4.4 Article

ADMET Predictability at Boehringer Ingelheim: State-of-the-Art, and Do Bigger Datasets or Algorithms Make a Difference?

期刊

MOLECULAR INFORMATICS
卷 41, 期 2, 页码 -

出版社

WILEY-V C H VERLAG GMBH
DOI: 10.1002/minf.202100113

关键词

ADMET modelling; machine learning; algorithm comparison; chemical representation; congeneric series

向作者/读者索取更多资源

Despite the widespread use of computational methods in drug discovery and development in the pharmaceutical industry, our study found that there is no significant impact on prediction from data volume, modeling algorithm, chemical representation and grouping, and temporal aspect relationships.
Computational methods assisting drug discovery and development are routine in the pharmaceutical industry. Digital recording of ADMET assays has provided a rich source of data for development of predictive models. Despite the accumulation of data and the public availability of advanced modeling algorithms, the utility of prediction in ADMET research is not clear. Here, we present a critical evaluation of the relationships between data volume, modeling algorithm, chemical representation and grouping, and temporal aspect (time sequence of assays) using an in-house ADMET database. We find no large difference in prediction algorithms nor any systemic and substantial gain from increasingly large datasets. Temporal-based data enlargement led to performance improvement in only in a limited number of assays, and with fractional improvement at best. Assays that are well-, intermediately-, or poorly-suited for ADMET predictions and reasons for such behavior are systematically identified, generating realistic expectations for areas in which computational models can be used to guide decision making in molecular design and development.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.4
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Chemistry, Medicinal

Chemogenomic Active Learning's Domain of Applicability on Small, Sparse qHTS Matrices: A Study Using Cytochrome P450 and Nuclear Hormone Receptor Families

Christin Rakers, Rifat Ara Najnin, Ahsan Habib Polash, Shunichi Takeda, J. B. Brown

CHEMMEDCHEM (2018)

Article Chemistry, Medicinal

Classifiers and their Metrics Quantified

J. B. Brown

MOLECULAR INFORMATICS (2018)

Article Biochemistry & Molecular Biology

Applicability Domain of Active Learning in Chemical Probe Identification: Convergence in Learning from Non-Specific Compounds and Decision Rule Clarification

Ahsan Habib Polash, Takumi Nakano, Shunichi Takeda, J. B. Brown

MOLECULES (2019)

Article Chemistry, Physical

Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models

Stephanie Maria Linker, Aniket Magarkar, Juergen Koefinger, Gerhard Hummer, Daniel Seeliger

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Medicinal

BIreactive: A Machine-Learning Model to Estimate Covalent Warhead Reactivity

Ferruccio Palazzesi, Markus R. Hermann, Marc A. Grundl, Alexander Pautsch, Daniel Seeliger, Christofer S. Tautermann, Alexander Weber

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Medicinal

Hybrid Screening Approach for Very Small Fragments: X-ray and Computational Screening on FKBP51

Sebastian W. Draxler, Margit Bauer, Christian Eickmeier, Simon Nadal, Herbert Nar, Daniel Rangel Rojas, Daniel Seeliger, Markus Zeeb, Dennis Fiegen

JOURNAL OF MEDICINAL CHEMISTRY (2020)

Article Biology

Comprehensive genomics in androgen receptor-dependent castration-resistant prostate cancer identifies an adaptation pathway mediated by opioid receptor kappa 1

Yuki Makino, Yuki Kamiyama, J. B. Brown, Toshiya Tanaka, Ryusuke Murakami, Yuki Teramoto, Takayuki Goto, Shusuke Akamatsu, Naoki Terada, Takahiro Inoue, Tatsuhiko Kodama, Osamu Ogawa, Takashi Kobayashi

Summary: The study reveals that OPRK1 plays an important role in the progression of castration resistance in prostate cancer. Loss of OPRK1 function can delay the acquisition of castration resistance and inhibit the growth of castration-resistant prostate cancer.

COMMUNICATIONS BIOLOGY (2022)

Correction Biology

Comprehensive genomics in androgen receptor-dependent castration-resistant prostate cancer identifies an adaptation pathway mediated by opioid receptor kappa 1 (vol 5, 299, 2022)

Yuki Makino, Yuki Kamiyama, J. B. Brown, Toshiya Tanaka, Ryusuke Murakami, Yuki Teramoto, Takayuki Goto, Shusuke Akamatsu, Naoki Terada, Takahiro Inoue, Tatsuhiko Kodama, Osamu Ogawa, Takashi Kobayashi

COMMUNICATIONS BIOLOGY (2022)

Article Oncology

Utility of Homologous Recombination Deficiency Biomarkers Across Cancer Types

Shiro Takamatsu, J. B. Brown, Ken Yamaguchi, Junzo Hamanishi, Koji Yamanoi, Hisamitsu Takaya, Tomoko Kaneyasu, Seiichi Mori, Masaki Mandai, Noriomi Matsumura

Summary: This study comprehensively analyzed the association between HRR pathway gene alterations and genomic scar scores, and found that biallelic alterations in HRR genes other than BRCA1/2 were also associated with elevated genomic scar scores. The combination of these indices can be used to identify HRD cases and provide better prognosis when treated with DNA-damaging agents.

JCO PRECISION ONCOLOGY (2022)

Article Oncology

Utility of Homologous Recombination Dificiency Biomarkers Across Cancer Types

Shiro Takamatsu, J. B. Brown, Ken Yamaguchi, Junzo Hamanishi, Koji Yamanoi, Hisamitsu Takaya, Tomoko Kaneyasu, Seiichi Mori, Masaki Mandai, Noriomi Matsumura

Summary: Biallelic alterations in HRR genes other than BRCA1/2 are associated with elevated genomic scar scores, and this association varies significantly by sex and the presence of somatic TP53 mutations. Tumors with HRD features in gene expression analysis due to a combination of indices show significantly higher sensitivity to DNA-damaging agents, both in clinical samples and cell lines. This study supports the utility of HRD analysis in all cancer types and enhances chemotherapy decision making and efficacy in clinical settings, marking a significant advancement in precision oncology.

JCO PRECISION ONCOLOGY (2021)

Article Chemistry, Multidisciplinary

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Vytautas Gapsys, Laura Perez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman Van Vlijmen, Gary Tresadern, Bert L. de Groot

CHEMICAL SCIENCE (2020)

暂无数据