Machine learning-based solubility prediction and methodology evaluation of active pharmaceutical ingredients in industrial crystallization

Yiming Ma, Zhenguo Gao, Peng Shi, Mingyang Chen, Songgu Wu, Chao Yang, Jing-Kang Wang, Jingcai Cheng, Junbo Gong

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Front. Chem. Sci. Eng. ›› 2022, Vol. 16 ›› Issue (4) : 523-535. DOI: 10.1007/s11705-021-2083-5
RESEARCH ARTICLE
RESEARCH ARTICLE

Machine learning-based solubility prediction and methodology evaluation of active pharmaceutical ingredients in industrial crystallization

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Abstract

Solubility has been widely regarded as a fundamental property of small molecule drugs and drug candidates, as it has a profound impact on the crystallization process. Solubility prediction, as an alternative to experiments which can reduce waste and improve crystallization process efficiency, has attracted increasing attention. However, there are still many urgent challenges thus far. Herein we used seven descriptors based on understanding dissolution behavior to establish two solubility prediction models by machine learning algorithms. The solubility data of 120 active pharmaceutical ingredients (APIs) in ethanol were considered in the prediction models, which were constructed by random decision forests and artificial neural network with optimized data structure and model accuracy. Furthermore, a comparison with traditional prediction methods including the modified solubility equation and the quantitative structure-property relationships model was carried out. The highest accuracy shown by the testing set proves that the ML models have the best solubility prediction ability. Multiple linear regression and stepwise regression were used to further investigate the critical factor in determining solubility value. The results revealed that the API properties and the solute-solvent interaction both provide a nonnegligible contribution to the solubility value.

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Keywords

solubility prediction / machine learning / artificial neural network / random decision forests

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Yiming Ma, Zhenguo Gao, Peng Shi, Mingyang Chen, Songgu Wu, Chao Yang, Jing-Kang Wang, Jingcai Cheng, Junbo Gong. Machine learning-based solubility prediction and methodology evaluation of active pharmaceutical ingredients in industrial crystallization. Front. Chem. Sci. Eng., 2022, 16(4): 523‒535 https://doi.org/10.1007/s11705-021-2083-5

References

[1]
Ma H, Qu Y, Zhou Z, Wang S, Li L. Solubility of thiotriazinone in binary solvent mixtures of water+ methanol and water+ ethanol from (283 to 330) K. Journal of Chemical & Engineering Data, 2012, 57(8): 2121–2127
CrossRef Google scholar
[2]
Maher A, Rasmuson Å, Croker D, Hodnett B. Solubility of the metastable polymorph of piracetam (Form II) in a range of solvents. Journal of Chemical & Engineering Data, 2012, 57(12): 3525–3531
CrossRef Google scholar
[3]
Ma Y, Wu S, Macaringue E, Zhang T, Gong J, Wang J. Recent progress in continuous crystallization of pharmaceutical products: precise preparation and control. Organic Process Research & Development, 2020, 24(10): 1785–1801
CrossRef Google scholar
[4]
Wang Y, Du S, Wu S, Li L, Zhang D, Yu B, Zhou L, Bekele H, Gong J. Thermodynamic and molecular investigation into the solubility, stability and self-assembly of gabapentin anhydrate and hydrate. Journal of Chemical Thermodynamics, 2017, 113: 132–143
CrossRef Google scholar
[5]
Wang X, Zhang D, Liu S, Chen Y, Jia L, Wu S. Thermodynamic study of solubility for imatinib mesylate in nine monosolvents and two binary solvent mixtures from 278.15 to 318.15 K. Journal of Chemical & Engineering Data, 2018, 63(11): 4114–4127
CrossRef Google scholar
[6]
Kiwala D, Olbrycht M, Balawejder M, Piątkowski W, Seidel-Morgenstern A, Antos D. Separation of stereoisomeric mixtures of nafronyl as a representative of compounds possessing two stereogenic centers by coupling crystallization, diastereoisomeric conversion and chromatography. Organic Process Research & Development, 2016, 20(3): 615–625
CrossRef Google scholar
[7]
Qi R, Wang J, Ye J, Hao H, Bao Y. The solubility of cefquinome sulfate in pure and mixed solvents. Frontiers of Chemical Science and Engineering, 2016, 10(2): 245–254
CrossRef Google scholar
[8]
Herrmannsdörfer D, Stierstorfer J, Klapötke T. Solubility behaviour of CL-20 and HMX in organic solvents and solvates of CL-20. Energetic Materials Frontiers, 2021, 2(1): 51–61
CrossRef Google scholar
[9]
Boobier S, Hose D, Blacker A, Nguyen B. Machine learning with physicochemical relationships: solubility prediction in organic solvents and water. Nature Communications, 2020, 11(1): 5753
CrossRef Google scholar
[10]
Cui Q, Lu S, Ni B, Zeng X, Tan Y, Chen Y, Zhao H. Improved prediction of aqueous solubility of novel compounds by going deeper with deep learning. Frontiers in Oncology, 2020, 10: 121
CrossRef Google scholar
[11]
Perryman A, Inoyama D, Patel J, Ekins S, Freundlich J. Pruned machine learning models to predict aqueous solubility. ACS Omega, 2020, 5(27): 16562–16567
CrossRef Google scholar
[12]
ChemAxon. ChemAxon Website, 2020
[13]
Ran Y, Yalkowsky S. Prediction of drug solubility by the general solubility equation (GSE). Journal of Chemical Information and Modeling, 2001, 32(22): 354–357
[14]
Ellegaard D, Abildskov J, O’Connell J. Molecular thermodynamic modeling of mixed solvent solubility. Industrial & Engineering Chemistry Research, 2010, 49(22): 11620–11632
CrossRef Google scholar
[15]
Acree W Jr, Che M, Lee G, Abraham M. Calculation of the Abraham model solute descriptors for the pharmaceutical compound acipimox based on experimental solubility data. Physics and Chemistry of Liquids, 2018, 57(3): 382–387
CrossRef Google scholar
[16]
Sun H, Shah P, Nguyen K, Yu K, Kerns E, Kabir M, Wang Y, Xu X. Predictive models of aqueous solubility of organic compounds built on A large dataset of high integrity. Bioorganic & Medicinal Chemistry, 2019, 27(14): 3110–3114
CrossRef Google scholar
[17]
Salahinejad M, Le T, Winkler D. Aqueous solubility prediction: do crystal lattice interactions help? Molecular Pharmaceutics, 2013, 10(7): 2757–2766
CrossRef Google scholar
[18]
Chinta S, Rengaswamy R. Machine learning derived quantitative structure property relationship (QSPR) to predict drug solubility in binary solvent systems. Industrial & Engineering Chemistry Research, 2019, 58(8): 3082–3092
CrossRef Google scholar
[19]
Fioressi S, Bacelo D, Rojas C, Aranda J, Duchowicz P. Conformation-independent quantitative structure-property relationships study on water solubility of pesticides. Ecotoxicology and Environmental Safety, 2019, 171: 47–53
CrossRef Google scholar
[20]
Wahab O, Olasunkanmi L, Govender K, Govender P. Prediction of aqueous solubility by treatment of COSMO-RS data with empirical solubility equations: the roles of global orbital cut-off and COSMO solvent radius. Theoretical Chemistry Accounts, 2019, 138(6): 80
CrossRef Google scholar
[21]
Abranches D, Benfica J, Shimizu S, Coutinho J. Solubility enhancement of hydrophobic substances in water/cyrene mixtures: a computational study. Industrial & Engineering Chemistry Research, 2020, 59(40): 18247–18253
CrossRef Google scholar
[22]
Modarresi E, Abildskov J, Gani R, Crafts P. Model-based calculation of solid solubility for solvent selections: a review. Industrial & Engineering Chemistry Research, 2008, 47(15): 5234–5242
CrossRef Google scholar
[23]
Shang C, You F. Data analytics and machine learning for smart process manufacturing: recent advances and perspectives in the big data era. Engineering, 2019, 5(6): 1010–1016
CrossRef Google scholar
[24]
Xie Y, Zhang C, Hu X, Zhang C, Kelley S, Atwood J, Lin J. Machine learning assisted synthesis of metal-organic nanocapsules. Journal of the American Chemical Society, 2020, 142(3): 1475–1481
CrossRef Google scholar
[25]
Dong Y, Wu C, Zhang C, Liu Y, Cheng J, Lin J. Bandgap prediction by deep learning in configurationally hybridized graphene and boron nitride. npj Computational Materials, 2019, 5, 26
[26]
Xin D, Gonnella N, He X, Horspool K. Solvate prediction for pharmaceutical organic molecules with machine learning. Crystal Growth & Design, 2019, 19(3): 1903–1911
CrossRef Google scholar
[27]
Ghosh A, Louis L, Arora K, Hancock B, Krzyzaniak J, Meenan P, Nakhmanson S, Wood G. Assessment of machine learning approaches for predicting the crystallization propensity of active pharmaceutical ingredients. CrystEngComm, 2019, 21(8): 1215–1223
CrossRef Google scholar
[28]
Paengjuntuek W, Thanasinthana L, Arpornwichanop A. Neural network-based optimal control of a batch crystallizer. Neurocomputing, 2012, 83: 158–164
CrossRef Google scholar
[29]
Han D, Karmakar T, Bjelobrk Z, Gong J, Parrinello M. Solvent-mediated morphology selection of the active pharmaceutical ingredient isoniazid: experimental and simulation studies. Chemical Engineering Science, 2018, 204: 320–328
CrossRef Google scholar
[30]
Wang N, Huang X, Gong H, Zhou Y, Li X, Li F, Bao Y, Xie C, Wang Z, Yin Q, Hao H. Thermodynamic mechanism of selective cocrystallization explored by MD simulation and phase diagram analysis. AIChE Journal. American Institute of Chemical Engineers, 2019, 65(5): e16570
CrossRef Google scholar
[31]
Ma Y, Cao Y, Yang Y, Li W, Shi P, Wang S, Tang W. Thermodynamic analysis and molecular dynamic simulation of the solubility of vortioxetine hydrobromide in three binary solvent mixtures. Journal of Molecular Liquids, 2018, 272: 676–688
CrossRef Google scholar
[32]
Zhang T, Li Z, Wang Y, Li C, Yu B, Zheng X, Jiang L, Gong J. Determination and correlation of solubility and thermodynamic properties of l-methionine in binary solvents of water+ (methanol, ethanol, acetone). Journal of Chemical Thermodynamics, 2016, 96: 82–92
CrossRef Google scholar
[33]
Raudino A, Sarpietro M, Pannuzzo M. Differential scanning calorimetry (DSC): theoretical fundamentals. In: Drug-Biomembrane Interaction Studies. Pignatello R, ed. Cambridge, UK: Woodhead Publishing Limited, 2013: 127–168
[34]
Foca G, Marchetti A, Tassi L, Ulrici A. Modelling of experimental thermophysical data by mixing of a ternary solvent system. Solution Chemistry Research Progress, 2011: 5–49
[35]
Price S, Brandenburg J. Molecular crystal structure prediction. Non-Covalent Interactions in Quantum Chemistry and Physics, 2017, 333–363
[36]
Shi P, Ma Y, Han D, Du S, Zhang T, Li Z. Uncovering the solubility behavior of vitamin B6 hydrochloride in three aqueous binary solvents by thermodynamic analysis and molecular dynamic simulation. Journal of Molecular Liquids, 2019, 283: 584–595
CrossRef Google scholar
[37]
Zhao S, Ma Y, Tang W. Thermodynamic analysis and molecular dynamic simulation of solid-liquid phase equilibrium of griseofulvin in three binary solvent systems. Journal of Molecular Liquids, 2019, 294: 111600
CrossRef Google scholar
[38]
Rong G, Mendez A, Bou Assi E, Zhao B, Sawan M. Artificial intelligence in healthcare: review and prediction case studies. Engineering, 2020, 6(3): 291–301
CrossRef Google scholar
[39]
Vegh J. How Amdahl’s Law limits the performance of large artificial neural networks: why the functionality of full-scale brain simulation on processor-based simulators is limited. Brain Informatics, 2019, 6(1): 4
CrossRef Google scholar
[40]
Xu J, Chen Y, Xie T, Zhao X, Xiong B, Chen Z. Prediction of triaxial behavior of recycled aggregate concrete using multivariable regression and artificial neural network techniques. Construction & Building Materials, 2019, 226: 534–554
CrossRef Google scholar
[41]
Rosenblatt F. The perception: a probabilistic model for information storage and organization in the brain. Psychological Review, 1988, 65(6): 89–114
[42]
McDonagh J, Nath N, De Ferrari L, van Mourik T, Mitchell J. Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules. Journal of Chemical Information and Modeling, 2014, 54(3): 844–856
CrossRef Google scholar
[43]
Rizkin B, Hartman R. Supervised machine learning for prediction of zirconocene-catalyzed α-olefin polymerization. Chemical Engineering Science, 2019, 210: 115224
CrossRef Google scholar
[44]
Breiman L. Random forests. Machine Learning, 2001, 45(1): 5–32
CrossRef Google scholar
[45]
Ho T. Random decision forest. In: Proceedings of 3rd International Conference on Document Analysis and Recongnition. Montreal, Canada, 1995, 278–282
[46]
Lee S, Kim J, Moon N. Random forest and WiFi fingerprint-based indoor location recognition system using smart watch. Human-centric Computing and Information Sciences, 2019, 9(1): 6
CrossRef Google scholar
[47]
de Santana F, Borges Neto W, Poppi R. Random forest as one-class classifier and infrared spectroscopy for food adulteration detection. Food Chemistry, 2019, 293: 323–332
CrossRef Google scholar
[48]
Zhou T, Sun X, Xia X, Li B, Chen X. Improving defect prediction with deep forest. Information and Software Technology, 2019, 114: 204–216
CrossRef Google scholar
[49]
Tarasova A, Burden F, Gasteiger J, Winkler D. Robust modelling of solubility in supercritical carbon dioxide using Bayesian methods. Journal of Molecular Graphics & Modelling, 2010, 28(7): 593–597
CrossRef Google scholar
[50]
Le T, Epa V, Burden F, Winkler D. Quantitative structure-property relationship modeling of diverse materials properties. Chemical Reviews, 2012, 112(5): 2889–2919
CrossRef Google scholar
[51]
Clark A, Labute P. Detection and assignment of common scaffolds in project databases of lead molecules. Journal of Medicinal Chemistry, 2009, 52(2): 469–483
CrossRef Google scholar
[52]
Molecular Operating Environment (MOE). Version 2019.0102. Montreal: Chemical Computing Group ULC, 2019

Acknowledgments

This work was financially supported by the National Natural Science Foundation of China (Grant No. 21938009).

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://dx.doi.org/10.1007/s11705-021-2083-5 and is accessible for authorized users.

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