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Siramshetty VB, Xu X, Shah P. Artificial Intelligence in ADME Property Prediction. Methods Mol Biol 2024; 2714:307-327. [PMID: 37676606 DOI: 10.1007/978-1-0716-3441-7_17] [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] [Indexed: 09/08/2023]
Abstract
Absorption, distribution, metabolism, excretion (ADME) are key properties of a small molecule that govern pharmacokinetic profiles and impact its efficacy and safety. Computational methods such as machine learning and artificial intelligence have gained significant interest in both academic and industrial settings to predict pharmacokinetic properties of small molecules. These methods are applied in drug discovery to optimize chemical libraries, prioritize hits from biological screens, and optimize ADME properties of lead molecules. In the recent years, the drug discovery community witnessed the use of a range of neural network architectures such as deep neural networks, recurrent neural networks, graph neural networks, and transformer neural networks, which marked a paradigm shift in computer-aided drug design and development. This chapter discusses recent developments with an emphasis on their application to predict ADME properties.
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Affiliation(s)
- Vishal B Siramshetty
- National Center for Advancing Translational Sciences, Rockville, MD, USA
- Department of Safety Assessment, Genentech, Inc., South San Francisco, CA, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, Rockville, MD, USA.
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2
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Stępnik K, Kukula-Koch W, Plazinski W, Rybicka M, Gawel K. Neuroprotective Properties of Oleanolic Acid-Computational-Driven Molecular Research Combined with In Vitro and In Vivo Experiments. Pharmaceuticals (Basel) 2023; 16:1234. [PMID: 37765042 PMCID: PMC10536188 DOI: 10.3390/ph16091234] [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: 07/27/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Oleanolic acid (OA), as a ubiquitous compound in the plant kingdom, is studied for both its neuroprotective and neurotoxic properties. The mechanism of acetylcholinesterase (AChE) inhibitory potential of OA is investigated using molecular dynamic simulations (MD) and docking as well as biomimetic tests. Moreover, the in vitro SH-SY5Y human neuroblastoma cells and the in vivo zebrafish model were used. The inhibitory potential towards the AChE enzyme is examined using the TLC-bioautography assay (the IC50 value is 9.22 μM). The CH-π interactions between the central fragment of the ligand molecule and the aromatic cluster created by the His440, Phe288, Phe290, Phe330, Phe331, Tyr121, Tyr334, Trp84, and Trp279 side chains are observed. The results of the in vitro tests using the SH-SY5Y cells indicate that the viability rate is reduced to 71.5%, 61%, and 43% at the concentrations of 100 µg/mL, 300 µg/mL, and 1000 µg/mL, respectively, after 48 h of incubation, whereas cytotoxicity against the tested cell line with the IC50 value is 714.32 ± 32.40 µg/mL. The in vivo tests on the zebrafish prove that there is no difference between the control and experimental groups regarding the mortality rate and morphology (p > 0.05).
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Affiliation(s)
- Katarzyna Stępnik
- Department of Physical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie–Sklodowska University in Lublin, Pl. M. Curie-Skłodowskiej 3, 20-031 Lublin, Poland
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland;
| | - Wirginia Kukula-Koch
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland;
| | - Wojciech Plazinski
- Department of Biopharmacy, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland;
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland
| | - Magda Rybicka
- Department of Photobiology and Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, ul. Abrahama 58, 80-307 Gdańsk, Poland;
| | - Kinga Gawel
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, ul. Jaczewskiego Str. 8b, 20-090 Lublin, Poland;
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3
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Meng F, Xi Y, Huang J, Ayers PW. A curated diverse molecular database of blood-brain barrier permeability with chemical descriptors. Sci Data 2021; 8:289. [PMID: 34716354 PMCID: PMC8556334 DOI: 10.1038/s41597-021-01069-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 01/31/2023] Open
Abstract
The highly-selective blood-brain barrier (BBB) prevents neurotoxic substances in blood from crossing into the extracellular fluid of the central nervous system (CNS). As such, the BBB has a close relationship with CNS disease development and treatment, so predicting whether a substance crosses the BBB is a key task in lead discovery for CNS drugs. Machine learning (ML) is a promising strategy for predicting the BBB permeability, but existing studies have been limited by small datasets with limited chemical diversity. To mitigate this issue, we present a large benchmark dataset, B3DB, complied from 50 published resources and categorized based on experimental uncertainty. A subset of the molecules in B3DB has numerical log BB values (1058 compounds), while the whole dataset has categorical (BBB+ or BBB-) BBB permeability labels (7807). The dataset is freely available at https://github.com/theochem/B3DB and https://doi.org/10.6084/m9.figshare.15634230.v3 (version 3). We also provide some physicochemical properties of the molecules. By analyzing these properties, we can demonstrate some physiochemical similarities and differences between BBB+ and BBB- compounds.
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Affiliation(s)
- Fanwang Meng
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Yang Xi
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Jinfeng Huang
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
| | - Paul W. Ayers
- grid.25073.330000 0004 1936 8227Department of Chemistry and Chemical Biology, McMaster University, Hamilton, L8S 4L8 Canada
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4
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Integration of evidence to evaluate the potential for neurobehavioral effects following exposure to USFDA-approved food colors. Food Chem Toxicol 2021; 151:112097. [DOI: 10.1016/j.fct.2021.112097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 01/02/2023]
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5
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Vatansever S, Schlessinger A, Wacker D, Kaniskan HÜ, Jin J, Zhou M, Zhang B. Artificial intelligence and machine learning-aided drug discovery in central nervous system diseases: State-of-the-arts and future directions. Med Res Rev 2021; 41:1427-1473. [PMID: 33295676 PMCID: PMC8043990 DOI: 10.1002/med.21764] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/30/2020] [Accepted: 11/20/2020] [Indexed: 01/11/2023]
Abstract
Neurological disorders significantly outnumber diseases in other therapeutic areas. However, developing drugs for central nervous system (CNS) disorders remains the most challenging area in drug discovery, accompanied with the long timelines and high attrition rates. With the rapid growth of biomedical data enabled by advanced experimental technologies, artificial intelligence (AI) and machine learning (ML) have emerged as an indispensable tool to draw meaningful insights and improve decision making in drug discovery. Thanks to the advancements in AI and ML algorithms, now the AI/ML-driven solutions have an unprecedented potential to accelerate the process of CNS drug discovery with better success rate. In this review, we comprehensively summarize AI/ML-powered pharmaceutical discovery efforts and their implementations in the CNS area. After introducing the AI/ML models as well as the conceptualization and data preparation, we outline the applications of AI/ML technologies to several key procedures in drug discovery, including target identification, compound screening, hit/lead generation and optimization, drug response and synergy prediction, de novo drug design, and drug repurposing. We review the current state-of-the-art of AI/ML-guided CNS drug discovery, focusing on blood-brain barrier permeability prediction and implementation into therapeutic discovery for neurological diseases. Finally, we discuss the major challenges and limitations of current approaches and possible future directions that may provide resolutions to these difficulties.
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Affiliation(s)
- Sezen Vatansever
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Avner Schlessinger
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Daniel Wacker
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - H. Ümit Kaniskan
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Jian Jin
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Therapeutics DiscoveryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ming‐Ming Zhou
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Oncological Sciences, Tisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute for Data Science and Genomic TechnologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of Pharmacological SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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6
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Stępnik K. Biomimetic Chromatographic Studies Combined with the Computational Approach to Investigate the Ability of Triterpenoid Saponins of Plant Origin to Cross the Blood-Brain Barrier. Int J Mol Sci 2021; 22:3573. [PMID: 33808219 PMCID: PMC8037809 DOI: 10.3390/ijms22073573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023] Open
Abstract
Biomimetic (non-cell based in vitro) and computational (in silico) studies are commonly used as screening tests in laboratory practice in the first stages of an experiment on biologically active compounds (potential drugs) and constitute an important step in the research on the drug design process. The main aim of this study was to evaluate the ability of triterpenoid saponins of plant origin to cross the blood-brain barrier (BBB) using both computational methods, including QSAR methodology, and biomimetic chromatographic methods, i.e., High Performance Liquid Chromatography (HPLC) with Immobilized Artificial Membrane (IAM) and cholesterol (CHOL) stationary phases, as well as Bio-partitioning Micellar Chromatography (BMC). The tested compounds were as follows: arjunic acid (Terminalia arjuna), akebia saponin D (Akebia quinata), bacoside A (Bacopa monnieri) and platycodin D (Platycodon grandiflorum). The pharmacokinetic BBB parameters calculated in silico show that three of the four substances, i.e., arjunic acid, akebia saponin D, and bacoside A exhibit similar values of brain/plasma equilibration rate expressed as logPSFubrain (the average logPSFubrain: -5.03), whereas the logPSFubrain value for platycodin D is -9.0. Platycodin D also shows the highest value of the unbound fraction in the brain obtained using the examined compounds (0.98). In these studies, it was found out for the first time that the logarithm of the analyte-micelle association constant (logKMA) calculated based on Foley's equation can describe the passage of substances through the BBB. The most similar logBB values were obtained for hydrophilic platycodin D, applying both biomimetic and computational methods. All of the obtained logBB values and physicochemical parameters of the molecule indicate that platycodin D does not cross the BBB (the average logBB: -1.681), even though the in silico estimated value of the fraction unbound in plasma is relatively high (0.52). As far as it is known, this is the first paper that shows the applicability of biomimetic chromatographic methods in predicting the penetration of triterpenoid saponins through the BBB.
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Affiliation(s)
- Katarzyna Stępnik
- Department of Physical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University in Lublin, 20-031 Lublin, Poland
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7
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Godyń J, Gucwa D, Kobrlova T, Novak M, Soukup O, Malawska B, Bajda M. Novel application of capillary electrophoresis with a liposome coated capillary for prediction of blood-brain barrier permeability. Talanta 2020; 217:121023. [DOI: 10.1016/j.talanta.2020.121023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/20/2022]
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8
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In Silico Studies on Triterpenoid Saponins Permeation through the Blood-Brain Barrier Combined with Postmortem Research on the Brain Tissues of Mice Affected by Astragaloside IV Administration. Int J Mol Sci 2020; 21:ijms21072534. [PMID: 32260588 PMCID: PMC7177733 DOI: 10.3390/ijms21072534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023] Open
Abstract
As the number of central nervous system (CNS) drug candidates is constantly growing, there is a strong need for precise a priori prediction of whether an administered compound is able to cross the blood–brain barrier (BBB). The aim of this study was to evaluate the ability to cross the BBB of triterpenoid saponins occurring in Astragalus mongholicus roots. The research was carried out using in silico methods combined with postmortem studies on the brain tissues of mice treated with isolated astragaloside IV (AIV). Firstly, to estimate the ability to cross the BBB by the tested saponins, new quantitative structure–activity relationship (QSAR) models were established. The reliability and predictability of the model based on the values of the blood–brain barrier penetration descriptor (logBB), the difference between the n-octanol/water and cyclohexane/water logP (ΔlogP), the logarithm of n-octanol/water partition coefficient (logPow), and the excess molar refraction (E) were both confirmed using the applicability domain (AD). The critical leverage value h* was found to be 0.128. The relationships between the standardized residuals and the leverages were investigated here. The application of an in vitro acetylcholinesterase-inhibition test showed that AIV can be recognized as the strongest inhibitor among the tested compounds. Therefore, it was isolated for the postmortem studies on brain tissues and blood using semi-preparative HPLC with the mobile phase composed of water, methanol, and ethyl acetate (1.7:2.1:16.2 v/v/v). The results of the postmortem studies on the brain tissues show a regular dependence of the final concentration of AIV in the analyzed brain samples of animals treated with 12.5 and 25 mg/kg b.w. of AIV (0.00012299 and 0.0002306 mg, respectively, per one brain). Moreover, the AIV logBB value was experimentally determined and found to be equal to 0.49 ± 0.03.
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9
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Janicka M, Sztanke M, Sztanke K. Predicting the Blood-Brain Barrier Permeability of New Drug-Like Compounds via HPLC with Various Stationary Phases. Molecules 2020; 25:molecules25030487. [PMID: 31979316 PMCID: PMC7037052 DOI: 10.3390/molecules25030487] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 11/30/2022] Open
Abstract
The permeation of the blood-brain barrier is a very important consideration for new drug candidate molecules. In this research, the reversed-phase liquid chromatography with different columns (Purosphere RP-18e, IAM.PC.DD2 and Cosmosil Cholester) was used to predict the penetration of the blood-brain barrier by 65 newly-synthesized drug-like compounds. The linear free energy relationships (LFERs) model (log BB = c + eE + sS + aA + bB + vV) was established for a training set of 23 congeneric biologically active azole compounds with known experimental log BB (BB = Cblood/Cbrain) values (R2 = 0.9039). The reliability and predictive potency of the model were confirmed by leave-one-out cross validation as well as leave-50%-out cross validation. Multiple linear regression (MLR) was used to develop the quantitative structure-activity relationships (QSARs) to predict the log BB values of compounds that were tested, taking into account the chromatographic lipophilicity (log kw), polarizability and topological polar surface area. The excellent statistics of the developed MLR equations (R2 > 0.8 for all columns) showed that it is possible to use the HPLC technique and retention data to produce reliable blood-brain barrier permeability models and to predict the log BB values of our pharmaceutically important molecules.
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Affiliation(s)
- Małgorzata Janicka
- Department of Physical Chemistry, Faculty of Chemistry, Institute of Chemical Science, Maria Curie-Skłodowska University, Maria Curie-Skłodowska Sq. 3, 20-031 Lublin, Poland;
| | - Małgorzata Sztanke
- Chair and Department of Medical Chemistry, Medical University, 4A Chodźki Street, 20-093 Lublin, Poland
- Correspondence: (M.S.); (K.S.); Tel.: +48-814486195 (M.S. & K.S.)
| | - Krzysztof Sztanke
- Laboratory of Bioorganic Synthesis and Analysis, Chair and Department of Medical Chemistry, Medical University, 4A Chodźki Street, 20-093 Lublin, Poland
- Correspondence: (M.S.); (K.S.); Tel.: +48-814486195 (M.S. & K.S.)
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Nembrini S. On what to permute in test-based approaches for variable importance measures in Random Forests. Bioinformatics 2019; 35:2701-2705. [PMID: 30561510 DOI: 10.1093/bioinformatics/bty1025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/09/2018] [Accepted: 12/12/2018] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION In bioinformatics applications, it is currently customary to permute the outcome variable in order to produce inference on covariates to test novel methods or statistics whose distributions are poorly known. The seminal publication of Altmann et al. in Bioinformatics uses the same permutation scheme to obtain P-values that can be treated as corrected measure of feature importance to rectify the bias of the Gini variable importance in Random Forests. Since then, such method has been used in applied work to also draw statistical conclusions on variable importance measures from resulting P-values. RESULTS In this paper, we show that permuting the outcome may produce unexpected results, including P-values with undesirable properties and illustrate how more refined permutation schemes can be appropriate to obtain desirable results, including high power in discovering relevant variables. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefano Nembrini
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
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Russo G, Barbato F, Grumetto L, Philippe L, Lynen F, Goetz GH. Entry of therapeutics into the brain: Influence of exposed polarity calculated in silico and measured in vitro by supercritical fluid chromatography. Int J Pharm 2019; 560:294-305. [DOI: 10.1016/j.ijpharm.2019.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/18/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022]
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12
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ADME properties evaluation in drug discovery: in silico prediction of blood-brain partitioning. Mol Divers 2018; 22:979-990. [PMID: 30083853 DOI: 10.1007/s11030-018-9866-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
The absorption, distribution, metabolism and excretion properties are important for drugs, and prediction of these properties in advance will save the cost of drug discovery substantially. The ability to penetrate the blood-brain barrier is critical for drugs targeting central nervous system, which is represented by the ratio of its concentration in brain and in blood. Herein, a quantitative structure-property relationship study was carried out to predict blood-brain partitioning coefficient (logBB) of a data set consisting of 287 compounds. Four different methods including support vector machine, multivariate linear regression, multivariate adaptive regression splines and random forest were employed to build prediction models with 116 molecular descriptors selected by Boruta algorithm. The RF model had best performance in training set ([Formula: see text] = 0.938), test set ([Formula: see text] = 0.840) and tenfold cross-validation ([Formula: see text] = 0.788). Finally, we found that the polar surface area and octanol-water partition coefficient have the greatest influence on blood-brain partitioning. Results suggest that the proposed model is a useful and practical tool to predict the logBB values of drug candidates.
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Yuan Y, Zheng F, Zhan CG. Improved Prediction of Blood-Brain Barrier Permeability Through Machine Learning with Combined Use of Molecular Property-Based Descriptors and Fingerprints. AAPS JOURNAL 2018; 20:54. [PMID: 29564576 DOI: 10.1208/s12248-018-0215-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/02/2018] [Indexed: 01/30/2023]
Abstract
Blood-brain barrier (BBB) permeability of a compound determines whether the compound can effectively enter the brain. It is an essential property which must be accounted for in drug discovery with a target in the brain. Several computational methods have been used to predict the BBB permeability. In particular, support vector machine (SVM), which is a kernel-based machine learning method, has been used popularly in this field. For SVM training and prediction, the compounds are characterized by molecular descriptors. Some SVM models were based on the use of molecular property-based descriptors (including 1D, 2D, and 3D descriptors) or fragment-based descriptors (known as the fingerprints of a molecule). The selection of descriptors is critical for the performance of a SVM model. In this study, we aimed to develop a generally applicable new SVM model by combining all of the features of the molecular property-based descriptors and fingerprints to improve the accuracy for the BBB permeability prediction. The results indicate that our SVM model has improved accuracy compared to the currently available models of the BBB permeability prediction.
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Affiliation(s)
- Yaxia Yuan
- Center for Pharmaceutical Innovation and Research, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA.,Molecular Modeling and Biopharmaceutical Center, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA
| | - Fang Zheng
- Center for Pharmaceutical Innovation and Research, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA.,Molecular Modeling and Biopharmaceutical Center, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA
| | - Chang-Guo Zhan
- Center for Pharmaceutical Innovation and Research, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA. .,Molecular Modeling and Biopharmaceutical Center, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA. .,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky, 40536, USA.
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14
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15
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Russo G, Grumetto L, Szucs R, Barbato F, Lynen F. Screening therapeutics according to their uptake across the blood-brain barrier: A high throughput method based on immobilized artificial membrane liquid chromatography-diode-array-detection coupled to electrospray-time-of-flight mass spectrometry. Eur J Pharm Biopharm 2018; 127:72-84. [PMID: 29427629 DOI: 10.1016/j.ejpb.2018.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 01/29/2023]
Abstract
The Blood-Brain Barrier (BBB) plays an essential role in protecting the brain tissues against possible injurious substances. In the present work, 79 neutral, basic, acidic and amphoteric structurally unrelated analytes were considered and their chromatographic retention coefficients on immobilized artificial membrane (IAM) stationary phase were determined employing a mass spectrometry (MS)-compatible buffer based on ammonium acetate. Their BBB passage predictive strength was evaluated and the statistical models based on IAM indexes and in silico physico-chemical descriptors showed solid statistics (r2 (n - 1) = 0.78). The predictive strength of the indexes achieved by the MS-compatible method was comparable to that achieved by employing the more "biomimetic" Dulbecco's phosphate buffered saline, even if some differences in the elution order were observed. The method was transferred to the MS, employing a diode-array-detection coupled to an electrospray ionization source and a time-of-flight analyzer. This setup allowed the simultaneous analysis of up to eight analytes, yielding a remarkable acceleration of the analysis time.
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Affiliation(s)
- Giacomo Russo
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4-bis, B-9000 Gent, Belgium; Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Lucia Grumetto
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Roman Szucs
- Pfizer Global R&D, Sandwich CT13 9NJ, Kent, United Kingdom
| | - Francesco Barbato
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Frederic Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4-bis, B-9000 Gent, Belgium.
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16
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Russo G, Grumetto L, Szucs R, Barbato F, Lynen F. Determination of in Vitro and in Silico Indexes for the Modeling of Blood–Brain Barrier Partitioning of Drugs via Micellar and Immobilized Artificial Membrane Liquid Chromatography. J Med Chem 2017; 60:3739-3754. [DOI: 10.1021/acs.jmedchem.6b01811] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Giacomo Russo
- Separation
Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4-bis, B-9000 Gent, Belgium
- Dipartimento
di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Lucia Grumetto
- Dipartimento
di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Roman Szucs
- Pfizer Global R&D, Sandwich CT13 9NJ, Kent, United Kingdom
| | - Francesco Barbato
- Dipartimento
di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano, 49, I-80131 Naples, Italy
| | - Frederic Lynen
- Separation
Science Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4-bis, B-9000 Gent, Belgium
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17
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Ceccarelli M, Wagner B, Alvarez-Sánchez R, Cruciani G, Goracci L. Use of the Distribution Coefficient in Brain Polar Lipids for the Assessment of Drug-Induced Phospholipidosis Risk. Chem Res Toxicol 2017; 30:1145-1156. [DOI: 10.1021/acs.chemrestox.6b00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M. Ceccarelli
- Laboratory
for Chemoinformatics and Molecular Modelling, Department of Chemistry,
Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - B. Wagner
- pRED,
Pharma Research and Early Development, Pharmaceutical Research, Innovation
Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - R. Alvarez-Sánchez
- pRED,
Pharma Research and Early Development, Pharmaceutical Research, Innovation
Center Basel, F. Hoffmann-La Roche Ltd., CH-4070 Basel, Switzerland
| | - G. Cruciani
- Laboratory
for Chemoinformatics and Molecular Modelling, Department of Chemistry,
Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
| | - L. Goracci
- Laboratory
for Chemoinformatics and Molecular Modelling, Department of Chemistry,
Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy
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18
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A Genetic Algorithm Based Support Vector Machine Model for Blood-Brain Barrier Penetration Prediction. BIOMED RESEARCH INTERNATIONAL 2015; 2015:292683. [PMID: 26504797 PMCID: PMC4609370 DOI: 10.1155/2015/292683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/07/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Blood-brain barrier (BBB) is a highly complex physical barrier determining what substances are allowed to enter the brain. Support vector machine (SVM) is a kernel-based machine learning method that is widely used in QSAR study. For a successful SVM model, the kernel parameters for SVM and feature subset selection are the most important factors affecting prediction accuracy. In most studies, they are treated as two independent problems, but it has been proven that they could affect each other. We designed and implemented genetic algorithm (GA) to optimize kernel parameters and feature subset selection for SVM regression and applied it to the BBB penetration prediction. The results show that our GA/SVM model is more accurate than other currently available log BB models. Therefore, to optimize both SVM parameters and feature subset simultaneously with genetic algorithm is a better approach than other methods that treat the two problems separately. Analysis of our log BB model suggests that carboxylic acid group, polar surface area (PSA)/hydrogen-bonding ability, lipophilicity, and molecular charge play important role in BBB penetration. Among those properties relevant to BBB penetration, lipophilicity could enhance the BBB penetration while all the others are negatively correlated with BBB penetration.
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19
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Tuning the predictive capacity of the PAMPA-BBB model. Eur J Pharm Sci 2015; 79:53-60. [PMID: 26344358 DOI: 10.1016/j.ejps.2015.08.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/28/2015] [Accepted: 08/29/2015] [Indexed: 11/23/2022]
Abstract
Due to its robustness and versatility, several variations of the blood-brain barrier specific parallel artificial membrane permeability assay (PAMPA-BBB) have been reported in the central nervous system (CNS) drug discovery practice. In this study, the impact of the main assay parameters on the predictive power of PAMPA-BBB was thoroughly investigated with 27, passively BBB-transported drug molecules with in vivo logBB data. The single and combined effects of the following variables were systematically studied and optimized: incubation time and temperature (4 vs. 18h, RT vs. 37°C), type of the read-out (UV-reader vs. HPLC), solvent composition (n-dodecane/n-hexane), lipid concentration (0-10w/v % PBLE), cholesterol content (0-1.66w/v %), and thickness of the lipid membrane, and the DMSO cosolvent content (5-20v/v %), respectively. Based on our results, solvent-driven and lipid-driven mechanisms of diffusion were identified in different assay conditions. Moreover, the analysis of membrane retention (MR%; the mole fraction of solute "lost" to the membrane) data obtained at various membrane compositions (volume of solvent and concentration of phospholipids) revealed the compound-specific nature of this parameter. The optimized conditions for the PAMPA-BBB were the following: 4h incubation at 37°C, detection by HPLC-DAD, iso-pH conditions (pH=7.4) with 5v/v % DMSO content in buffer solutions, and PBLE (10w/v %; without cholesterol) as membrane dissolved in the mixture of n-hexane:n-dodecane 3:1.
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20
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Lavecchia A. Machine-learning approaches in drug discovery: methods and applications. Drug Discov Today 2014; 20:318-31. [PMID: 25448759 DOI: 10.1016/j.drudis.2014.10.012] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 09/27/2014] [Accepted: 10/24/2014] [Indexed: 12/19/2022]
Abstract
During the past decade, virtual screening (VS) has evolved from traditional similarity searching, which utilizes single reference compounds, into an advanced application domain for data mining and machine-learning approaches, which require large and representative training-set compounds to learn robust decision rules. The explosive growth in the amount of public domain-available chemical and biological data has generated huge effort to design, analyze, and apply novel learning methodologies. Here, I focus on machine-learning techniques within the context of ligand-based VS (LBVS). In addition, I analyze several relevant VS studies from recent publications, providing a detailed view of the current state-of-the-art in this field and highlighting not only the problematic issues, but also the successes and opportunities for further advances.
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Affiliation(s)
- Antonio Lavecchia
- Department of Pharmacy, Drug Discovery Laboratory, University of Napoli 'Federico II', via D. Montesano 49, I-80131 Napoli, Italy.
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21
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Raevsky OA, Trepalin SV, Grigor’ev VY, Solodova SL, Yarkov AV, Raevskaya OE. Computer Calculation of Drug Penetration Through the Blood–Brain Barrier. Pharm Chem J 2014. [DOI: 10.1007/s11094-014-1039-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Plowright AT, Nilsson K, Antonsson M, Amin K, Broddefalk J, Jensen J, Lehmann A, Jin S, St-Onge S, Tomaszewski MJ, Tremblay M, Walpole C, Wei Z, Yang H, Ulander J. Discovery of Agonists of Cannabinoid Receptor 1 with Restricted Central Nervous System Penetration Aimed for Treatment of Gastroesophageal Reflux Disease. J Med Chem 2012; 56:220-40. [DOI: 10.1021/jm301511h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alleyn T. Plowright
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Karolina Nilsson
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Madeleine Antonsson
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Kosrat Amin
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Johan Broddefalk
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Jörgen Jensen
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Anders Lehmann
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
| | - Shujuan Jin
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Stephane St-Onge
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Mirosław J. Tomaszewski
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Maxime Tremblay
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Christopher Walpole
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Zhongyong Wei
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Hua Yang
- AstraZeneca Research and Development, 7171 Frederick-Banting, Saint-Laurent,
Quebec, H4S 1Z9, Canada
| | - Johan Ulander
- AstraZeneca Research and Development, Pepparedsleden 1, Mölndal, 43183,
Sweden
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23
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Mente S, Doran A, Wager TT. Getting the MAX out of Computational Models: The Prediction of Unbound-Brain and Unbound-Plasma Maximum Concentrations. ACS Med Chem Lett 2012; 3:515-9. [PMID: 24900502 DOI: 10.1021/ml300029a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/16/2012] [Indexed: 11/28/2022] Open
Abstract
The objective of this work was to establish that unbound maximum concentrations may be reasonably predicted from a combination of computed molecular properties assuming subcutaneous (SQ) dosing. Additionally, we show that the maximum unbound plasma and brain concentrations may be projected from a mixture of in vitro absorption, distribution, metabolism, excretion experimental parameters in combination with computed properties (volume of distribution, fraction unbound in microsomes). Finally, we demonstrate the utility of the underlying equations by showing that the maximum total plasma concentrations can be projected from the experimental parameters for a set of compounds with data collected from clinical research.
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Affiliation(s)
- Scot Mente
- Groton Laboratories, Pfizer Worldwide Research and Development, 1 Eastern Point Road, Groton,
Connecticut 06340, United States
| | - Angela Doran
- Groton Laboratories, Pfizer Worldwide Research and Development, 1 Eastern Point Road, Groton,
Connecticut 06340, United States
| | - Travis T. Wager
- Groton Laboratories, Pfizer Worldwide Research and Development, 1 Eastern Point Road, Groton,
Connecticut 06340, United States
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24
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Wager TT, Liras JL, Mente S, Trapa P. Strategies to minimize CNS toxicity:in vitrohigh-throughput assays and computational modeling. Expert Opin Drug Metab Toxicol 2012; 8:531-42. [DOI: 10.1517/17425255.2012.677028] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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25
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Muehlbacher M, Spitzer GM, Liedl KR, Kornhuber J. Qualitative prediction of blood-brain barrier permeability on a large and refined dataset. J Comput Aided Mol Des 2011; 25:1095-106. [PMID: 22109848 PMCID: PMC3241963 DOI: 10.1007/s10822-011-9478-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Accepted: 10/10/2011] [Indexed: 12/14/2022]
Abstract
The prediction of blood-brain barrier permeation is vitally important for the optimization of drugs targeting the central nervous system as well as for avoiding side effects of peripheral drugs. Following a previously proposed model on blood-brain barrier penetration, we calculated the cross-sectional area perpendicular to the amphiphilic axis. We obtained a high correlation between calculated and experimental cross-sectional area (r = 0.898, n = 32). Based on these results, we examined a correlation of the calculated cross-sectional area with blood-brain barrier penetration given by logBB values. We combined various literature data sets to form a large-scale logBB dataset with 362 experimental logBB values. Quantitative models were calculated using bootstrap validated multiple linear regression. Qualitative models were built by a bootstrapped random forest algorithm. Both methods found similar descriptors such as polar surface area, pKa, logP, charges and number of positive ionisable groups to be predictive for logBB. In contrast to our initial assumption, we were not able to obtain models with the cross-sectional area chosen as relevant parameter for both approaches. Comparing those two different techniques, qualitative random forest models are better suited for blood-brain barrier permeability prediction, especially when reducing the number of descriptors and using a large dataset. A random forest prediction system (n(trees) = 5) based on only four descriptors yields a validated accuracy of 88%.
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Affiliation(s)
- Markus Muehlbacher
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen-Nuremberg, Germany
| | - Gudrun M. Spitzer
- Theoretical Chemistry, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Theoretical Chemistry, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen-Nuremberg, Germany
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26
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Bayat Z, Movaffagh J, Noruzi S. Development of a computational approach to predict blood-brain permeability on anti-viral Nucleoside Analogues. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2011. [DOI: 10.1134/s0036024411110021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Kornhuber J, Muehlbacher M, Trapp S, Pechmann S, Friedl A, Reichel M, Mühle C, Terfloth L, Groemer TW, Spitzer GM, Liedl KR, Gulbins E, Tripal P. Identification of novel functional inhibitors of acid sphingomyelinase. PLoS One 2011; 6:e23852. [PMID: 21909365 PMCID: PMC3166082 DOI: 10.1371/journal.pone.0023852] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 07/26/2011] [Indexed: 12/19/2022] Open
Abstract
We describe a hitherto unknown feature for 27 small drug-like molecules, namely functional inhibition of acid sphingomyelinase (ASM). These entities named FIASMAs (Functional Inhibitors of Acid SphingoMyelinAse), therefore, can be potentially used to treat diseases associated with enhanced activity of ASM, such as Alzheimer's disease, major depression, radiation- and chemotherapy-induced apoptosis and endotoxic shock syndrome. Residual activity of ASM measured in the presence of 10 µM drug concentration shows a bimodal distribution; thus the tested drugs can be classified into two groups with lower and higher inhibitory activity. All FIASMAs share distinct physicochemical properties in showing lipophilic and weakly basic properties. Hierarchical clustering of Tanimoto coefficients revealed that FIASMAs occur among drugs of various chemical scaffolds. Moreover, FIASMAs more frequently violate Lipinski's Rule-of-Five than compounds without effect on ASM. Inhibition of ASM appears to be associated with good permeability across the blood-brain barrier. In the present investigation, we developed a novel structure-property-activity relationship by using a random forest-based binary classification learner. Virtual screening revealed that only six out of 768 (0.78%) compounds of natural products functionally inhibit ASM, whereas this inhibitory activity occurs in 135 out of 2028 (6.66%) drugs licensed for medical use in humans.
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Affiliation(s)
- Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University of Erlangen, Erlangen, Germany.
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28
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Wager TT, Villalobos A, Verhoest PR, Hou X, Shaffer CL. Strategies to optimize the brain availability of central nervous system drug candidates. Expert Opin Drug Discov 2011; 6:371-81. [DOI: 10.1517/17460441.2011.564158] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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29
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Sakiyama Y. The use of machine learning and nonlinear statistical tools for ADME prediction. Expert Opin Drug Metab Toxicol 2010; 5:149-69. [PMID: 19239395 DOI: 10.1517/17425250902753261] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Absorption, distribution, metabolism and excretion (ADME)-related failure of drug candidates is a major issue for the pharmaceutical industry today. Prediction of ADME by in silico tools has now become an inevitable paradigm to reduce cost and enhance efficiency in pharmaceutical research. Recently, machine learning as well as nonlinear statistical tools has been widely applied to predict routine ADME end points. To achieve accurate and reliable predictions, it would be a prerequisite to understand the concepts, mechanisms and limitations of these tools. Here, we have devised a small synthetic nonlinear data set to help understand the mechanism of machine learning by 2D-visualisation. We applied six new machine learning methods to four different data sets. The methods include Naive Bayes classifier, classification and regression tree, random forest, Gaussian process, support vector machine and k nearest neighbour. The results demonstrated that ensemble learning and kernel machine displayed greater accuracy of prediction than classical methods irrespective of the data set size. The importance of interaction with the engineering field is also addressed. The results described here provide insights into the mechanism of machine learning, which will enable appropriate usage in the future.
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Affiliation(s)
- Yojiro Sakiyama
- Pharmacokinetics Dynamics Metabolism, Pfizer Global Research and Development, Sandwich Laboratories, Kent, UK.
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30
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Vilar S, Chakrabarti M, Costanzi S. Prediction of passive blood-brain partitioning: straightforward and effective classification models based on in silico derived physicochemical descriptors. J Mol Graph Model 2010; 28:899-903. [PMID: 20427217 DOI: 10.1016/j.jmgm.2010.03.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 03/29/2010] [Indexed: 11/30/2022]
Abstract
The distribution of compounds between blood and brain is a very important consideration for new candidate drug molecules. In this paper, we describe the derivation of two linear discriminant analysis (LDA) models for the prediction of passive blood-brain partitioning, expressed in terms of logBB values. The models are based on computationally derived physicochemical descriptors, namely the octanol/water partition coefficient (logP), the topological polar surface area (TPSA) and the total number of acidic and basic atoms, and were obtained using a homogeneous training set of 307 compounds, for all of which the published experimental logBB data had been determined in vivo. In particular, since molecules with logBB>0.3 cross the blood-brain barrier (BBB) readily while molecules with logBB<-1 are poorly distributed to the brain, on the basis of these thresholds we derived two distinct models, both of which show a percentage of good classification of about 80%. Notably, the predictive power of our models was confirmed by the analysis of a large external dataset of compounds with reported activity on the central nervous system (CNS) or lack thereof. The calculation of straightforward physicochemical descriptors is the only requirement for the prediction of the logBB of novel compounds through our models, which can be conveniently applied in conjunction with drug design and virtual screenings.
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Affiliation(s)
- Santiago Vilar
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
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31
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Mehdipour AR, Hamidi M. Brain drug targeting: a computational approach for overcoming blood–brain barrier. Drug Discov Today 2009; 14:1030-6. [DOI: 10.1016/j.drudis.2009.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 06/29/2009] [Accepted: 07/20/2009] [Indexed: 01/04/2023]
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32
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Shen J, Du Y, Zhao Y, Liu G, Tang Y. In SilicoPrediction of Blood–Brain Partitioning Using a Chemometric Method Called Genetic Algorithm Based Variable Selection. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200710129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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34
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Chapter 29 Computational Models for ADME. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2007. [DOI: 10.1016/s0065-7743(07)42029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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35
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Leonard AK, Sileno AP, Brandt GC, Foerder CA, Quay SC, Costantino HR. In vitro formulation optimization of intranasal galantamine leading to enhanced bioavailability and reduced emetic response in vivo. Int J Pharm 2006; 335:138-146. [PMID: 17174048 DOI: 10.1016/j.ijpharm.2006.11.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 11/02/2006] [Accepted: 11/03/2006] [Indexed: 11/20/2022]
Abstract
The purpose of the current investigation was to optimize an intranasal (IN) galantamine (an acetylcholinesterase inhibitor used for treatment of Alzheimer's disease) formulation using an in vitro tissue model, to correlate those results to in vivo bioavailability, and to compare emetic response to oral dosing. A design-of-experiments (DOE) based formulation screening employing an in vitro tissue model of human nasal epithelium was used to assess drug permeability, tight junction modulation, and cellular toxicity. In vivo studies in rats compared pharmacokinetic (PK) profiles of different formulations dosed intranasally. Finally, studies in ferrets evaluated PK and gastrointestinal (GI) related side effects of oral compared to nasal dosage forms. Galantamine permeation was enhanced without increasing cytotoxicity. Pharmacokinetic testing in rats confirmed the improved drug bioavailability and demonstrated an in vitro-in vivo correlation. Compared to oral dosing, IN galantamine resulted in a dramatically lowered incidence of GI-related side effects, e.g., retching and emesis. These findings illustrate that IN delivery represents an attractive alternative to oral dosing for this important Alzheimer's disease therapeutic. To our knowledge, the data herein represent the first direct confirmation of reducing GI-related side effects for IN galantamine compared to oral dosing.
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Affiliation(s)
- Alexis Kays Leonard
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA
| | - Anthony P Sileno
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA
| | - Gordon C Brandt
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA
| | - Charles A Foerder
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA
| | - Steven C Quay
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA
| | - Henry R Costantino
- Nastech Pharmaceutical Company Inc., 3450 Monte Villa Parkway, Bothell, WA 98021, USA.
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