1
|
Epoxides: Developability as Active Pharmaceutical Ingredients and Biochemical Probes. Bioorg Chem 2022; 125:105862. [DOI: 10.1016/j.bioorg.2022.105862] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
|
2
|
Malaspina LA, Genoni A, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Grabowsky S. The advanced treatment of hydrogen bonding in quantum crystallography. J Appl Crystallogr 2021; 54:718-729. [PMID: 34188611 PMCID: PMC8202034 DOI: 10.1107/s1600576721001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/31/2021] [Indexed: 11/16/2022] Open
Abstract
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
Collapse
Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Michael J. Turner
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute/Diffraction and Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| |
Collapse
|
3
|
Kleemiss F, Wieduwilt EK, Hupf E, Shi MW, Stewart SG, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Schirmeister T, Schmidt TC, Engels B, Grabowsky S. Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules. Chemistry 2021; 27:3407-3419. [PMID: 33090581 PMCID: PMC7898524 DOI: 10.1002/chem.202003978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Indexed: 01/28/2023]
Abstract
The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.
Collapse
Affiliation(s)
- Florian Kleemiss
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| | - Erna K. Wieduwilt
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019Université de Lorraine & CNRSBoulevard Arago, 57078 MetzFrance
| | - Emanuel Hupf
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
| | - Ming W. Shi
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Scott G. Stewart
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Dylan Jayatilaka
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Michael J. Turner
- School of Molecular SciencesUniversity of Western Australia35 Stirling Highway, Perth WA 6009Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research InstituteSPring-81-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198Japan
- Institute for Integrated Cell-Materials SciencesKyoto UniversityYoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501Japan
| | - Eiji Nishibori
- Division of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials ScienceUniversity of TsukubaTsukubaJapan
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical SciencesJohannes-Gutenberg University MainzStaudingerweg 5, 55128 MainzGermany
| | - Thomas C. Schmidt
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Bernd Engels
- Institute for Physical and Theoretical ChemistryJulius-Maximilians-University WürzburgEmil-Fischer-Str. 42, 97074 WürzburgGermany
| | - Simon Grabowsky
- Department 2 – Biology/Chemistry, Institute of Inorganic Chemistry and CrystallographyUniversity of BremenLeobener Str. 3 and 7, 28359 BremenGermany
- Department of Chemistry and BiochemistryUniversity of BernFreiestrasse 3, 3012 BernSwitzerland
| |
Collapse
|
4
|
Khrenova MG, Tsirelson VG, Nemukhin AV. Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors. Phys Chem Chem Phys 2020; 22:19069-19079. [PMID: 32812956 DOI: 10.1039/d0cp03560b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A dynamical approach is proposed to discriminate between reactive (rES) and nonreactive (nES) enzyme-substrate complexes taking the SARS-CoV-2 main protease (Mpro) as an important example. Molecular dynamics simulations with the quantum mechanics/molecular mechanics potentials (QM(DFT)/MM-MD) followed by the electron density analysis are employed to evaluate geometry and electronic properties of the enzyme with different substrates along MD trajectories. We demonstrate that mapping the Laplacian of the electron density and the electron localization function provides easily visible images of the substrate activation that allow one to distinguish rES and nES. The computed fractions of reactive enzyme-substrate complexes along MD trajectories well correlate with the findings of recent experimental studies on the substrate specificity of Mpro. The results of our simulations demonstrate the role of the theory level used in QM subsystems for a proper description of the nucleophilic attack of the catalytic cysteine residue in Mpro. The activation of the carbonyl group of a substrate is correctly characterized with the hybrid DFT functional PBE0, whereas the use of a GGA-type PBE functional, that lacks the admixture of the Hartree-Fock exchange fails to describe activation.
Collapse
Affiliation(s)
- Maria G Khrenova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Prospect, 33, bld. 2, Moscow, 119071, Russia and Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vladimir G Tsirelson
- Mendeleev University of Chemical Technology, Miusskaya Square, 9, Moscow, 125047, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia. and Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| |
Collapse
|
5
|
Spackman PR, Yu L, Morton CJ, Parker MW, Bond CS, Spackman MA, Jayatilaka D, Thomas SP. Bridging Crystal Engineering and Drug Discovery by Utilizing Intermolecular Interactions and Molecular Shapes in Crystals. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Peter R. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Li‐Juan Yu
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Research School of Chemistry Australian National University Canberra Australia
| | - Craig J. Morton
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
- St Vincent's Institute of Medical Research Fitz-roy VIC 3065 Australia
| | - Charles S. Bond
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Department of Chemistry and iNano Aarhus University Langelandsgade 140 Aarhus 8000 Denmark
| |
Collapse
|
6
|
Spackman PR, Yu L, Morton CJ, Parker MW, Bond CS, Spackman MA, Jayatilaka D, Thomas SP. Bridging Crystal Engineering and Drug Discovery by Utilizing Intermolecular Interactions and Molecular Shapes in Crystals. Angew Chem Int Ed Engl 2019; 58:16780-16784. [DOI: 10.1002/anie.201906602] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Peter R. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Li‐Juan Yu
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Research School of Chemistry Australian National University Canberra Australia
| | - Craig J. Morton
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
- St Vincent's Institute of Medical Research Fitz-roy VIC 3065 Australia
| | - Charles S. Bond
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Department of Chemistry and iNano Aarhus University Langelandsgade 140 Aarhus 8000 Denmark
| |
Collapse
|
7
|
Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| |
Collapse
|
8
|
Dittrich B, Luger P. Invariom-based comparative electron density studies of iso-sildenafil and sildenafil. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2016. [DOI: 10.1515/znb-2016-0178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The title compounds have raised considerable medical and broad public interest in that sildenafil is used as an agent against male erectile dysfunction; iso-sildenafil is not in clinical use. A comparison of their structural and electronic properties therefore seems of interest. The electron densities of iso-sildenafil and the cationic and neutral forms of sildenafil were examined by the application of the invariom formalism relying on diffraction data reported in the literature. The electron-density distributions obtained were subjected to topological analysis using the quantum theory of atoms in molecules (QTAIM) formalism to yield bond topological and atomic properties. Moreover, molecular Hirshfeld surfaces and electrostatic potentials (ESPs) were calculated. A number of structural and electronic differences were thus identified between sildenafil and the iso-analog. In both sildenafil structures, the phenyl ring and the pyrazolopyrimidine fragment are practically coplanar (planar conformation), whereas in the iso-analog they exhibit an angle of 44° (inclined form). Related to differences in molecular structure are completely different hydrogen bonding patterns and differences in the ESPs, the latter ones being influenced by different methylation at the pyrazolopyrimidine fragment. Iso-sildenafil is present as a hydrogen-bond dimer in the crystal, and the ESP of this dimer is dominated by a surrounding positive potential.
Collapse
Affiliation(s)
- Birger Dittrich
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany
| |
Collapse
|
9
|
Wandtke CM, Lübben J, Dittrich B. Molecular Electrostatic Potentials from Invariom Point Charges. Chemphyschem 2016; 17:2238-46. [DOI: 10.1002/cphc.201600213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Claudia M. Wandtke
- Institut für Anorganische Chemie; Georg-August-Universität; Tammannstr. 4 37077 Göttingen Germany
| | - Jens Lübben
- Anorganische Chemie und Strukturchemie; Heinrich-Heine Universität Düsseldorf; Universitätsstraße 1, Gebäude 26.42.01.21 40225 Düsseldorf Germany
- Institut für Anorganische Chemie; Georg-August-Universität; Tammannstr. 4 37077 Göttingen Germany
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie; Heinrich-Heine Universität Düsseldorf; Universitätsstraße 1, Gebäude 26.42.01.21 40225 Düsseldorf Germany
| |
Collapse
|