrome P450 (CYP) 2D6 and P-glycoprotein (P-gp) and is therefore recommended for use in clinical drug-drug interaction (DDI) studies. However, as quinidine is also a substrate of CYP3A4 and P-gp, it is susceptible to DDIs involving these proteins. Physiologically-based pharmacokinetic (PBPK) modeling can help to mechanistically assess the absorption, distribution, metabolism, and excretion processes of a drug and has proven its usefulness in predicting even complex interaction scenarios. The objectives of the presented work were to develop a PBPK model of quinidine and to integrate the model into a comprehensive drug-drug(-gene) interaction (DD(G)I) network with a diverse set of CYP3A4 and P-gp perpetrators as well as CYP2D6 and P-gp victims. The quinidine parent-metabolite model including 3-hydroxyquinidine was developed using pharmacokinetic profiles from clinical studies after intravenous and oral administration covering a broad dosing range (0.1-600 mg). The model covers efflux transport via P-gp and metabolic transformation to either 3-hydroxyquinidine or unspecified metabolites via CYP3A4. The 3-hydroxyquinidine model includes further metabolism by CYP3A4 as well as an unspecific hepatic clearance. Model performance was assessed graphically and quantitatively with greater than 90% of predicted pharmacokinetic parameters within two-fold of corresponding observed values. The model was successfully used to simulate various DD(G)I scenarios with greater than 90% of predicted DD(G)I pharmacokinetic parameter ratios within two-fold prediction success limits. The presented network will be provided to the research community and can be extended to include further perpetrators, victims, and targets, to support investigations of DD(G)Is.
MeSH term(s)	Humans ; Cytochrome P-450 CYP2D6/genetics ; Cytochrome P-450 CYP2D6/metabolism ; Cytochrome P-450 CYP3A/genetics ; Cytochrome P-450 CYP3A/metabolism ; Quinidine ; ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics ; Drug Interactions ; Models, Biological ; Cytochrome P-450 CYP3A Inhibitors/pharmacokinetics
Chemical Substances	Cytochrome P-450 CYP2D6 (EC 1.14.14.1) ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Quinidine (ITX08688JL) ; ATP Binding Cassette Transporter, Subfamily B, Member 1 ; Cytochrome P-450 CYP3A Inhibitors ; CYP3A4 protein, human (EC 1.14.14.55)
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697010-7
ISSN	2163-8306 ; 2163-8306
ISSN (online)	2163-8306
ISSN	2163-8306
DOI	10.1002/psp4.12981
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Physiologically based pharmacokinetic modeling of tacrolimus for food-drug and CYP3A drug-drug-gene interaction predictions.

Loer, Helena Leonie Hanae / Feick, Denise / Rüdesheim, Simeon / Selzer, Dominik / Schwab, Matthias / Teutonico, Donato / Frechen, Sebastian / van der Lee, Maaike / Moes, Dirk Jan A R / Swen, Jesse J / Lehr, Thorsten

CPT: pharmacometrics & systems pharmacology

2023 Volume 12, Issue 5, Page(s) 724–738

Abstract: The immunosuppressant and narrow therapeutic index drug tacrolimus is metabolized mainly via cytochrome P450 (CYP) 3A4 and CYP3A5. For its pharmacokinetics (PK), high inter- and intra-individual variability can be observed. Underlying causes include the ... ...

Abstract	The immunosuppressant and narrow therapeutic index drug tacrolimus is metabolized mainly via cytochrome P450 (CYP) 3A4 and CYP3A5. For its pharmacokinetics (PK), high inter- and intra-individual variability can be observed. Underlying causes include the effect of food intake on tacrolimus absorption as well as genetic polymorphism in the CYP3A5 gene. Furthermore, tacrolimus is highly susceptible to drug-drug interactions, acting as a victim drug when coadministered with CYP3A perpetrators. This work describes the development of a whole-body physiologically based pharmacokinetic model for tacrolimus as well as its application for investigation and prediction of (i) the impact of food intake on tacrolimus PK (food-drug interactions [FDIs]) and (ii) drug-drug(-gene) interactions (DD[G]Is) involving the CYP3A perpetrator drugs voriconazole, itraconazole, and rifampicin. The model was built in PK-Sim® Version 10 using a total of 37 whole blood concentration-time profiles of tacrolimus (training and test) compiled from 911 healthy individuals covering the administration of tacrolimus as intravenous infusions as well as immediate-release and extended-release capsules. Metabolism was incorporated via CYP3A4 and CYP3A5, with varying activities implemented for different CYP3A5 genotypes and study populations. The good predictive model performance is demonstrated for the examined food effect studies with 6/6 predicted FDI area under the curve determined between first and last concentration measurements (AUC
MeSH term(s)	Humans ; Tacrolimus ; Cytochrome P-450 CYP3A/genetics ; Cytochrome P-450 CYP3A/metabolism ; Pharmaceutical Preparations ; Immunosuppressive Agents ; Drug Interactions ; Genotype
Chemical Substances	Tacrolimus (WM0HAQ4WNM) ; Cytochrome P-450 CYP3A (EC 1.14.14.1) ; Pharmaceutical Preparations ; Immunosuppressive Agents
Language	English
Publishing date	2023-03-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2697010-7
ISSN	2163-8306 ; 2163-8306
ISSN (online)	2163-8306
ISSN	2163-8306
DOI	10.1002/psp4.12946
Database	MEDical Literature Analysis and Retrieval System OnLINE

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