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Perspective

Improving on in-silico prediction of oral drug bioavailability

Pages 665-670 | Received 09 Jul 2023, Accepted 18 Sep 2023, Published online: 25 Sep 2023

References

  • Agoram B, Woltosz WS, Bolger MB. Predicting the impact of physiological and biochemical processes on oral drug bioavailability. Adv Drug Deliv Rev. 2001 Oct 1;50(Suppl 1):S41–67.
  • Lobenberg R, Amidon GL. Modern bioavailability, bioequivalence and biopharmaceutics classification system. New scientific approaches to international regulatory standards. Eur J Pharm Biopharm. 2000 Jul;50(1):3–12. doi: 10.1016/S0939-6411(00)00091-6
  • Jamei M, Turner D, Yang J, et al. Population-based mechanistic prediction of oral drug absorption. AAPS J. 2009 Jun;11(2):225–237. doi: 10.1208/s12248-009-9099-y
  • Alqahtani S. In silico ADME-Tox modeling: progress and prospects. Expert Opin Drug Metab Toxicol. 2017 Nov;13(11):1147–1158. doi: 10.1080/17425255.2017.1389897
  • Huang W, Lee SL, Yu LX. Mechanistic approaches to predicting oral drug absorption. AAPS J. 2009 Jun;11(2):217–224. doi: 10.1208/s12248-009-9098-z
  • Yu LX, Lipka E, Crison JR, et al. Transport approaches to the biopharmaceutical design of oral drug delivery systems: prediction of intestinal absorption. Adv Drug Deliv Rev. 1996 Jun 12;19(3):359–376. doi: 10.1016/0169-409X(96)00009-9
  • Xia B, Yang Z, Zhou H, et al. Development of a novel oral cavity compartmental absorption and transit model for sublingual administration: illustration with zolpidem. AAPS J. 2015 May;17(3):631–642. doi: 10.1208/s12248-015-9727-7
  • Ahmed SS, Ramakrishnan V, Khan AU. Systems biological approach of molecular descriptors connectivity: optimal descriptors for oral bioavailability prediction. PLoS One. 2012;7(7):e40654. doi: 10.1371/journal.pone.0040654
  • Xu X, Zhang W, Huang C, et al. A novel chemometric method for the prediction of human oral bioavailability. Int J Mol Sci. 2012;13(6):6964–6982. doi: 10.3390/ijms13066964
  • Olivares-Morales A, Hatley OJ, Turner D, et al. The use of ROC analysis for the qualitative prediction of human oral bioavailability from animal data. Pharm Res. 2014 Mar;31(3):720–730. doi: 10.1007/s11095-013-1193-2
  • Kim MT, Sedykh A, Chakravarti SK, et al. Critical evaluation of human oral bioavailability for pharmaceutical drugs by using various cheminformatics approaches. Pharm Res. 2014 Apr;31(4):1002–1014. doi: 10.1007/s11095-013-1222-1
  • Pires DE, Blundell TL, Ascher DB. pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem. 2015 May 14;58(9):4066–4072. doi: 10.1021/acs.jmedchem.5b00104
  • Miteva MA, Violas S, Montes M, et al. FAF-Drugs: free ADME/tox filtering of compound collections. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W738–44. doi: 10.1093/nar/gkl065
  • Lagorce D, Maupetit J, Baell J, et al. The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. Bioinformatics. 2011 Jul 15;27(14):2018–2020. doi: 10.1093/bioinformatics/btr333
  • Lagorce D, Sperandio O, Baell JB, et al. FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res. 2015 Jul 1;43(W1):W200–7. doi: 10.1093/nar/gkv353
  • Lagorce D, Bouslama L, Becot J, et al. FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics. 2017 Nov 15;33(22):3658–3660. doi: 10.1093/bioinformatics/btx491
  • Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017 Mar 3;7(1):42717.
  • Falcon-Cano G, Molina C, Cabrera-Perez MA. ADME prediction with KNIME: development and validation of a publicly available workflow for the prediction of human oral bioavailability. J Chem Inf Model. 2020 Jun 22;60(6):2660–2667.
  • Dong J, Wang NN, Yao ZJ, et al. Admetlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. J Cheminform. 2018 Jun 26;10(1):29. doi: 10.1186/s13321-018-0283-x
  • Xiong G, Wu Z, Yi J, et al. Admetlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 2021 Jul 2;49(W1):W5–W14. doi: 10.1093/nar/gkab255
  • Cheng F, Li W, Zhou Y, et al. admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model. 2012 Nov 26;52(11):3099–3105. doi: 10.1021/ci300367a
  • Yang H, Lou C, Sun L, et al. admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties. Bioinformatics. 2019 Mar 15;35(6):1067–1069. doi: 10.1093/bioinformatics/bty707
  • Wei M, Zhang X, Pan X, et al. HobPre: accurate prediction of human oral bioavailability for small molecules. J Cheminform. 2022 Jan 6;14(1):1. doi: 10.1186/s13321-021-00580-6
  • Alqahtani S, Bukhari I, Albassam A, et al. An update on the potential role of intestinal first-pass metabolism for the prediction of drug-drug interactions: the role of PBPK modeling. Expert Opin Drug Metab Toxicol. 2018 Jun;14(6):625–634. doi: 10.1080/17425255.2018.1482277
  • Lawless MD, DiBella J, Bolger MB, et al. Simulations Plus, Inc. In Silico Prediction of Oral Bioavailability. 2016. https://www.simulations-plus.com/assets/ASCPT-2016-San-Diego-In-silico-prediction-oral-bioavailability.pdf?utm_source=qsar_pbpk_brochure
  • Fagerholm U, Hellberg S, Spjuth O. Advances in predictions of oral bioavailability of candidate drugs in man with new machine learning methodology. Molecules. 2021 Apr 28;26(9):2572.
  • Obrezanova O, Martinsson A, Whitehead T, et al. Prediction of in vivo pharmacokinetic parameters and time-exposure curves in rats using machine learning from the chemical structure. Mol Pharm. 2022 May 2;19(5):1488–1504. doi: 10.1021/acs.molpharmaceut.2c00027
  • Hens B, Augustijns P, Lennernas H, et al. Leveraging oral drug development to a next level: impact of the IMI-Funded OrBiTo project on patient healthcare. Front Med. 2021;8:480706. doi: 10.3389/fmed.2021.480706
  • Margolskee A, Darwich AS, Pepin X, et al. IMI - oral biopharmaceutics tools project - evaluation of bottom-up PBPK prediction success part 1: characterisation of the OrBiTo database of compounds. Eur J Pharm Sci. 2017 Jan 1;96:598–609.
  • Ghosh J, Lawless MS, Waldman M, et al. Modeling ADMET. Methods Mol Biol. 2016;1425:63–83.
  • Waring MJ, Arrowsmith J, Leach AR, et al. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat Rev Drug Discov. 2015 Jul;14(7):475–486. doi: 10.1038/nrd4609
  • Cao D, Wang J, Zhou R, et al. ADMET evaluation in drug discovery. 11. PharmacoKinetics knowledge base (PKKB): a comprehensive database of pharmacokinetic and toxic properties for drugs. J Chem Inf Model. 2012 May 25;52(5):1132–1137. doi: 10.1021/ci300112j
  • Schmidt U, Struck S, Gruening B, et al. SuperToxic: a comprehensive database of toxic compounds. Nucleic Acids Res. 2009 Jan;37(Database issue):D295–9. doi: 10.1093/nar/gkn850
  • Shang J, Sun H, Liu H, et al. Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. J Cheminform. 2017 Apr 21;9(1):25. doi: 10.1186/s13321-017-0212-4
  • Williams AJ, Grulke CM, Edwards J, et al. The CompTox chemistry dashboard: a community data resource for environmental chemistry. J Cheminform. 2017 Nov 28;9(1):61. doi: 10.1186/s13321-017-0247-6
  • Mouchlis VD, Afantitis A, Serra A, et al. Advances in de novo drug design: from conventional to machine learning methods. Int J Mol Sci. 2021 Feb 7;22(4):1676. doi: 10.3390/ijms22041676
  • Ramey G, Vargas S, Alwis DD, et al. An artificial intelligence framework for optimal drug design. bioRxiv. 2022 Oct 29: 514379.
  • Obrezanova O. Artificial intelligence for compound pharmacokinetics prediction. Curr Opin Struct Biol. 2023 Apr;79:102546. doi: 10.1016/j.sbi.2023.102546

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