1
|
Bursik B, Eller J, Gross J. Predicting Solvation Free Energies from the Minnesota Solvation Database Using Classical Density Functional Theory Based on the PC-SAFT Equation of State. J Phys Chem B 2024; 128:3677-3688. [PMID: 38579126 DOI: 10.1021/acs.jpcb.3c07447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
We critically assess the capabilities of classical density functional theory (DFT) based on the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state to predict the solvation free energies of small molecules in various hydrocarbon solvents. We compare DFT results with experimental data from the Minnesota solvation database and utilize statistical methods to analyze the accuracy of our approach, as well as its weaknesses. The mean absolute error of the solvation free energies is 3.7 kJ mol-1 for n-alkane solvents, ranging from pentane to hexadecane, with 473 solute-solvent systems. For solvents consisting of cyclic hydrocarbons (cyclohexane, benzene, toluene, and ethylbenzene) with 245 solute-solvent systems, we report a slightly larger mean absolute error of 4.2 kJ mol-1. We identify three possible sources of errors: (i) the neglect of solute-solvent and solvent-solvent Coulomb interactions, which limits the applicability of PC-SAFT DFT to nonpolar and weakly polar molecules; (ii) the solute's Lennard-Jones parameters supplied by the general AMBER force field, which are not parametrized toward solvation free energies; and (iii) the application of the Lorentz-Berthelot combining rules to the dispersive interactions between a segment of the PC-SAFT solvent and a Lennard-Jones interaction site of the solute. The approach is more accurate than standard implementations of phenomenological models in common chemistry software packages, which exhibit mean absolute errors larger than 9.12 kJ mol-1, even though newer phenomenological models achieve a mean absolute error of about 2 kJ mol-1. PC-SAFT DFT is more computationally efficient than state of the art explicit molecular simulations in combination with free energy perturbation methods. It is predictive with respect to solvation free energies, i.e., the input for the model is the (element-specific) molecular force field, the solute configuration from molecular dynamics simulations, and the (substance-specific) PC-SAFT parameters. The PC-SAFT parametrization uses pure-component data and does not require experimental solvation free energies. The PC-SAFT equation of state, without applying a DFT formalism, can also be used to calculate solvation free energies, provided that the PC-SAFT parameters for the solute are available. A large number of substances was recently parametrized by members of our group (Esper, T.; Bauer, G.; Rehner, P.; Gross, J. Ind. Eng. Chem. Res. 2023, 62), which enables a comparison to the DFT approach for 103 substances. Accurate results are obtained from the PC-SAFT equation of state with an MAE below 2.51 kJ mol-1. The DFT approach does not require PC-SAFT parameters for the solute and can be applied to all solutes that can be represented by the molecular force field.
Collapse
Affiliation(s)
- Benjamin Bursik
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Johannes Eller
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Stuttgart 70569, Germany
| |
Collapse
|
2
|
Reppas C, Kuentz M, Bauer-Brandl A, Carlert S, Dallmann A, Dietrich S, Dressman J, Ejskjaer L, Frechen S, Guidetti M, Holm R, Holzem FL, Karlsson Ε, Kostewicz E, Panbachi S, Paulus F, Senniksen MB, Stillhart C, Turner DB, Vertzoni M, Vrenken P, Zöller L, Griffin BT, O'Dwyer PJ. Leveraging the use of in vitro and computational methods to support the development of enabling oral drug products: An InPharma commentary. Eur J Pharm Sci 2023; 188:106505. [PMID: 37343604 DOI: 10.1016/j.ejps.2023.106505] [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: 03/13/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023]
Abstract
Due to the strong tendency towards poorly soluble drugs in modern development pipelines, enabling drug formulations such as amorphous solid dispersions, cyclodextrins, co-crystals and lipid-based formulations are frequently applied to solubilize or generate supersaturation in gastrointestinal fluids, thus enhancing oral drug absorption. Although many innovative in vitro and in silico tools have been introduced in recent years to aid development of enabling formulations, significant knowledge gaps still exist with respect to how best to implement them. As a result, the development strategy for enabling formulations varies considerably within the industry and many elements of empiricism remain. The InPharma network aims to advance a mechanistic, animal-free approach to the assessment of drug developability. This commentary focuses current status and next steps that will be taken in InPharma to identify and fully utilize 'best practice' in vitro and in silico tools for use in physiologically based biopharmaceutic models.
Collapse
Affiliation(s)
- Christos Reppas
- Department of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Martin Kuentz
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz CH 4132, Switzerland
| | - Annette Bauer-Brandl
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark
| | | | - André Dallmann
- Pharmacometrics/Modeling and Simulation, Research and Development, Pharmaceuticals, Bayer AG, Leverkusen, Germany
| | - Shirin Dietrich
- Department of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Jennifer Dressman
- Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | - Lotte Ejskjaer
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sebastian Frechen
- Pharmacometrics/Modeling and Simulation, Research and Development, Pharmaceuticals, Bayer AG, Leverkusen, Germany
| | - Matteo Guidetti
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark; Solvias AG, Department for Solid-State Development, Römerpark 2, 4303 Kaiseraugst, Switzerland
| | - René Holm
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark
| | - Florentin Lukas Holzem
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark; Pharmaceutical R&D, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | | | - Edmund Kostewicz
- Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | - Shaida Panbachi
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz CH 4132, Switzerland
| | - Felix Paulus
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark
| | - Malte Bøgh Senniksen
- Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany; Pharmaceutical R&D, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Cordula Stillhart
- Pharmaceutical R&D, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | | | - Maria Vertzoni
- Department of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Paul Vrenken
- Department of Pharmacy, National and Kapodistrian University of Athens, Greece; Pharmacometrics/Modeling and Simulation, Research and Development, Pharmaceuticals, Bayer AG, Leverkusen, Germany
| | - Laurin Zöller
- AstraZeneca R&D, Gothenburg, Sweden; Fraunhofer Institute of Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | | | | |
Collapse
|
3
|
Iyer J, Brunsteiner M, Modhave D, Paudel A. Role of Crystal Disorder and Mechanoactivation in Solid-State Stability of Pharmaceuticals. J Pharm Sci 2023; 112:1539-1565. [PMID: 36842482 DOI: 10.1016/j.xphs.2023.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/28/2023]
Abstract
Common energy-intensive processes applied in oral solid dosage development, such as milling, sieving, blending, compaction, etc. generate particles with surface and bulk crystal disorder. An intriguing aspect of the generated crystal disorder is its evolution and repercussion on the physical- and chemical stabilities of drugs. In this review, we firstly examine the existing literature on crystal disorder and its implications on solid-state stability of pharmaceuticals. Secondly, we discuss the key aspects related to the generation and evolution of crystal disorder, dynamics of the disordered/amorphous phase, analytical techniques to measure/quantify them, and approaches to model the disordering propensity from first principles. The main objective of this compilation is to provide special impetus to predict or model the chemical degradation(s) resulting from processing-induced manifestation in bulk solid manufacturing. Finally, a generic workflow is proposed that can be useful to investigate the relevance of crystal disorder on the degradation of pharmaceuticals during stability studies. The present review will cater to the requirements for developing physically- and chemically stable drugs, thereby enabling early and rational decision-making during candidate screening and in assessing degradation risks associated with formulations and processing.
Collapse
Affiliation(s)
- Jayant Iyer
- Research Center Pharmaceutical Engineering GmbH (RCPE), Graz, Austria
| | | | - Dattatray Modhave
- Research Center Pharmaceutical Engineering GmbH (RCPE), Graz, Austria
| | - Amrit Paudel
- Research Center Pharmaceutical Engineering GmbH (RCPE), Graz, Austria; Graz University of Technology, Institute of Process and Particle Engineering, Graz Austria.
| |
Collapse
|
4
|
Discovery solubility measurement and assessment of small molecules with drug development in mind. Drug Discov Today 2022; 27:1315-1325. [PMID: 35114363 DOI: 10.1016/j.drudis.2022.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/04/2022] [Accepted: 01/27/2022] [Indexed: 12/24/2022]
Abstract
Solubility is a key physicochemical property for the success of any drug candidate. Although the methods used and their rationales for determining solubility are subject to project needs and stages along the drug discovery-drug development pipeline, an artificial boundary can exist at the discovery-development interface. This boundary results in less effective solubility knowledge sharing and data integration among scientists in both drug discovery and drug development. Herein, we present a refreshed perspective on solubility. Solubility experimentation is not a one-size-fits-all measurement; instead, we stress the importance of constructing a seamless solubility understanding of a molecule as it progresses from a new chemical entity into a drug product.
Collapse
|
5
|
Fowles DJ, Palmer DS, Guo R, Price SL, Mitchell JBO. Toward Physics-Based Solubility Computation for Pharmaceuticals to Rival Informatics. J Chem Theory Comput 2021; 17:3700-3709. [PMID: 33988381 PMCID: PMC8190954 DOI: 10.1021/acs.jctc.1c00130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
We demonstrate that
physics-based calculations of intrinsic aqueous
solubility can rival cheminformatics-based machine learning predictions.
A proof-of-concept was developed for a physics-based approach via
a sublimation thermodynamic cycle, building upon previous work that
relied upon several thermodynamic approximations, notably the 2RT approximation, and limited conformational sampling. Here,
we apply improvements to our sublimation free-energy model with the
use of crystal phonon mode calculations to capture the contributions
of the vibrational modes of the crystal. Including these improvements
with lattice energies computed using the model-potential-based Ψmol method leads to accurate estimates of sublimation free
energy. Combining these with hydration free energies obtained from
either molecular dynamics free-energy perturbation simulations or
density functional theory calculations, solubilities comparable to
both experiment and informatics predictions are obtained. The application
to coronene, succinic acid, and the pharmaceutical desloratadine shows
how the methods must be adapted for the adoption of different conformations
in different phases. The approach has the flexibility to extend to
applications that cannot be covered by informatics methods.
Collapse
Affiliation(s)
- Daniel J Fowles
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Rui Guo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - John B O Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Scotland KY16 9ST, U.K
| |
Collapse
|
6
|
Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
Collapse
Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
| |
Collapse
|
7
|
Abramov YA, Sun G, Zeng Q, Zeng Q, Yang M. Guiding Lead Optimization for Solubility Improvement with Physics-Based Modeling. Mol Pharm 2020; 17:666-673. [DOI: 10.1021/acs.molpharmaceut.9b01138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Yuriy A. Abramov
- XtalPi Inc, 245 Main Street, Cambridge, Massachusetts 02142, United States
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Guangxu Sun
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Qiao Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Qun Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Mingjun Yang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| |
Collapse
|
8
|
Duarte Ramos Matos G, Mobley DL. Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules. F1000Res 2019; 7:686. [PMID: 30109026 PMCID: PMC6069752 DOI: 10.12688/f1000research.14960.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule. Methods: Chemical potentials were estimated from all-atom molecular dynamics simulations. We used the Einstein molecule method (EMM) to predict the absolute chemical potential of the solid and solvation free energy calculations to predict the excess chemical potentials of the liquid-phase systems. Results: Reliable estimations of the chemical potentials for the solid and for a single ASA molecule using the EMM required an extremely large number of intermediate states for the free energy calculations, meaning that the calculations were extremely demanding computationally. Despite the computational cost, however, the computed value did not agree well with the experimental value, potentially due to limitations with the underlying energy model. Perhaps better values could be obtained with a better energy model; however, it seems likely computational cost may remain a limiting factor for use of this particular approach to solubility estimation. Conclusions: Solubility prediction of drug-like solids remains computationally challenging, and it appears that both the underlying energy model and the computational approach applied may need improvement before the approach is suitable for routine use.
Collapse
Affiliation(s)
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Irvine, California, USA.,Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine, Irvine, California, USA
| |
Collapse
|
9
|
Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2017; 62:1559-1569. [PMID: 29056756 PMCID: PMC5648357 DOI: 10.1021/acs.jced.7b00104] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.
Collapse
Affiliation(s)
- Guilherme Duarte Ramos Matos
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Daisy Y Kyu
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Hannes H Loeffler
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - John D Chodera
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - Michael R Shirts
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine
| |
Collapse
|
10
|
Palmer DS, Mitchell JBO. Is Experimental Data Quality the Limiting Factor in Predicting the Aqueous Solubility of Druglike Molecules? Mol Pharm 2014; 11:2962-72. [DOI: 10.1021/mp500103r] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David S. Palmer
- Department
of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral
Street, Glasgow, Scotland G1 1XL, U.K
| | - John B. O. Mitchell
- Biomedical
Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews, Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, U.K
| |
Collapse
|
11
|
McDonagh JL, Nath N, De Ferrari L, van Mourik T, Mitchell JBO. Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules. J Chem Inf Model 2014; 54:844-56. [PMID: 24564264 PMCID: PMC3965570 DOI: 10.1021/ci4005805] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We
present four models of solution free-energy prediction for druglike
molecules utilizing cheminformatics descriptors and theoretically
calculated thermodynamic values. We make predictions of solution free
energy using physics-based theory alone and using machine learning/quantitative
structure–property relationship (QSPR) models. We also develop
machine learning models where the theoretical energies and cheminformatics
descriptors are used as combined input. These models are used to predict
solvation free energy. While direct theoretical calculation does not
give accurate results in this approach, machine learning is able to
give predictions with a root mean squared error (RMSE) of ∼1.1
log S units in a 10-fold cross-validation for our
Drug-Like-Solubility-100 (DLS-100) dataset of 100 druglike molecules.
We find that a model built using energy terms from our theoretical
methodology as descriptors is marginally less predictive than one
built on Chemistry Development Kit (CDK) descriptors. Combining both
sets of descriptors allows a further but very modest improvement in
the predictions. However, in some cases, this is a statistically significant
enhancement. These results suggest that there is little complementarity
between the chemical information provided by these two sets of descriptors,
despite their different sources and methods of calculation. Our machine
learning models are also able to predict the well-known Solubility
Challenge dataset with an RMSE value of 0.9–1.0 log S units.
Collapse
Affiliation(s)
- James L McDonagh
- Biomedical Sciences Research Complex and ‡EaStCHEM, School of Chemistry, Purdie Building, University of St. Andrews , North Haugh, St. Andrews, Scotland , KY16 9ST, United Kingdom
| | | | | | | | | |
Collapse
|
12
|
Dandapani S, Rosse G, Southall N, Salvino JM, Thomas CJ. Selecting, Acquiring, and Using Small Molecule Libraries for High-Throughput Screening. ACTA ACUST UNITED AC 2012; 4:177-191. [PMID: 26705509 DOI: 10.1002/9780470559277.ch110252] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The selection, acquisition and use of high quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libraries continue to evolve as researchers gain a greater appreciation of the suitability of small molecules for specific biological targets, processes and environments. The decisions surrounding the make-up of any given small molecule library is informed by a multitude of variables and opinions vary on best-practices. The fitness of any collection relies upon upfront filtering to avoiding problematic compounds, assess appropriate physicochemical properties, install the ideal level of structural uniqueness and determine the desired extent of molecular complexity. These criteria are under constant evaluation and revision as academic and industrial organizations seek out collections that yield ever improving results from their screening portfolios. Practical questions including cost, compound management, screening sophistication and assay objective also play a significant role in the choice of library composition. This overview attempts to offer advice to all organizations engaged in small molecule screening based upon current best practices and theoretical considerations in library selection and acquisition.
Collapse
Affiliation(s)
- Sivaraman Dandapani
- Chemical Biology Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge Massachusetts 02142 USA
| | - Gerard Rosse
- Dart NeuroScience LLC, 7473 Lusk Boulevard, San Diego, CA 92121 USA
| | - Noel Southall
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Joseph M Salvino
- Alliance Discovery, Inc, Biotechnology Center 3805 Old Easton Road, Doylestown, PA 18902 USA
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| |
Collapse
|
13
|
Palmer DS, McDonagh JL, Mitchell JBO, van Mourik T, Fedorov MV. First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules. J Chem Theory Comput 2012; 8:3322-37. [PMID: 26605739 DOI: 10.1021/ct300345m] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that the intrinsic aqueous solubility of crystalline druglike molecules can be estimated with reasonable accuracy from sublimation free energies calculated using crystal lattice simulations and hydration free energies calculated using the 3D Reference Interaction Site Model (3D-RISM) of the Integral Equation Theory of Molecular Liquids (IET). The solubilities of 25 crystalline druglike molecules taken from different chemical classes are predicted by the model with a correlation coefficient of R = 0.85 and a root mean square error (RMSE) equal to 1.45 log10S units, which is significantly more accurate than results obtained using implicit continuum solvent models. The method is not directly parametrized against experimental solubility data, and it offers a full computational characterization of the thermodynamics of transfer of the drug molecule from crystal phase to gas phase to dilute aqueous solution.
Collapse
Affiliation(s)
- David S Palmer
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
| | - James L McDonagh
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - John B O Mitchell
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Tanja van Mourik
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Maxim V Fedorov
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
| |
Collapse
|
14
|
Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. J Chem Theory Comput 2012; 8:1721-1736. [PMID: 22582032 PMCID: PMC3348590 DOI: 10.1021/ct300035u] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.
Collapse
Affiliation(s)
- Michael J. Schnieders
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Jonas Baltrusaitis
- Departments of Chemistry and Chemical/Biochemical Engineering, University of Iowa, Iowa City, IA, 52242
| | - Yue Shi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Gaurav Chattree
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Lianqing Zheng
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| |
Collapse
|
15
|
Guha R, Dexheimer TS, Kestranek AN, Jadhav A, Chervenak AM, Ford MG, Simeonov A, Roth GP, Thomas CJ. Exploratory analysis of kinetic solubility measurements of a small molecule library. Bioorg Med Chem 2011; 19:4127-34. [PMID: 21640593 PMCID: PMC3236531 DOI: 10.1016/j.bmc.2011.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 04/29/2011] [Accepted: 05/04/2011] [Indexed: 11/20/2022]
Abstract
Kinetic solubility measurements using prototypical assay buffer conditions are presented for a ∼58,000 member library of small molecules. Analyses of the data based upon physical and calculated properties of each individual molecule were performed and resulting trends were considered in the context of commonly held opinions of how physicochemical properties influence aqueous solubility. We further analyze the data using a decision tree model for solubility prediction and via a multi-dimensional assessment of physicochemical relationships to solubility in the context of specific 'rule-breakers' relative to common dogma. The role of solubility as a determinant of assay outcome is also considered based upon each compound's cross-assay activity score for a collection of publicly available screening results. Further, the role of solubility as a governing factor for colloidal aggregation formation within a specified assay setting is examined and considered as a possible cause of a high cross-assay activity score. The results of this solubility profile should aid chemists during library design and optimization efforts and represent a useful training set for computational solubility prediction.
Collapse
Affiliation(s)
- Rajarshi Guha
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Thomas S. Dexheimer
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Aimee N. Kestranek
- Analiza, Inc., 3615 Superior Avenue, Suite 4407B, Cleveland, OH 44114 USA
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | | | - Michael G. Ford
- Analiza, Inc., 3615 Superior Avenue, Suite 4407B, Cleveland, OH 44114 USA
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| | - Gregory P. Roth
- Sanford–Burnham Medical Research Institute at Lake Nona, Conrad Prebys Center for Chemical Genomics, 6400 Sanger Road, Orlando, Florida 32827
| | - Craig J. Thomas
- NIH Chemical Genomics Center, National Human Genome Research Institute, NIH 9800 Medical Center Drive, MSC 3370 Bethesda, MD 20892-3370 USA
| |
Collapse
|
16
|
Moučka F, Lísal M, Škvor J, Jirsák J, Nezbeda I, Smith WR. Molecular Simulation of Aqueous Electrolyte Solubility. 2. Osmotic Ensemble Monte Carlo Methodology for Free Energy and Solubility Calculations and Application to NaCl. J Phys Chem B 2011; 115:7849-61. [DOI: 10.1021/jp202054d] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filip Moučka
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
| | - Martin Lísal
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - Jiří Škvor
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
| | - Jan Jirsák
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - Ivo Nezbeda
- E. Hála Laboratory of Thermodynamics, Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6, Czech Republic
| | - William R. Smith
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON L1H7K4, Canada
| |
Collapse
|
17
|
Persson R, Nordholm S, Perlovich G, Lindfors L. Monte Carlo Studies of Drug Nucleation 1: Formation of Crystalline Clusters of Bicalutamide in Water. J Phys Chem B 2011; 115:3062-72. [DOI: 10.1021/jp111817h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rasmus Persson
- Department of Chemistry, University of Gothenburg, Sweden
| | - Sture Nordholm
- Department of Chemistry, University of Gothenburg, Sweden
| | - German Perlovich
- Institute of Solution Chemistry, Russian Academy of Science, Ivanovo, Russia
| | | |
Collapse
|
18
|
Abstract
This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein–ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.
Collapse
|
19
|
Chebil L, Chipot C, Archambault F, Humeau C, Engasser JM, Ghoul M, Dehez F. Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents. J Phys Chem B 2010; 114:12308-13. [DOI: 10.1021/jp104569k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Latifa Chebil
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Christophe Chipot
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Fabien Archambault
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Catherine Humeau
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Jean Marc Engasser
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Mohamed Ghoul
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - François Dehez
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| |
Collapse
|
20
|
Shayanfar A, Fakhree M, Jouyban A. A simple QSPR model to predict aqueous solubility of drugs. J Drug Deliv Sci Technol 2010. [DOI: 10.1016/s1773-2247(10)50080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|