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Computational Study of Furosemide-Piperazine (FS – PZ) and 2,3,5,6-tetramethylpyrazine (FS-TP) Co-Crystals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Quantum study of DHA, DPA and EPA anticancer fatty acids for microscopic explanation of their biological functions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Latosińska JN, Latosińska M, Szafrański M, Seliger J, Žagar V, Burchardt DV. Impact of structural differences in carcinopreventive agents indole-3-carbinol and 3,3'-diindolylmethane on biological activity. An X-ray, ¹H-¹⁴N NQDR, ¹³C CP/MAS NMR, and periodic hybrid DFT study. Eur J Pharm Sci 2015; 77:141-53. [PMID: 26066413 DOI: 10.1016/j.ejps.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
Three experimental techniques (1)H-(14)N NQDR, (13)C CP/MAS NMR and X-ray and Density Functional Theory (GGA/BLYP with PBC) and Hirshfeld surfaces were applied for the structure-activity oriented studies of two phyto-antioxidants and anticarcinogens: indole-3-carbinol, I3C, and 3,3'-diindolylmethane, DIM, (its bioactive metabolite). One set of (14)N NQR frequencies for DIM (2.310, 2.200 and 0.110 MHz at 295K) and I3C (2.315, 1.985 and 0.330 MHz at 160K) was recorded. The multiplicity of NQR lines recorded at RT revealed high symmetry (chemical and physical equivalence) of both methyl indazole rings of DIM. Carbonyl (13)C CSA tensor components were calculated from the (13)C CP/MAS solid state NMR spectrum of I3C recorded under fast and slow spinning. At room temperature the crystal structure of I3C is orthorhombic: space group Pca21, Z=4, a=5.78922(16), b=15.6434(7) and c=8.4405(2)Å. The I3C molecules are aggregated into ribbons stacked along [001]. The oxygen atomsare disorderedbetween the two sites of different occupancy factors. It implies that the crystal is built of about 70% trans and 30% gauche conformers, and apart from the weak OH⋯O hydrogen bonds (O⋯O=3.106Å) the formation of alternative O'H⋯O bonds (O'⋯O=2.785Å) is possible within the 1D ribbons. The adjacent ribbons are further stabilised by O'H⋯O bonds (O'⋯O=2.951Å). The analysis of spectra and intermolecular interactions pattern by experimental techniques was supported by solid (periodic) DFT calculations. The knowledge of the topology and competition of the interactions in crystalline state shed some light on the preferred conformations of CH2OH in I3C and steric hindrance of methyl indole rings in DIM. A comparison of the local environment in gas phase and solid permitted drawing some conclusions on the nature of the interactions required for effective processes of recognition and binding of a given anticarcinogen to the protein or nucleic acid.
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Affiliation(s)
| | - Magdalena Latosińska
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Marek Szafrański
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland
| | - Janez Seliger
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia; "Jozef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Veselko Žagar
- "Jozef Stefan" Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Dorota V Burchardt
- Department of Paediatric Dentistry, Poznan University of Medical Sciences, Bukowska 70, 60-812 Poznań, Poland
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Honarparvar B, Pawar SA, Alves CN, Lameira J, Maguire GE, Silva JRA, Govender T, Kruger HG. Pentacycloundecane lactam vs lactone norstatine type protease HIV inhibitors: binding energy calculations and DFT study. J Biomed Sci 2015; 22:15. [PMID: 25889635 PMCID: PMC4387594 DOI: 10.1186/s12929-015-0115-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/16/2015] [Indexed: 01/12/2023] Open
Abstract
Background Novel pentacycloundecane (PCU)-lactone-CO-EAIS peptide inhibitors were designed, synthesized, and evaluated against wild-type C-South African (C-SA) HIV-1 protease. Three compounds are reported herein, two of which displayed IC50 values of less than 1.00 μM. A comparative MM-PB(GB)SA binding free energy of solvation values of PCU-lactam and lactone models and their enantiomers as well as the PCU-lactam-NH-EAIS and lactone-CO-EAIS peptide inhibitors and their corresponding diastereomers complexed with South African HIV protease (C-SA) was performed. This will enable us to rationalize the considerable difference between inhibitory concentration (IC50) of PCU-lactam-NH-EAIS and PCU-lactone-CO-EAIS peptides. Results The PCU-lactam model exhibited more negative calculated binding free energies of solvation than the PCU-lactone model. The same trend was observed for the PCU-peptide inhibitors, which correspond to the experimental activities for the PCU-lactam-NH-EAIS peptide (IC50 = 0.076 μM) and the PCU-lactone-CO-EAIS peptide inhibitors (IC50 = 0.850 μM). Furthermore, a density functional theory (DFT) study on the natural atomic charges of the nitrogen and oxygen atoms of the three PCU-lactam, PCU-lactim and PCU-lactone models were performed using natural bond orbital (NBO) analysis. Electrostatic potential maps were also used to visualize the electron density around electron-rich regions. The asymmetry parameter (η) and quadrupole coupling constant (χ) values of the nitrogen and oxygen nuclei of the model compounds were calculated at the same level of theory. Electronic molecular properties including polarizability and electric dipole moments were also calculated and compared. The Gibbs theoretical free solvation energies of solvation (∆Gsolv) were also considered. Conclusions A general trend is observed that the lactam species appears to have a larger negative charge distribution around the heteroatoms, larger quadrupole constant, dipole moment and better solvation energy, in comparison to the PCU-lactone model. It can be argued that these characteristics will ensure better eletronic interaction between the lactam and the receptor, corresponding to the observed HIV protease activities in terms of experimental IC50 data. Electronic supplementary material The online version of this article (doi:10.1186/s12929-015-0115-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Sachin A Pawar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110, Belém, PA, Brazil.
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110, Belém, PA, Brazil.
| | - Glenn Em Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CP 11101, 66075-110, Belém, PA, Brazil.
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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Latosinńska JN. Applications of nuclear quadrupole resonance spectroscopy in drug development. Expert Opin Drug Discov 2013; 2:225-48. [PMID: 23496079 DOI: 10.1517/17460441.2.2.225] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this review, fundamentals of nuclear quadrupole resonance (NQR) spectroscopy are briefly outlined. Examples of its applications in drug development are discussed to demonstrate that the NQR method is a sophisticated, non-destructive and valuable analytical technique for studying pharmaceuticals, providing effective assistance at the two main steps of drug development: the physical and chemical characterization of the active pharmaceutical ingredients (API) at the analytical step and API development. This review covers different aspects of the use of NQR spectroscopy for drug development and analysis and illustrates the power and versatility of this method in the determination of impurities, polymorphic forms, the drug's structure and conformation, characterization of the interactions between the drug and ligands, search for analogs (second- or third-generation drugs) and the drug's thermal stability. Lastly, NQR advantages and restrictions in the aspect of application in drug development studies are summarized.
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Affiliation(s)
- Jolanta N Latosinńska
- Adam Mickiewicz University, Institute of Physics, Umultowska 85, 61-614 Poznańn, Poland.
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Shi JQ, Qiu J, Sun L, Wang M, Wang FY, Wang ZY. Partial physicochemical properties and relative stability of polyhydroxylated dibenzofurans: theoretical and experimental study. J Mol Graph Model 2012; 38:396-410. [PMID: 23085181 DOI: 10.1016/j.jmgm.2012.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 05/10/2012] [Accepted: 05/15/2012] [Indexed: 11/16/2022]
Abstract
Polyhydroxylated dibenzofuran (PHODF) is an important degradation product of polychlorinated dibenzofuran (PCDF). Four types of hydrogen bonds (the one between a hydroxyl and the oxygen atom in the matrix, between hydroxyls at ortho positions, between the oxygen atom of hydroxyl at position 1 and the hydrogen atom of the matrix at position 9, and between hydroxyls at positions 1 and 9) exist in PHODFs. The energies of the hydrogen bonds were ascertained by comparing the two configurational isomers as approximately 8-11 kJ mol⁻¹, 16-21 kJ mol⁻¹, 5-8 kJ mol⁻¹ and 23-25 kJ mol⁻¹, respectively. An experiment was designed to verify the bond energies, and the entrance geometry on main paths was studied by AIM 2000 program. The most stable in each group of configurational isomers was ascertained on the basis of evaluating the effect of hydrogen bonds. Their thermodynamic properties (standard state entropy S°, standard enthalpy Δ(f)H° and standard Gibbs energy of formation Δ(f)G°) were calculated from the combination of density functional theory (DFT) at B3LYP/6-311G** level and isodesmic reactions. Octanol/water partition coefficients (log K(ow)) were calculated on line with molinspiration methodology based on group contributions. The number and position of hydroxyl substitution (N(PHOS)) can be a good indicator of these properties for all stable PHODF congeners. The configurations most likely to form are those with a hydrogen bond (Type IV). How intramolecular hydrogen bond influences ionization was also investigated and the first-order ionization constant for each stable conformation was obtained with the self-consistent reaction field (SCRF) method.
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Affiliation(s)
- Jia-Qi Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210046, PR China
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Mollaamin F, Monajjemi M. DFT outlook of solvent effect on function of nano bioorganic drugs. PHYSICS AND CHEMISTRY OF LIQUIDS 2012. [DOI: 10.1080/00319104.2011.646444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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An innovative method for the non-destructive identification of photodegradation products in solid state: 1H–14N NMR–NQR and DFT/QTAIM study of photodegradation of nifedipine (anti-hypertensive) to nitrosonifedipine (potential anti-oxidative). Eur J Pharm Sci 2012; 47:97-107. [DOI: 10.1016/j.ejps.2012.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/15/2012] [Accepted: 05/02/2012] [Indexed: 11/18/2022]
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Latosińska JN, Latosińska M, Tomczak MA, Seliger J, Zagar V. Supramolecular synthon pattern in solid clioquinol and cloxiquine (APIs of antibacterial, antifungal, antiaging and antituberculosis drugs) studied by ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR and DFT/QTAIM. J Mol Model 2010; 17:1781-800. [PMID: 21080020 PMCID: PMC3126996 DOI: 10.1007/s00894-010-0876-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 10/11/2010] [Indexed: 11/29/2022]
Abstract
The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via 35Cl NQR, 1H-17O and 1H-14N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O–H···N hydrogen bonds linking dimers and π–π stacking interactions were described within the QTAIM (quantum theory of atoms in molecules) /DFT (density functional theory) formalism. Both proton donor and acceptor sites in O–H···N bonds were characterized using 1H-17O and 1H-14N NQDR spectroscopies and QTAIM. The possibility of the existence of O–H···H–O dihydrogen bonds was excluded. The weak intermolecular interactions in the crystals of clioquinol and cloxiquine were detected and examined. The results obtained in this work suggest that considerable differences in the NQR parameters for the planar and twisted supramolecular synthons permit differentiation between specific polymorphic forms, and indicate that the more planar supramolecular synthons are accompanied by a greater number of weaker hydrogen bonds linking them and stronger π···π stacking interactions. The 1H-14N solid effect double resonance spectra and the relief map of the Laplacian of electron density in the OH...N plane for clioquinol and cloxiquine ![]()
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Seliger J, Žagar V, Latosińska JN. 14N NQR, 1H NMR and DFT/QTAIM study of hydrogen bonding and polymorphism in selected solid 1,3,4-thiadiazole derivatives. Phys Chem Chem Phys 2010; 12:13007-19. [DOI: 10.1039/c0cp00195c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chiş V, Pîrnău A, Vasilescu M, Varga RA, Oniga O. X-ray, 1H NMR and DFT study on 5-para-X-benzylidene-thiazolidine derivatives with X=Br, F. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.10.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Latosińska JN. Nuclear Quadrupole Resonance spectroscopy in studies of biologically active molecular systems—a review. J Pharm Biomed Anal 2005; 38:577-87. [PMID: 15908157 DOI: 10.1016/j.jpba.2005.03.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 03/17/2005] [Indexed: 11/19/2022]
Abstract
The main idea of this work was to give an overview of the NQR capabilities in the search for a correlation between electronic structure and biological activity of certain compounds, mainly drugs. A correlation between the parameters characterising biological activity and the NQR spectral parameters describing chemical properties of a given compound, permits drawing conclusions on biological effectiveness of compounds from a certain group. The quadrupole coupling constants, which are very well correlated with atomic charges, can be treated as descriptors in QSAR. The information inferred from NQR study on local electron density distribution together with analysis of charge distribution, provides excellent means for determination of reactive sites and hence, can indicate possible promising directions to be followed in drugs design.
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Affiliation(s)
- J N Latosińska
- Institute of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznań, Poland.
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