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Bettadj FZY, Benchouk W. Computer-aided analysis for identification of novel analogues of ketoprofen based on molecular docking, ADMET, drug-likeness and DFT studies for the treatment of inflammation. J Biomol Struct Dyn 2023; 41:9915-9930. [PMID: 36444967 DOI: 10.1080/07391102.2022.2148750] [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: 08/11/2022] [Accepted: 11/12/2022] [Indexed: 11/30/2022]
Abstract
Computer-based drug design is increasingly used in strategies for discovering new molecules for therapeutic purposes. The targeted drug is ketoprofen (KTP), which belongs to the family of non-steroidal anti-inflammatory drugs, which are widely used for the treatment of pain, fever, inflammation and certain types of cancers. In an attempt to rationalize the search for 72 new potential anti-inflammatory compounds on the COX-2 enzyme, we carried out an in silico protocol that successfully combines molecular docking towards COX-2 receptor (5F1A), ADMET pharmacokinetic parameters, drug-likeness rules and molecular electrostatic potential (MEP). It was found that six of the compounds analyzed satisfy with the associated values to physico-chemical properties as key evaluation parameters for the drug-likeness and demonstrate a hydrophobic character which makes their solubility in aqueous media difficult and easy in lipids. All the compounds presented good ADMET profile and they showed an interaction with the amino acids responsible for anti-inflammatory activity of the COX-2 isoenzyme. The calculation of the MEP of the six analogues reveals new preferential sites involving the formation of new bonds. Consequently, this result allowed us to understand the origin of the potential increase in the anti-inflammatory activity of the candidates. Finally, it was obtained that six compounds have a binding mode, binding energy, and stability in the active site of COX-2 like the reference drug ketoprofen, suggesting that these compounds could become a powerful candidate in the inhibition of the COX-2 enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatima Zohra Yasmine Bettadj
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
| | - Wafaa Benchouk
- Laboratory of Applied Thermodynamics and Molecular Modeling, Department of Chemistry, Faculty of Science, University of Tlemcen, Tlemcen, Algeria
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2
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Kozakiewicz-Latała M, Marciniak D, Krajewska K, Złocińska A, Prusik K, Karolewicz B, Nartowski KP, Pudło W. Hierarchical Macro-Mesoporous Silica Monolithic Tablets as a Novel Dose-Structure-Dependent Delivery System for the Release of Confined Dexketoprofen. Mol Pharm 2023; 20:641-649. [PMID: 36533661 PMCID: PMC9811460 DOI: 10.1021/acs.molpharmaceut.2c00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This study reports the application of hierarchical porous monoliths as carriers for controlled and dose-adjustable release of model pharmaceutical (dexketoprofen, DEX). The synthesis and detailed characterization of the hierarchical porous scaffolds are provided before and after the adsorption of three doses of DEX─a widely used nonsteroidal anti-inflammatory drug. The drug incorporated in the mesopores of silica was stabilized in an amorphous state, while the presence of macropores provided sufficient space for drug crystallization as we demonstrated via a combination of powder X-ray diffraction, differential scanning calorimetry, and imaging techniques (scanning electron microscopy and EDX analysis). Drug release from silica matrices was tested, and a mechanistic model of this release based on the Fick diffusion equation was proposed. The hierarchical structure of the carrier, due to the presence of micrometric macropores and nanometric mesopores, turned out to be critical for the control of the drug phase and drug release from the monoliths. It was found that at low drug content, the presence of an amorphous component in the pores promoted the rapid release of the drug, while at higher drug contents, the presence of macropores favored the crystallization of DEX, which naturally slowed down its release. Both the hierarchical porous structure and the control of the drug phase (amorphous and/or crystalline) were proven important for adjustable (fast or prolonged) release kinetics, desirable for effective pharmacotherapy and patient compliance. Therefore, the developed materials may serve as a versatile formulation platform for the smart manipulation of drug release kinetics.
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Affiliation(s)
- Marta Kozakiewicz-Latała
- Department
of Drug Forms Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland
| | - Dominik Marciniak
- Department
of Drug Forms Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland
| | - Karolina Krajewska
- Department
of Drug Forms Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland
| | - Adrianna Złocińska
- Laboratory
of Elemental Analysis Structural Research, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland
| | - Krystian Prusik
- Institute
of Materials Engineering, University of
Silesia in Katowice, 75 Pulku Piechoty 1A, Chorzow40-007, Poland,Silesian
Center for Education and Interdisciplinary Research, University of Silesia in Katowice, 75 Pulku Piechoty 1A, Chorzow40-007, Poland
| | - Bożena Karolewicz
- Department
of Drug Forms Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland
| | - Karol P. Nartowski
- Department
of Drug Forms Technology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, Wroclaw50-556, Poland,
| | - Wojciech Pudło
- Department
of Chemical Engineering and Process Design, Silesian University of Technology, Gliwice44-100, Poland,
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3
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Rodríguez-Ortega PG, Sánchez-Valera M, López-González JJ, Montejo M. Fourier Transform Infrared Spectroscopy and Vibrational Circular Dichroism Assisted Elucidation of the Solution-State Supramolecular Speciation in Racemic and Enantiopure Ketoprofen. APPLIED SPECTROSCOPY 2022; 76:216-227. [PMID: 35001646 DOI: 10.1177/00037028211060073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The molecular structure and solution-state molecular interactions in the popular non-steroidal anti-inflammatory drug, ketoprofen, are extensively studied with the aim of gaining a better understanding of the chemical behavior of its solution state and its connection to its nucleation pathway and crystallization outcome. Using as reference solid-state X-ray structures of enantiomeric and racemic forms of ketoprofen, a set of self-assembly models underpinned by density functional theory calculations has been considered for the analysis of spectroscopic data, infrared (IR) and vibrational circular dichroism (VCD), obtained for solutions of the samples as a function of composition and solvent. From our results it can be concluded that, contrary to the general belief for generic carboxylic acids, there are no cyclic dimeric structures of ketoprofen present in solution, but rather linear arrays made up of two (in high polar or diluted media) or more units (in low polar or low dilution media). This observation is in line with the idea that the weak contacts (other than H-bonding) would hold the key to molecular self-assembly, in agreement with recent studies on other aromatic carboxylic acids.
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Affiliation(s)
| | | | | | - Manuel Montejo
- Department of Physical and Analytical Chemistry, 16747University of Jaén, Jaén, Spain
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4
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de Oliveira Junior H, Borges BA, Barbosa TWL, Batista A, Braga MTL, de Araújo MB, Bonfilio R. A New Crystalline Ketoprofen Sodium Salt: Solid-State Characterization, Solubility, and Stability. J Pharm Sci 2021; 111:1674-1681. [PMID: 34808219 DOI: 10.1016/j.xphs.2021.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
Ketoprofen (KTP) is an Active Pharmaceutical Ingredient (API) that has low solubility in aqueous solvents. The use of KTP salts has attracted attention due to its improvements in terms of solubility, tolerability, higher rate and extent of absorption, and faster onset of the therapeutic effect. In this work, a crystalline KTP sodium salt (coded as KTP-Na) was successfully obtained and widely characterized by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), solubility and accelerated stability studies. XRD results showed that KTP-Na is not yet reported in the literature. Moreover, FTIR, DSC and TGA were useful for differentiation of KTP-Na from the KTP commercialized form (coded as KTP-R1). The solubility of KTP-Na in water was about 80 times greater than the KTP-R1. However, KTP-Na showed lower physical stability in storage conditions at 40 ± 2°C/ 75% ± 5% RH when compared to KTP-R1, which was shown to be related to a high hygroscopicity of KTP-Na. Therefore, due to its higher solubility, KTP-Na may be a viable alternative for use in solid dosage forms. However, the presence of moisture must be strictly controlled to avoid water absorption and consequent amorphization.
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Affiliation(s)
- Homero de Oliveira Junior
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil
| | - Bruno Arantes Borges
- Institute of Chemistry, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil
| | | | - Ataislaine Batista
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil
| | - Maria Teresa Leite Braga
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil
| | - Magali Benjamim de Araújo
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil
| | - Rudy Bonfilio
- Faculty of Pharmaceutical Sciences, Federal University of Alfenas (UNIFAL-MG), Alfenas, Minas Gerais 37130-001, Brazil.
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5
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Stanton SA, Du JJ, Lai F, Stanton G, Hawkins BA, Ong JA, Groundwater PW, Platts JA, Hibbs DE. Understanding Hygroscopicity of Theophylline via a Novel Cocrystal Polymorph: A Charge Density Study. J Phys Chem A 2021; 125:9736-9756. [PMID: 34731566 DOI: 10.1021/acs.jpca.0c09536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The charge density distribution in a novel cocrystal (1) complex of 1,3-dimethylxanthine (theophylline) and propanedioic acid (malonic acid) has been determined. The molecules crystallize in the triclinic, centrosymmetric space group P1̅, with four independent molecules (Z = 4) in the asymmetric unit (two molecules each of theophylline and malonic acid). Theophylline has a notably high hygroscopic nature, and numerous cocrystals have shown a significant improvement in stability to humidity. A charge density study of the novel polymorph has identified interesting theoretical results correlating the stability enhancement of theophylline via cocrystallization. Topological analysis of the electron density highlighted key differences (up to 17.8) in Laplacian (∇2ρ) between the experimental (EXP) and single-point (SP) models, mainly around intermolecular-bonded carbonyls. Further investigation via molecular electrostatic potential maps reaffirmed that the charge redistribution enhanced intramolecular hydrogen bonding, predominantly for N(2') and N(2) (61.2 and 61.8 kJ mol-1, respectively). An overall weaker lattice energy of the triclinic form (-126.1 kJ mol-1) compared to that of the monoclinic form (-133.8 kJ mol-1) suggests a lower energy threshold to overcome to initiate dissociation. Future work via physical testing of the novel cocrystal in both dissolution and solubility will further solidify the correlation between theoretical and experimental results.
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Affiliation(s)
- Stephen A Stanton
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathan J Du
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Felcia Lai
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gyte Stanton
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Bryson A Hawkins
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jennifer A Ong
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Paul W Groundwater
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - James A Platts
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - David E Hibbs
- Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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6
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Betlejewska-Kielak K, Bednarek E, Budzianowski A, Michalska K, Maurin JK. Comprehensive Characterisation of the Ketoprofen-β-Cyclodextrin Inclusion Complex Using X-ray Techniques and NMR Spectroscopy. Molecules 2021; 26:molecules26134089. [PMID: 34279429 PMCID: PMC8271474 DOI: 10.3390/molecules26134089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022] Open
Abstract
Racemic ketoprofen (KP) and β-cyclodextrin (β-CD) powder samples from co-precipitation (1), evaporation (2), and heating-under-reflux (3) were analysed using X-ray techniques and nuclear magnetic resonance (NMR) spectroscopy. On the basis of NMR studies carried out in an aqueous solution, it was found that in the samples obtained by methods 1 and 2, there were large excesses of β-CD in relation to KP, 10 and 75 times, respectively, while the sample obtained by method 3 contained equimolar amounts of β-CD and KP. NMR results indicated that KP/β-CD inclusion complexes were formed and the estimated binding constants were approximately 2400 M-1, showing that KP is quite strongly associated with β-CD. On the other hand, the X-ray single-crystal technique in the solid state revealed that the (S)-KP/β-CD inclusion complex with a stoichiometry of 2:2 was obtained as a result of heating-under-reflux, for which the crystal and molecular structure were examined. Among the methods used for the preparation of the KP/β-CD complex, only method 3 is suitable.
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Affiliation(s)
| | - Elżbieta Bednarek
- Falsified Medicines and Medical Devices Department, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (E.B.); (J.K.M.)
| | | | - Katarzyna Michalska
- Department of Synthetic Drugs, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland;
- Correspondence: ; Tel.: +48-(22)-841-18-88 (ext. 369)
| | - Jan K. Maurin
- Falsified Medicines and Medical Devices Department, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (E.B.); (J.K.M.)
- National Centre for Nuclear Research, A. Sołtana 7, 05-400 Otwock, Poland;
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7
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Ziemniak M, Zawadzka-Kazimierczuk A, Pawlędzio S, Malinska M, Sołtyka M, Trzybiński D, Koźmiński W, Skora S, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose. Int J Mol Sci 2021; 22:3720. [PMID: 33918425 PMCID: PMC8038202 DOI: 10.3390/ijms22073720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maja Sołtyka
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Stanisław Skora
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
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8
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Gobbo D, Ballone P, Decherchi S, Cavalli A. Solubility Advantage of Amorphous Ketoprofen. Thermodynamic and Kinetic Aspects by Molecular Dynamics and Free Energy Approaches. J Chem Theory Comput 2020; 16:4126-4140. [PMID: 32463689 DOI: 10.1021/acs.jctc.0c00166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermodynamic and kinetic aspects of crystalline (c-KTP) and amorphous (a-KTP) ketoprofen dissolution in water have been investigated by molecular dynamics simulation focusing on free energy properties. Absolute free energies of all relevant species and phases have been determined by thermodynamic integration on a novel path, first connecting the harmonic to the anharmonic system Hamiltonian at low T and then extending the result to the temperature of interest. The free energy required to transfer one ketoprofen molecule from the crystal to the solution is in fair agreement with the experimental value. The absolute free energy of the amorphous form is 19.58 kJ/mol higher than for the crystal, greatly enhancing the ketoprofen concentration in water, although as a metastable species in supersaturated solution. The kinetics of the dissolution process has been analyzed by computing the free energy profile along a reaction coordinate bringing one ketoprofen molecule from the crystal or amorphous phase to the solvated state. This computation confirms that, compared to the crystal form, the dissolution rate is nearly 7 orders of magnitude faster for the amorphous form, providing one further advantage to the latter in terms of bioavailability. The problem of drug solubility, of great practical importance, is used here as a test bed for a refined method to compute absolute free energies, which could be of great interest in biophysics and drug discovery in particular.
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Affiliation(s)
- D Gobbo
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - P Ballone
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy.,School of Physics, University College Dublin, Dublin, Ireland.,Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - S Decherchi
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - A Cavalli
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy.,University of Bologna, Bologna 40126, Italy
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9
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Jagan R, Boopathi K. Hydrogen-Bonded Supramolecular Framework, Hirshfeld Surface Analysis and Interaction Energy Studies on 2-Amino-5-Chloropyridinium P-Toluenesulfonate. J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620010163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Köhler C, Lübben J, Krause L, Hoffmann C, Herbst-Irmer R, Stalke D. Comparison of different strategies for modelling hydrogen atoms in charge density analyses. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:434-441. [PMID: 32830665 DOI: 10.1107/s2052520619004517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/03/2019] [Indexed: 06/11/2023]
Abstract
The quality of various approximation methods for modelling anisotropic displacement parameters (ADPs) for hydrogen atoms was investigated in a comparative study. A multipole refinement was performed against high-resolution single crystal X-ray data of 9-diphenylthiophosphoranylanthracene (SPAnH) and 9,10-bis-diphenylthiophosphoranylanthracene·toluene (SPAnPS). Hydrogen-atom parameters and structural properties derived from our collected neutron data sets were compared with those obtained from the SHADE-server, the software APD-Toolkit based on the invariom database, the results from Hirshfeld atom refinement conducted in the OLEX2 GUI (HARt), and the results of anisotropic hydrogen refinement within XD2016. Additionally, a free refinement of H-atom positions against X-ray data was performed with fixed ADPs from various methods. The resulting C-H bond distances were compared with distances from neutron diffraction experiments and the HARt results. Surprisingly, the refinement of anisotropic hydrogen displacement parameters against the X-ray data yielded the smallest deviations from the neutron values. However, the refinement of bond-directed quadrupole parameters turned out to be vital for the quality of the resulting ADPs. In both model structures, SHADE and, to a lesser extent, APD-Toolkit showed problems in dealing with atoms bonded to carbon atoms with refined Gram-Charlier parameters for anharmonic motion. The HARt method yields the most accurate C-H bond distances compared to neutron data results. Unconstrained refinement of hydrogen atom positions using ADPs derived from all other used approximation methods showed that even with well approximated hydrogen ADPs, the resulting distances were still significantly underestimated.
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Affiliation(s)
- Christian Köhler
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Jens Lübben
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Lennard Krause
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus, 8000, Denmark
| | - Christina Hoffmann
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
| | - Regine Herbst-Irmer
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Dietmar Stalke
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany
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