1
|
Cysewski P, Przybyłek M, Jeliński T. Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures. MATERIALS (BASEL, SWITZERLAND) 2023; 16:6336. [PMID: 37763610 PMCID: PMC10532775 DOI: 10.3390/ma16186336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
Dapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS: 112-57-2), and diethylene glycol bis(3-aminopropyl) ether (CAS: 4246-51-9). Furthermore, the study proposes the use of intermolecular interactions as molecular descriptors to predict the solubility of dapsone in neat solvents and binary mixtures using machine learning models. An ensemble of regressors was used, including support vector machines, random forests, gradient boosting, and neural networks. Affinities of dapsone to solvent molecules were calculated using COSMO-RS and used as input for model training. Due to the polymorphic nature of dapsone, fusion data are not available, which prohibits the direct use of COSMO-RS for solubility calculations. Therefore, a consonance solvent approach was tested, which allows an indirect estimation of the fusion properties. Unfortunately, the resulting accuracy is unsatisfactory. In contrast, the developed regressors showed high predictive potential. This work documents that intermolecular interactions characterized by solute-solvent contacts can be considered valuable molecular descriptors for solubility modeling and that the wealth of encoded information is sufficient for solubility predictions for new systems, including those for which experimental measurements of thermodynamic properties are unavailable.
Collapse
Affiliation(s)
- Piotr Cysewski
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-096 Bydgoszcz, Poland; (M.P.); (T.J.)
| | | | | |
Collapse
|
2
|
Przybyłek M, Miernicka A, Nowak M, Cysewski P. New Screening Protocol for Effective Green Solvents Selection of Benzamide, Salicylamide and Ethenzamide. Molecules 2022; 27:3323. [PMID: 35630800 PMCID: PMC9144492 DOI: 10.3390/molecules27103323] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023] Open
Abstract
New protocol for screening efficient and environmentally friendly solvents was proposed and experimentally verified. The guidance for solvent selection comes from computed solubility via COSMO-RS approach. Furthermore, solute-solvent affinities computed using advanced quantum chemistry level were used as a rationale for observed solvents ranking. The screening protocol pointed out that 4-formylomorpholine (4FM) is an attractive solubilizer compared to commonly used aprotic solvents such as DMSO and DMF. This was tested experimentally by measuring the solubility of the title compounds in aqueous binary mixtures in the temperature range between 298.15 K and 313.15 K. Additional measurements were also performed for aqueous binary mixtures of DMSO and DMF. It has been found that the solubility of studied aromatic amides is very high and quite similar in all three aprotic solvents. For most aqueous binary mixtures, a significant decrease in solubility with a decrease in the organic fraction is observed, indicating that all systems can be regarded as efficient solvent-anti-solvent pairs. In the case of salicylamide dissolved in aqueous-4FM binary mixtures, a strong synergistic effect has been found leading to the highest solubility for 0.6 mole fraction of 4-FM.
Collapse
Affiliation(s)
- Maciej Przybyłek
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland; (A.M.); (M.N.)
| | | | | | - Piotr Cysewski
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland; (A.M.); (M.N.)
| |
Collapse
|
3
|
Recent Developments of Computational Methods for pKa Prediction Based on Electronic Structure Theory with Solvation Models. J 2021. [DOI: 10.3390/j4040058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The protonation/deprotonation reaction is one of the most fundamental processes in solutions and biological systems. Compounds with dissociative functional groups change their charge states by protonation/deprotonation. This change not only significantly alters the physical properties of a compound itself, but also has a profound effect on the surrounding molecules. In this paper, we review our recent developments of the methods for predicting the Ka, the equilibrium constant for protonation reactions or acid dissociation reactions. The pKa, which is a logarithm of Ka, is proportional to the reaction Gibbs energy of the protonation reaction, and the reaction free energy can be determined by electronic structure calculations with solvation models. The charge of the compound changes before and after protonation; therefore, the solvent effect plays an important role in determining the reaction Gibbs energy. Here, we review two solvation models: the continuum model, and the integral equation theory of molecular liquids. Furthermore, the reaction Gibbs energy calculations for the protonation reactions require special attention to the handling of dissociated protons. An efficient method for handling the free energy of dissociated protons will also be reviewed.
Collapse
|
4
|
Mbous YP, Hayyan M, Wong WF, Hayyan A, Looi CY, Hashim MA. Simulation of Deep Eutectic Solvents' Interaction with Membranes of Cancer Cells Using COSMO-RS. J Phys Chem B 2020; 124:9086-9094. [PMID: 32930594 DOI: 10.1021/acs.jpcb.0c04801] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deep eutectic solvent (DES) affinities with cellular membranes structures dictate the degree of cytotoxicity that results from these interactions. The physicochemical properties of choline chloride (ChCl)-DESs suggest non-negligible cytotoxicities that were attested by published researches. In this study, the profiles of novel N,N-diethylammonium chloride (DAC)-based-deep eutectic solvents (DESs) prepared with various hydrogen bond donors (urea, glycerol, ethylene glycol, malonic acid, and zinc chloride) were compared to those of ChCl-DESs by using HelaS3, AGS, MCF-7, and WRL-68 cancer cell lines. The molecular interactions between salts and cellular membranes were investigated to explain the observed cytotoxicity. The results show that ChCl-based DESs (279 ≤ IC50 ≥ 1260 mM) were less toxic than DAC-based DESs (37 ≤ IC50 ≥ 109 mM). COSMO-RS analysis emphasized the importance of salt hydrophobicity with regards to DESs cytotoxicity. Malonic acid increased hydrophobicity and cytotoxicity in general, thus highlighting the potential of ammonium salt-based DESs as anticancer agents.
Collapse
Affiliation(s)
- Yves Paul Mbous
- Department of Pharmaceutical Systems and Policy, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Maan Hayyan
- Chemical Engineering Program, Faculty of Engineering and Technology, Muscat University, P.O. Box 550, Muscat P.C. 130, Oman.,University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Won Fen Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Adeeb Hayyan
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia.,Centre for Separation Science & Technology (CSST), Faculty of Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chung Yeng Looi
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Mohd Ali Hashim
- University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, Kuala Lumpur 50603, Malaysia.,Department of Chemical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur 50603, Malaysia
| |
Collapse
|
5
|
Pracht P, Wilcken R, Udvarhelyi A, Rodde S, Grimme S. High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge. J Comput Aided Mol Des 2018; 32:1139-1149. [PMID: 30141103 DOI: 10.1007/s10822-018-0145-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.
Collapse
Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Rainer Wilcken
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland.
| | - Anikó Udvarhelyi
- Novartis Pharma AG, Technical Research and Development, 4002, Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany.
| |
Collapse
|
6
|
Bochevarov AD, Watson MA, Greenwood JR, Philipp DM. Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups. J Chem Theory Comput 2016; 12:6001-6019. [PMID: 27951674 DOI: 10.1021/acs.jctc.6b00805] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Art D. Bochevarov
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark A. Watson
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jeremy R. Greenwood
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dean M. Philipp
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States
| |
Collapse
|
7
|
Hayyan M, Mbous YP, Looi CY, Wong WF, Hayyan A, Salleh Z, Mohd-Ali O. Natural deep eutectic solvents: cytotoxic profile. SPRINGERPLUS 2016; 5:913. [PMID: 27386357 PMCID: PMC4927554 DOI: 10.1186/s40064-016-2575-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/15/2016] [Indexed: 01/15/2023]
Abstract
The purpose of this study was to investigate the cytotoxic profiles of different ternary natural deep eutectic solvents (NADESs) containing water. For this purpose, five different NADESs were prepared using choline chloride as a salt, alongside five hydrogen bond donors (HBD) namely glucose, fructose, sucrose, glycerol, and malonic acid. Water was added as a tertiary component during the eutectics preparation, except for the malonic acid-based mixture. Coincidentally, the latter was found to be more toxic than any of the water-based NADESs. A trend was observed between the cellular requirements of cancer cells, the viscosity of the NADESs, and their cytotoxicity. This study also highlights the first time application of the conductor-like screening model for real solvent (COSMO-RS) software for the analysis of the cytotoxic mechanism of NADESs. COSMO-RS simulation of the interactions between NADESs and cellular membranes' phospholipids suggested that NADESs strongly interacted with cell surfaces and that their accumulation and aggregation possibly defined their cytotoxicity. This reinforced the idea that careful selection of NADESs components is necessary, as it becomes evident that organic acids as HBD highly contribute to the increasing toxicity of these neoteric mixtures. Nevertheless, NADESs in general seem to possess relatively less acute toxicity profiles than their DESs parents. This opens the door for future large scale utilization of these mixtures.
Collapse
Affiliation(s)
- Maan Hayyan
- />University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, 50603 Kuala Lumpur, Malaysia
- />Department of Civil Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yves Paul Mbous
- />University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, 50603 Kuala Lumpur, Malaysia
- />Department of Chemical Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chung Yeng Looi
- />Department of Pharmacology, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Won Fen Wong
- />Department of Medical Microbiology, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Adeeb Hayyan
- />University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, 50603 Kuala Lumpur, Malaysia
- />Institute of Halal Research University of Malaya (IHRUM), Academy of Islamic Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Zulhaziman Salleh
- />University of Malaya Centre for Ionic Liquids (UMCiL), University of Malaya, 50603 Kuala Lumpur, Malaysia
- />Department of Chemical Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ozair Mohd-Ali
- />UiTM Medical Specialist Centre, University of Technology MARA, Jalan Hospital, 47000 Sungai Buloh, Selangor, Malaysia
| |
Collapse
|
8
|
Theoretical description of 2D-cluster formation of nonionic surfactants at the air/water interface. Colloid Polym Sci 2015. [DOI: 10.1007/s00396-015-3630-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
Collapse
Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| |
Collapse
|
10
|
Andersson MP, Bennetzen MV, Klamt A, Stipp SLS. First-Principles Prediction of Liquid/Liquid Interfacial Tension. J Chem Theory Comput 2014; 10:3401-8. [DOI: 10.1021/ct500266z] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- M. P. Andersson
- Nano-Science
Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen
Ø DK-2100, Denmark
| | | | - A. Klamt
- COSMOlogic GmbH&CoKG, Imbacher Weg 46, D-51379 Leverkusen, Germany
- Institute
of Physical and Theoretical Chemistry, Universität Regensburg, 93053 Regensburg, Germany
| | - S. L. S Stipp
- Nano-Science
Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen
Ø DK-2100, Denmark
| |
Collapse
|
11
|
Andersson MP, Olsson MHM, Stipp SLS. Predicting the pKa and stability of organic acids and bases at an oil-water interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:6437-45. [PMID: 24823316 DOI: 10.1021/la5008318] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We have used density functional theory and the implicit solvent model, COSMO-RS, to investigate how the acidity constant, pKa, of organic acids and bases adsorbed at the organic compound-aqueous solution interface changes, compared to its value in the aqueous phase. The pKa determine the surface charge density of the molecules that accumulate at the fluid-fluid interface. We have estimated the pKa by comparing the stability of the protonated and unprotonated forms of a series of molecules in the bulk aqueous solution and at an interface where parts of each molecule reside in the hydrophobic phase and the rest remains in the hydrophilic phase. We found that the pKa for acids is shifted by ∼1 pH unit to higher values compared to the bulk water pKa, whereas they are shifted to lower values by a similar amount for bases. Because this pKa shift is similar in magnitude for each of the molecules studied, we propose that the pKa for molecules at a water-organic compound interface can easily be predicted by adding a small shift to the aqueous pKa. This shift is general and correlates with the functional group. We also found that the relative composition of molecules at the fluid-fluid interface is not the same as in the bulk. For example, species such as carboxylic acids are enriched at the interface, where they can dominate surface properties, even when they are a modest component in the bulk fluid. For high surface concentrations of carboxylic acid groups at an interface, such as a self-assembled monolayer, we have demonstrated that the pKa depends on the degree of deprotonation through direct hydrogen bonding between protonated and deprotonated acidic headgroups.
Collapse
Affiliation(s)
- M P Andersson
- Nano-Science Center, Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen OE, Denmark
| | | | | |
Collapse
|