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Sheng M, Ma L, Li Z, Peng X, Cen S, Feng M, Tian Y, Dai X, Shi X. A hybrid evaluation of the intestinal absorption performance of compounds from molecular structure. Chem Biol Drug Des 2024; 104:e14576. [PMID: 38969623 DOI: 10.1111/cbdd.14576] [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: 08/14/2023] [Revised: 11/30/2023] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
Intestinal absorption of compounds is significant in drug research and development. To evaluate this efficiently, a method combining mathematical modeling and molecular simulation was proposed, from the perspective of molecular structure. Based on the quantitative structure-property relationship study, the model between molecular structure and their apparent permeability coefficients was successfully constructed and verified, predicting intestinal absorption of drugs and interpreting decisive structural factors, such as AlogP98, Hydrogen bond donor and Ellipsoidal volume. The molecules with strong lipophilicity, less hydrogen bond donors and receptors, and small molecular volume are more easily absorbed. Then, the molecular dynamics simulation and molecular docking were utilized to study the mechanism of differences in intestinal absorption of drugs and investigate the role of molecular structure. Results indicated that molecules with strong lipophilicity and small volume interacted with the membrane at a lower energy and were easier to penetrate the membrane. Likewise, they had weaker interaction with P-glycoprotein and were easier to escape from it and harder to export from the body. More in, less out, is the main reason these molecules absorb well.
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Affiliation(s)
- Mengke Sheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Lina Ma
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhixun Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinhui Peng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuai Cen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Minfang Feng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yuting Tian
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xingxing Dai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinyuan Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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2
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Ta GH, Jhang CS, Weng CF, Leong MK. Development of a Hierarchical Support Vector Regression-Based In Silico Model for Caco-2 Permeability. Pharmaceutics 2021; 13:pharmaceutics13020174. [PMID: 33525340 PMCID: PMC7911528 DOI: 10.3390/pharmaceutics13020174] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/09/2021] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Drug absorption is one of the critical factors that should be taken into account in the process of drug discovery and development. The human colon carcinoma cell layer (Caco-2) model has been frequently used as a surrogate to preliminarily investigate the intestinal absorption. In this study, a quantitative structure–activity relationship (QSAR) model was generated using the innovative machine learning-based hierarchical support vector regression (HSVR) scheme to depict the exceedingly confounding passive diffusion and transporter-mediated active transport. The HSVR model displayed good agreement with the experimental values of the training samples, test samples, and outlier samples. The predictivity of HSVR was further validated by a mock test and verified by various stringent statistical criteria. Consequently, this HSVR model can be employed to forecast the Caco-2 permeability to assist drug discovery and development.
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Affiliation(s)
- Giang Huong Ta
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
| | - Cin-Syong Jhang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
| | - Ching-Feng Weng
- Department of Physiology, School of Basic Medical Science, Xiamen Medical College, Xiamen 361023, China;
| | - Max K. Leong
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien 974301, Taiwan; (G.H.T.); (C.-S.J.)
- Correspondence: ; Tel.: +886-3-890-3609
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3
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Poulsen JA, Tannergren C, Borde A, Westergren J, Lindfors L. Atomistic Modeling of Drug Permeability. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11530-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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4
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Wang Y, Chen X. QSPR model for Caco-2 cell permeability prediction using a combination of HQPSO and dual-RBF neural network. RSC Adv 2020; 10:42938-42952. [PMID: 35514900 PMCID: PMC9058322 DOI: 10.1039/d0ra08209k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of this study is to establish a promising QSPR model for the Caco-2 permeability prediction.
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Affiliation(s)
- Yukun Wang
- School of Chemical Engineering
- University of Science and Technology Liaoning
- Anshan 114051
- China
- School of Electronic and Information Engineering
| | - Xuebo Chen
- School of Electronic and Information Engineering
- University of Science and Technology Liaoning
- Anshan 114051
- China
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5
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Pham-The H, Cabrera-Pérez MÁ, Nam NH, Castillo-Garit JA, Rasulev B, Le-Thi-Thu H, Casañola-Martin GM. In Silico Assessment of ADME Properties: Advances in Caco-2 Cell Monolayer Permeability Modeling. Curr Top Med Chem 2019; 18:2209-2229. [PMID: 30499410 DOI: 10.2174/1568026619666181130140350] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/16/2018] [Accepted: 11/19/2018] [Indexed: 11/22/2022]
Abstract
One of the main goals of in silico Caco-2 cell permeability models is to identify those drug substances with high intestinal absorption in human (HIA). For more than a decade, several in silico Caco-2 models have been made, applying a wide range of modeling techniques; nevertheless, their capacity for intestinal absorption extrapolation is still doubtful. There are three main problems related to the modest capacity of obtained models, including the existence of inter- and/or intra-laboratory variability of recollected data, the influence of the metabolism mechanism, and the inconsistent in vitro-in vivo correlation (IVIVC) of Caco-2 cell permeability. This review paper intends to sum up the recent advances and limitations of current modeling approaches, and revealed some possible solutions to improve the applicability of in silico Caco-2 permeability models for absorption property profiling, taking into account the above-mentioned issues.
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Affiliation(s)
- Hai Pham-The
- Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hanoi, Vietnam
| | - Miguel Á Cabrera-Pérez
- Unit of Modeling and Experimental Biopharmaceutics, Chemical Bioactive Center, Central University of Las Villas, Santa Clara, 54830, Villa Clara, Cuba.,Department of Engineering, Area of Pharmacy and Pharmaceutical Technology, Miguel Hernández University, 03550 Sant Juan d'Alacant, Alicante, Spain
| | - Nguyen-Hai Nam
- Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hanoi, Vietnam
| | - Juan A Castillo-Garit
- Unidad de Toxicologia Experimental, Universidad de Ciencias Medicas "Dr. Serafín Ruiz de Zarate Ruiz" de Villa Clara, Santa Clara, 50200, Villa Clara, Cuba
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, Fargo, ND, 58102, United States
| | - Huong Le-Thi-Thu
- School of Medicine and Pharmacy, Vietnam National University, 144 Xuan Thuy, Hanoi, Vietnam
| | - Gerardo M Casañola-Martin
- Department of Coatings and Polymer Materials, North Dakota State University, Fargo, ND, 58102, United States
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6
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Wang NN, Dong J, Deng YH, Zhu MF, Wen M, Yao ZJ, Lu AP, Wang JB, Cao DS. ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting. J Chem Inf Model 2016; 56:763-73. [DOI: 10.1021/acs.jcim.5b00642] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ning-Ning Wang
- School
of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
| | - Jie Dong
- School
of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
| | - Yin-Hua Deng
- School
of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
| | - Min-Feng Zhu
- School
of Mathematics and Statistics, Central South University, Changsha 410083, P. R. China
| | - Ming Wen
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhi-Jiang Yao
- School
of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P. R. China
| | - Jian-Bing Wang
- College
of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Dong-Sheng Cao
- School
of Pharmaceutical Sciences, Central South University, Changsha 410013, P. R. China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P. R. China
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7
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Potter T, Ermondi G, Newbury G, Caron G. Relating Caco-2 permeability to molecular properties using block relevance analysis. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00470a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New insights into physicochemical drivers for Caco-2 permeability have been gained using a modelling technique known as block relevance analysis.
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Affiliation(s)
- T. Potter
- Cyprotex Discovery Limited
- Macclesfield
- UK
| | - G. Ermondi
- CASSMedChem Research Group
- Molecular Biotechnology and Health Sciences Department
- University of Turin
- Italy
| | - G. Newbury
- Cyprotex Discovery Limited
- Macclesfield
- UK
| | - G. Caron
- CASSMedChem Research Group
- Molecular Biotechnology and Health Sciences Department
- University of Turin
- Italy
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8
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Structure-based prediction of human intestinal membrane permeability for rapidin silicoBCS classification. Biopharm Drug Dispos 2013; 34:321-35. [DOI: 10.1002/bdd.1848] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 05/16/2013] [Accepted: 05/23/2013] [Indexed: 11/07/2022]
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9
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Larregieu CA, Benet LZ. Drug discovery and regulatory considerations for improving in silico and in vitro predictions that use Caco-2 as a surrogate for human intestinal permeability measurements. AAPS JOURNAL 2013; 15:483-97. [PMID: 23344793 DOI: 10.1208/s12248-013-9456-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/10/2013] [Indexed: 11/30/2022]
Abstract
There is a growing need for highly accurate in silico and in vitro predictive models to facilitate drug discovery and development. Results from in vitro permeation studies across the Caco-2 cell monolayer are commonly used for drug permeability screening in industry and are also accepted as a surrogate for human intestinal permeability measurements by the US FDA to support new drug applications. Countless studies carried out in this cell line with published permeability measurements have enabled the development of many in silico prediction models. We identify several common cases that illustrate how using Caco-2 permeability measurements in these in silico and in vitro predictive models will not correlate with human intestinal permeability and will further lead to inaccuracies in these models. We provide guidelines and recommendations for improving these models to more accurately predict clinically relevant information, thereby enhancing the drug discovery, development, and regulatory approval processes.
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Affiliation(s)
- Caroline A Larregieu
- Department of Bioengineering & Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, 533 Parnassus Avenue, Room U-68, San Francisco, CA 94143-0912, USA
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10
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Hakkarainen JJ, Pajander J, Laitinen R, Suhonen M, Forsberg MM. Similar molecular descriptors determine the in vitro drug permeability in endothelial and epithelial cells. Int J Pharm 2012; 436:426-43. [DOI: 10.1016/j.ijpharm.2012.06.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 06/21/2012] [Accepted: 06/22/2012] [Indexed: 11/26/2022]
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11
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Paixão P, Gouveia LF, Morais JA. Prediction of the human oral bioavailability by using in vitro and in silico drug related parameters in a physiologically based absorption model. Int J Pharm 2012; 429:84-98. [DOI: 10.1016/j.ijpharm.2012.03.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 12/13/2022]
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12
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Karelson M, Dobchev D. Using artificial neural networks to predict cell-penetrating compounds. Expert Opin Drug Discov 2011; 6:783-96. [DOI: 10.1517/17460441.2011.586689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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13
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Hecht D. Applications of machine learning and computational intelligence to drug discovery and development. Drug Dev Res 2010. [DOI: 10.1002/ddr.20402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- David Hecht
- Southwestern College, Chula Vista, California
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14
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Prediction of the in vitro permeability determined in Caco-2 cells by using artificial neural networks. Eur J Pharm Sci 2010; 41:107-17. [DOI: 10.1016/j.ejps.2010.05.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 05/12/2010] [Accepted: 05/30/2010] [Indexed: 11/24/2022]
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15
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Fernandez M, Caballero J, Fernandez L, Sarai A. Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). Mol Divers 2010; 15:269-89. [PMID: 20306130 DOI: 10.1007/s11030-010-9234-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 01/25/2010] [Indexed: 10/19/2022]
Abstract
Many articles in "in silico" drug design implemented genetic algorithm (GA) for feature selection, model optimization, conformational search, or docking studies. Some of these articles described GA applications to quantitative structure-activity relationships (QSAR) modeling in combination with regression and/or classification techniques. We reviewed the implementation of GA in drug design QSAR and specifically its performance in the optimization of robust mathematical models such as Bayesian-regularized artificial neural networks (BRANNs) and support vector machines (SVMs) on different drug design problems. Modeled data sets encompassed ADMET and solubility properties, cancer target inhibitors, acetylcholinesterase inhibitors, HIV-1 protease inhibitors, ion-channel and calcium entry blockers, and antiprotozoan compounds as well as protein classes, functional, and conformational stability data. The GA-optimized predictors were often more accurate and robust than previous published models on the same data sets and explained more than 65% of data variances in validation experiments. In addition, feature selection over large pools of molecular descriptors provided insights into the structural and atomic properties ruling ligand-target interactions.
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Affiliation(s)
- Michael Fernandez
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), 680-4 Kawazu, Iizuka, 820-8502, Japan.
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16
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Winkler DA. Network models in drug discovery and regenerative medicine. BIOTECHNOLOGY ANNUAL REVIEW 2008; 14:143-70. [PMID: 18606362 DOI: 10.1016/s1387-2656(08)00005-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Network motifs and modelling paradigms are attracting increasing attention as modelling tools in drug design and development, and in regenerative medicine. There is a gradual but inexorable convergence between these hitherto disparate disciplines. This review summarizes some very recent work in these areas, leading to an understanding of the complementary roles networks play and factors driving this convergence: network paradigms can be excellent ways of modelling and understanding drug molecules and their action, an understanding of the robustness and vulnerabilities of biological targets may improve the efficacy of drug design and discovery, drug design has an increasingly large role to play in directing stem cell properties, stem cell regulatory networks can be modelled in useful ways using network models at a reasonable level of scale, and the network tools of drug design are also very useful for the design of biomaterials used in regenerative medicine.
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Affiliation(s)
- David A Winkler
- CSIRO Molecular and Health Technologies, Clayton 3168, Australia.
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17
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Kalyanaraman C, Jacobson MP. An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des 2007; 21:675-9. [PMID: 17989930 DOI: 10.1007/s10822-007-9141-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 10/15/2007] [Indexed: 10/22/2022]
Abstract
We apply an atomistic model of passive membrane permeability to a series of weakly basic drugs. The computational model uses conformational sampling in combination with an all-atom force field and implicit solvent model to estimate relative passive membrane permeabilities. The model does not require the use of training data for rank-ordering compounds, and as such represents a different approach from the more commonly employed QSPR models. We compare the computational results to previously published experimental PAMPA and Caco-2 permeabilities.
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