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Pacoste L, Ignat’ev VM, Dominiak PM, Zou X. On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors. IUCRJ 2024; 11:878-890. [PMID: 39146197 PMCID: PMC11364031 DOI: 10.1107/s2052252524006730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/09/2024] [Indexed: 08/17/2024]
Abstract
This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.
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Affiliation(s)
- Laura Pacoste
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSweden
| | | | - Paulina Maria Dominiak
- Biological and Chemical Research Center, Faculty of ChemistryUniversity of WarsawWarsawPoland
| | - Xiaodong Zou
- Department of Materials and Environmental ChemistryStockholm UniversityStockholmSweden
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2
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Krawczuk A, Genoni A. Current developments and trends in quantum crystallography. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:S2052520624003421. [PMID: 38888407 PMCID: PMC11301899 DOI: 10.1107/s2052520624003421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/17/2024] [Indexed: 06/20/2024]
Abstract
Quantum crystallography is an emerging research field of science that has its origin in the early days of quantum physics and modern crystallography when it was almost immediately envisaged that X-ray radiation could be somehow exploited to determine the electron distribution of atoms and molecules. Today it can be seen as a composite research area at the intersection of crystallography, quantum chemistry, solid-state physics, applied mathematics and computer science, with the goal of investigating quantum problems, phenomena and features of the crystalline state. In this article, the state-of-the-art of quantum crystallography will be described by presenting developments and applications of novel techniques that have been introduced in the last 15 years. The focus will be on advances in the framework of multipole model strategies, wavefunction-/density matrix-based approaches and quantum chemical topological techniques. Finally, possible future improvements and expansions in the field will be discussed, also considering new emerging experimental and computational technologies.
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Affiliation(s)
- Anna Krawczuk
- Institut für Anorganische Chemie, Georg-August-Universität, Tammannstraße 4, Göttingen, 37077, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRSLaboratoire de Physique et Chimie Théoriques1 Boulevard AragoMetz57078France
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3
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Zwolenik A, Tchoń D, Makal A. Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure. IUCRJ 2024; 11:519-527. [PMID: 38727170 PMCID: PMC11220879 DOI: 10.1107/s2052252524003634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 07/04/2024]
Abstract
A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV-Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of -55.8 (57) MK-1 in the direction of C-H...O interactions.
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Affiliation(s)
- A. Zwolenik
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawŻwirki i Wigury 10102-089WarszawaPoland
| | - D. Tchoń
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawŻwirki i Wigury 10102-089WarszawaPoland
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National Laboratory,1 Cyclotron RoadBerkeleyCA94720USA
| | - A. Makal
- Biological and Chemical Research Centre, Faculty of ChemistryUniversity of WarsawŻwirki i Wigury 10102-089WarszawaPoland
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4
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Kumar A, Jha KK, Olech B, Goral T, Malinska M, Woźniak K, Dominiak PM. TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules. Acta Crystallogr C Struct Chem 2024; 80:264-277. [PMID: 38934273 PMCID: PMC11225613 DOI: 10.1107/s2053229624005357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.
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Affiliation(s)
- Anil Kumar
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
| | - Kunal Kumar Jha
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Barbara Olech
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Tomasz Goral
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Maura Malinska
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
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5
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Hawash M, Qneibi M, Natsheh H, Mohammed NH, Hamda LA, Kumar A, Olech B, Dominiak PM, Bdir S, Bdair M. Evaluating the Neuroprotective Potential of Novel Benzodioxole Derivatives in Parkinson's Disease via AMPA Receptor Modulation. ACS Chem Neurosci 2024; 15:2334-2349. [PMID: 38747411 DOI: 10.1021/acschemneuro.4c00163] [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] [Indexed: 06/06/2024] Open
Abstract
Parkinson's disease (PD) is a significant health issue because it gradually damages the nervous system. α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors play a significant role in the development of PD. The current investigation employed hybrid benzodioxole-propanamide (BDZ-P) compounds to get information on AMPA receptors, analyze their biochemical and biophysical properties, and assess their neuroprotective effects. Examining the biophysical characteristics of all the subunits of the AMPA receptor offers insights into the impact of BDZ-P on the desensitization and deactivation rate. It demonstrates a partial improvement in the locomotor capacities in a mouse model of Parkinson's disease. In addition, the in vivo experiment assessed the locomotor activity by utilizing the open-field test. Our findings demonstrated that BDZ-P7 stands out with its remarkable potency, inhibiting the GluA2 subunit nearly 8-fold with an IC50 of 3.03 μM, GluA1/2 by 7.5-fold with an IC50 of 3.14 μM, GluA2/3 by nearly 7-fold with an IC50 of 3.19 μM, and GluA1 by 6.5-fold with an IC50 of 3.2 μM, significantly impacting the desensitization and deactivation rate of the AMPA receptor. BDZ-P7 showed an in vivo impact of partially reinstating locomotor abilities in a mouse model of PD. The results above suggest that the BDZ-P7 compounds show great promise as top contenders for the development of novel neuroprotective therapies.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Hiba Natsheh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Noor Haj Mohammed
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Lubaba Abu Hamda
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Anil Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Barbara Olech
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Centre of New Technologies, University of Warsaw, ul. S. Banacha 2c, 02-097 Warsaw, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Sosana Bdir
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
| | - Mohammad Bdair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, P403, Nablus 00970, Palestine
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6
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Olech B, Brázda P, Palatinus L, Dominiak PM. Dynamical refinement with multipolar electron scattering factors. IUCRJ 2024; 11:309-324. [PMID: 38512772 PMCID: PMC11067749 DOI: 10.1107/s2052252524001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024]
Abstract
Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.
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Affiliation(s)
- Barbara Olech
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Petr Brázda
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Lukas Palatinus
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czechia
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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7
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Chodkiewicz M, Patrikeev L, Pawlędzio S, Woźniak K. Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors. IUCRJ 2024; 11:249-259. [PMID: 38446457 PMCID: PMC10916294 DOI: 10.1107/s2052252524001507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen-Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen-Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.
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Affiliation(s)
- Michał Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Leonid Patrikeev
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
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8
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Bick T, Dominiak PM, Wendler P. Exploiting the full potential of cryo-EM maps. BBA ADVANCES 2024; 5:100113. [PMID: 38292063 PMCID: PMC10825613 DOI: 10.1016/j.bbadva.2024.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024] Open
Abstract
The Coulomb potential maps generated by electron microscopy (EM) experiments contain not only information about the position but also about the charge state of the atom. This feature of EM maps allows the identification of specific ions and the protonation state of amino acid side chains in the sample. Here, we summarize qualitative observations of charges in EM maps, discuss the difficulties in interpreting the charge in Coulomb potential maps with respect to distinguishing it from radiation damage, and outline considerations to implement the correct charge in fitting algorithms.
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Affiliation(s)
- Thomas Bick
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
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9
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Hawash M, Al-Smadi D, Kumar A, Olech B, Dominiak PM, Jaradat N, Antari S, Mohammed S, Nasasrh A, Abualhasan M, Musa A, Suboh S, Çapan İ, Qneibi M, Natsheh H. Characterization and Investigation of Novel Benzodioxol Derivatives as Antidiabetic Agents: An In Vitro and In Vivo Study in an Animal Model. Biomolecules 2023; 13:1486. [PMID: 37892167 PMCID: PMC10604990 DOI: 10.3390/biom13101486] [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: 08/19/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
In this study, we synthesized benzodioxol carboxamide derivatives and investigated their antidiabetic potential. The synthesized compounds (Ia-Ic and IIa-IId) underwent characterization via HRMS, 1H-, 13CAPT-NMR, and MicroED. Their efficacy against α-amylase was assessed in vitro, while MTS assays were employed to gauge cytotoxicity across cancer and normal cell lines. Additionally, the antidiabetic impact of compound IIc was evaluated in vivo using a streptozotocin-induced diabetic mice model. Notably, IIa and IIc displayed potent α-amylase inhibition (IC50 values of 0.85 and 0.68 µM, respectively) while exhibiting a negligible effect on the Hek293t normal cell line (IC50 > 150 µM), suggesting their safety. Compound IId demonstrated significant activity against four cancer cell lines (26-65 µM). In vivo experiments revealed that five doses of IIc substantially reduced mice blood glucose levels from 252.2 mg/dL to 173.8 mg/dL in contrast to the control group. The compelling in vitro anticancer efficacy of IIc and its safety for normal cells underscores the need for further in vivo assessment of this promising compound. This research highlights the potential of benzodioxol derivatives as candidates for the future development of synthetic antidiabetic drugs.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Derar Al-Smadi
- Department of Chemistry, Faculty of Sciences, An-Najah National University, Nablus 00970, Palestine;
| | - Anil Kumar
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.K.); (B.O.); (P.M.D.)
| | - Barbara Olech
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.K.); (B.O.); (P.M.D.)
- Centre of New Technologies, University of Warsaw, ul. S. Banacha 2c, 02-097 Warsaw, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland; (A.K.); (B.O.); (P.M.D.)
| | - Nidal Jaradat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Sarah Antari
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Sarah Mohammed
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Ala’a Nasasrh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Murad Abualhasan
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
| | - Ahmed Musa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (A.M.); (S.S.); (M.Q.)
| | - Shorooq Suboh
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (A.M.); (S.S.); (M.Q.)
| | - İrfan Çapan
- Department of Material and Material Processing Technologies, Technical Sciences Vocational College, Gazi University, 06560 Ankara, Turkey;
- Basic and Engineering Sciences Central Laboratory Application and Research Center (GUTMAM), Gazi University, 06500 Ankara, Turkey
| | - Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (A.M.); (S.S.); (M.Q.)
| | - Hiba Natsheh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 00970, Palestine; (N.J.); (S.A.); (S.M.); (A.N.); (M.A.)
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10
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Jelsch C, Bibila Mayaya Bisseyou Y. Deciphering the driving forces in crystal packing by analysis of electrostatic energies and contact enrichment ratios. IUCRJ 2023; 10:557-567. [PMID: 37449972 PMCID: PMC10478513 DOI: 10.1107/s2052252523005675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Hirshfeld surface analysis is a widely used tool for identifying the types of intermolecular contacts that contribute most significantly to crystal packing stabilization. One useful metric for analyzing these contacts is the contact enrichment descriptor, which indicates the types of contacts that are over- or under-represented. In this statistical study, enrichment ratios were combined with electrostatic energy (Eelec) data for a variety of compound families. To compute the electrostatic interaction energy between atoms, charge density models from the ELMAM2 database of multipolar atoms were used. As expected, strong hydrogen bonds such as O/N-H...N and O/N-H...O typically display large enrichment values and have the most negative (i.e. favorable) electrostatic energies. Conversely, contacts that are repulsive from an electrostatic perspective are usually the most under-represented. Analyzing the enrichment ratio and electrostatic energy indicators was shown to help identify which favorable contacts are the most competitive with each other. For weaker interactions, such as hydrophobic contacts, the behavior is less clear cut and can depend on other factors such as the chemical content of the molecule. The anticorrelation between contact enrichment and Eelec is generally lost for weaker contacts. However, we observed that C...C contacts are often enriched in crystal structures containing heterocycles, despite the low electrostatic attraction. For molecules with only weak hydrogen bond donors/acceptors and hydrophobic groups, the correlation between contact enrichment and Eelec is still evident for the strongest of these interactions. However, there are some exceptions where the most favorable contacts from an electrostatic perspective are not the most over-represented. This can occur in cases where the shape of the molecule is complex or elongated, favoring dispersion forces and shape complementarity in the packing.
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Affiliation(s)
- Christian Jelsch
- CRM2, UMR CNRS 7036, Université de Lorraine, Nancy 54500, France
| | - Yvon Bibila Mayaya Bisseyou
- Laboratoire des Sciences de la Matière, de l’Environnement et de l’Energie Solaire, UFR SSMT, Université Félix Houphouët-Boigny, 22 BP 582 Abidjan 22, Cote d’Ivoire
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11
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Jha KK, Kleemiss F, Chodkiewicz ML, Dominiak PM. Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time-accuracy trade-off. J Appl Crystallogr 2023; 56:116-127. [PMID: 36777135 PMCID: PMC9901929 DOI: 10.1107/s1600576722010883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/13/2022] [Indexed: 12/24/2022] Open
Abstract
Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal-organic compounds and network structures such as covalent organic frameworks and metal-organic frameworks is now possible in a hybrid mode such as IAM-TAAM or HAR-TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.
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Affiliation(s)
- Kunal Kumar Jha
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Florian Kleemiss
- Fakultät für Chemie und Pharmazie, Universität Regensburg, Universitätstrasse 31, Regensburg, Bayern 93053, Germany
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
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Rybicka PM, Kulik M, Chodkiewicz ML, Dominiak PM. Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis. J Chem Inf Model 2022; 62:3766-3783. [PMID: 35943739 PMCID: PMC9400106 DOI: 10.1021/acs.jcim.2c00145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The multipole model (MM) uses an aspherical approach
to describe
electron density and can be used to interpret data from X-ray diffraction
in a more accurate manner than using the spherical approximation.
The MATTS (multipolar atom types from theory and statistical clustering)
data bank gathers MM parameters specific for atom types in proteins,
nucleic acids, and organic molecules. However, it was not fully understood
how the electron density of particular atoms responds to their surroundings
and which factors describe the electron density in molecules within
the MM. In this work, by applying clustering using descriptors available
in the MATTS data bank, that is, topology and multipole parameters,
we found the topology features with the biggest impact on the multipole
parameters: the element of the central atom, the number of first neighbors,
and planarity of the group. The similarities in the spatial distribution
of electron density between and within atom type classes revealed
distinct and unique atom types. The quality of existing types can
be improved by adding better parametrization, definitions, and local
coordinate systems. Future development of the MATTS data bank should
lead to a wider range of atom types necessary to construct the electron
density of any molecule.
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Affiliation(s)
- Paulina Maria Rybicka
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Marta Kulik
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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