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Spiwoková P, Horn M, Fanfrlík J, Jílková A, Fajtová P, Leontovyč A, Houštecká R, Bieliková L, Brynda J, Chanová M, Mertlíková-Kaiserová H, Caro-Diaz EJE, Almaliti J, El-Sakkary N, Gerwick WH, Caffrey CR, Mareš M. Nature-Inspired Gallinamides Are Potent Antischistosomal Agents: Inhibition of the Cathepsin B1 Protease Target and Binding Mode Analysis. ACS Infect Dis 2024. [PMID: 38757505 DOI: 10.1021/acsinfecdis.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Schistosomiasis, caused by a parasitic blood fluke of the genus Schistosoma, is a global health problem for which new chemotherapeutic options are needed. We explored the scaffold of gallinamide A, a natural peptidic metabolite of marine cyanobacteria that has previously been shown to inhibit cathepsin L-type proteases. We screened a library of 19 synthetic gallinamide A analogs and identified nanomolar inhibitors of the cathepsin B-type protease SmCB1, which is a drug target for the treatment of schistosomiasis mansoni. Against cultured S. mansoni schistosomula and adult worms, many of the gallinamides generated a range of deleterious phenotypic responses. Imaging with a fluorescent-activity-based probe derived from gallinamide A demonstrated that SmCB1 is the primary target for gallinamides in the parasite. Furthermore, we solved the high-resolution crystal structures of SmCB1 in complex with gallinamide A and its two analogs and describe the acrylamide covalent warhead and binding mode in the active site. Quantum chemical calculations evaluated the contribution of individual positions in the peptidomimetic scaffold to the inhibition of the target and demonstrated the importance of the P1' and P2 positions. Our study introduces gallinamides as a powerful chemotype that can be exploited for the development of novel antischistosomal chemotherapeutics.
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Affiliation(s)
- Petra Spiwoková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 5, Prague 6 16628, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Adéla Jílková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - Adrian Leontovyč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Radka Houštecká
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, Praha 2 12108, Czech Republic
| | - Lucia Bieliková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
- First Faculty of Medicine, Charles University, Kateřinská 32, Praha 2 12108, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Marta Chanová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2028/7, Prague 2 12800, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
| | - Eduardo J E Caro-Diaz
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - Jehad Almaliti
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - Nelly El-Sakkary
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - William H Gerwick
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, California 92093, United States
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, Prague 6 16610, Czech Republic
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Pecina A, Fanfrlík J, Lepšík M, Řezáč J. SQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein-ligand binding affinity predictions in minutes. Nat Commun 2024; 15:1127. [PMID: 38321025 PMCID: PMC10847445 DOI: 10.1038/s41467-024-45431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Accurate estimation of protein-ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets. In contrast to DFT, SQM2.20 provides affinity predictions in minutes, making it suitable for practical applications in hit identification or lead optimization.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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Keller W, Hofmann M, Wadepohl H, Enders M, Fanfrlík J, Hnyk D. Chlorinated polyhedral selenaboranes revisited by joint experimental/computational efforts: the formation of closo-1-SeB 9Cl 9 and the crystal structure of closo-SeB 11Cl 11. Dalton Trans 2023; 52:16886-16893. [PMID: 37916993 DOI: 10.1039/d3dt02987e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
The recent success in the formation of chlorinated telluraboranes and the reactivities of pnictogenaboranes prompted us to re-examine the vacuum co-pyrolysis of B2Cl4 with Se2Cl2 at various molar ratios and temperatures in order to search for the generation of other polyhedral selenaboranes than closo-SeB5Cl5 (1a) and closo-SeB11Cl11 (1b), the latter being observed earlier. Interestingly, a new compound with the elemental composition SeB9Cl9 (2) was detected, this time by high- and low-resolution mass spectrometry. Further characterization by 1- and 2-D 11B-NMR spectroscopy suggests that 2 should adopt a closed bicapped square-antiprismatic geometry with selenium at the apical position. Moreover, vacuum sublimation gave suitable crystals of 1b, which were subjected to single-crystal X-ray structure determination. Crystallographic data analysis confirmed that 1b, consistent with its 26 skeletal electron count, adopts a distorted icosahedral structure close to the symmetry of C5v. Computations at the DFT-D3 level have revealed that 33% of the total computed binding motifs in the grown 1b crystals are due to the very strong chalcogen bonding. Moreover, SAPT decomposition has shown that the bonding motifs in the crystals are stabilized mainly by dispersion and electrostatic terms. Homodecoupling and high resolution 11B NMR and 77Se NMR experiments have resolved both coupling constants 1J(11B11B) and 1J(77Se11B) as well as the 77Se chemical shift of 1a and 1b, which are in reasonable agreement with the corresponding computed values. The computed 11B chemical shifts of 2 were determined by the well-established DFT/GIAO/NMR structural tool based on its B3LYP/6-311+G** internal coordinates. They agree well with the experimental values and provide a good representation of the molecular structure of 2 in solution. The extraordinary downfield 11B NMR chemical shift of B(10) in 2 has been ascribed to the intensive paramagnetic contribution to the shielding tensor in this bicapped square-antiprismatic motif. Calculations of the synproportionation free energies of smaller (n - 1) closo-selenaboranes with larger-sized (n + 1) ones support the extraordinary stability of octahedral, bicapped square-antiprismatic and icosahedral closo motifs in the SeBnCln family (n = 4-12).
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Affiliation(s)
- Willi Keller
- Institut für Chemie, Universität Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany.
| | - Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Markus Enders
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic.
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Keller W, Sárosi MB, Fanfrlík J, Straka M, Holub J, McKee ML, Hnyk D. Boron-based octahedral dication experimentally detected: DFT surface confirms its availability. RSC Adv 2023; 13:19627-19637. [PMID: 37388141 PMCID: PMC10305729 DOI: 10.1039/d3ra03665k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Borane and heteroborane clusters have been known as neutral or anionic species. In contrast to them, several ten-vertex monocationic nido and closo dicarbaborane-based systems have recently emerged from the reaction of the parent bicapped-square antiprismatic dicarbaboranes with N-heterocyclic carbenes followed by the protonization of the corresponding nido intermediates. The expansion of these efforts has afforded the very first closo-dicationic octahedral phosphahexaborane along with new closo-monocationic pnictogenahexaboranes of the same shapes. All are the products of the one-pot procedure that consists in the reaction of the same carbenes with the parent closo-1,2-Pn2B4Br4 (Pn = As, P). Whereas in the case of phosphorus such a monocation appears to be a mixture of stable intermediates, and arsenahexaboranyl monocation has occurred as the final product, all of them without using any subsequent reaction. The well-established DFT/ZORA/NMR approach has unambiguously confirmed the existence of these species in solution, and computed electrostatic potentials have revealed the delocalization of the positive charge in these monocations and in the very first dication, namely within the octahedral shapes in both cases.
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Affiliation(s)
- Willi Keller
- Institut für Chemie, Universität Hohenheim Garbenstrasse 30 D-70599 Stuttgart Germany
| | - Menyhárt B Sárosi
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig Linnéstrasse 2 04103 Leipzig Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2, CZ-166 10 Praha 6 Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2, CZ-166 10 Praha 6 Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences CZ-250 68 Husinec-Řež Czech Republic
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University Auburn AL 36849 USA
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences CZ-250 68 Husinec-Řež Czech Republic
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McKee ML, Vrána J, Holub J, Fanfrlík J, Hnyk D. DFT Surface Infers Ten-Vertex Cationic Carboranes from the Corresponding Neutral closo Ten-Vertex Family: The Computed Background Confirming Their Experimental Availability. Molecules 2023; 28:molecules28083645. [PMID: 37110879 PMCID: PMC10141709 DOI: 10.3390/molecules28083645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Modern computational protocols based on the density functional theory (DFT) infer that polyhedral closo ten-vertex carboranes are key starting stationary states in obtaining ten-vertex cationic carboranes. The rearrangement of the bicapped square polyhedra into decaborane-like shapes with open hexagons in boat conformations is caused by attacks of N-heterocyclic carbenes (NHCs) on the closo motifs. Single-point computations on the stationary points found during computational examinations of the reaction pathways have clearly shown that taking the "experimental" NHCs into account requires the use of dispersion correction. Further examination has revealed that for the purposes of the description of reaction pathways in their entirety, i.e., together with all transition states and intermediates, a simplified model of NHCs is sufficient. Many of such transition states resemble in their shapes those that dictate Z-rearrangement among various isomers of closo ten-vertex carboranes. Computational results are in very good agreement with the experimental findings obtained earlier.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Jan Vrána
- Faculty of Chemical Technology, University of Pardubice, CZ-532 10 Pardubice, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68 Husinec-Řež, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, CZ-166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68 Husinec-Řež, Czech Republic
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Farka D, Kříž K, Fanfrlík J. Strategies for the Design of PEDOT Analogues Unraveled: the Use of Chalcogen Bonds and σ-Holes. J Phys Chem A 2023; 127:3779-3787. [PMID: 37075228 PMCID: PMC10165655 DOI: 10.1021/acs.jpca.2c08965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
In this theoretical study, we set out to demonstrate the substitution effect of PEDOT analogues on planarity as an intrinsic indicator for electronic performance. We perform a quantum mechanical (DFT) study of PEDOT and analogous model systems and demonstrate the usefulness of the ωB97X-V functional to simulate chalcogen bonds and other noncovalent interactions. We confirm that the chalcogen bond stabilizes the planar conformation and further visualize its presence via the electrostatic potential surface. In comparison to the prevalent B3LYP, we gain 4-fold savings in computational time and simulate model systems of up to a dodecamer. Implications for design of conductive polymers can be drawn from the results, and an example for self-doped polymers is presented where modulation of the strength of the chalcogen bond plays a significant role.
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Affiliation(s)
- Dominik Farka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Prague, Czech Republic
| | - Kristian Kříž
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Prague, Czech Republic
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Keller W, Ballmann J, Sárosi MB, Fanfrlík J, Hnyk D. The Telluraboranes closo‐TeB5Cl5 and closo‐TeB11Cl11 with Exceptionally Long Body Diagonals: Synthetic and Bonding Motifs for Innovative Octahedral and Icosahedral Geometries. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202219018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Affiliation(s)
- Willi Keller
- Universitat Hohenheim Fakultat fur Naturwissenschaften Chemie GERMANY
| | - Joachim Ballmann
- Ruprecht-Karls-Universität Heidelberg: Universitat Heidelberg Anorganisch-Chemisches GERMANY
| | | | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Computational Chemistry CZECH REPUBLIC
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry Czech Academy of Sciences: Ustav anorganicke chemie Akademie ved Ceske republiky Department of Syntheses Dlouha 1001 CZ - 250 68 Husinec - Rez CZECH REPUBLIC
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Keller W, Ballmann J, Sárosi MB, Fanfrlík J, Hnyk D. The Telluraboranes closo-TeB5Cl5 and closo-TeB11Cl11 with Exceptionally Long Body Diagonals: Synthetic and Bonding Motifs for Innovative Octahedral and Icosahedral Geometries. Angew Chem Int Ed Engl 2023:e202219018. [PMID: 36912896 DOI: 10.1002/anie.202219018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/14/2023]
Abstract
Six-vertex closo-TeB5Cl5 (1) and twelve-vertex closo-TeB11Cl11 (2) telluraboranes have been prepared via co-pyrolysis of B2Cl4 with TeCl4in vacuo at temperatures between 360ºC and 400°C. Both compounds are sublimable, off-white solids, and they have been characterized by one- and two-dimensional 11B-NMR and high-resolution mass spectroscopy. Both ab initio/GIAO/NMR and DFT/ZORA/NMR computations support octahedral and icosahedral geometries for 1 and 2, respectively, as expected due to their closo-electron counts. The octahedral structure of 1 has been confirmed by single-crystal X-ray diffraction on an incommensurately modulated crystal. The corresponding bonding properties have been analyzed in terms of the intrinsic bond orbital (IBO) approach. 1 is the first example of a polyhedral telluraborane with a cluster size smaller than 11 vertices.
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Affiliation(s)
- Willi Keller
- Universitat Hohenheim Fakultat fur Naturwissenschaften, Chemie, GERMANY
| | - Joachim Ballmann
- Ruprecht-Karls-Universität Heidelberg: Universitat Heidelberg, Anorganisch-Chemisches, GERMANY
| | | | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Computational Chemistry, CZECH REPUBLIC
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry Czech Academy of Sciences: Ustav anorganicke chemie Akademie ved Ceske republiky, Department of Syntheses, Dlouha 1001, CZ - 250 68, Husinec - Rez, CZECH REPUBLIC
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Fanfrlík J, Brynda J, Kugler M, Lepšík M, Pospíšilová K, Holub J, Hnyk D, Nekvinda J, Grüner B, Řezáčová P. B-H⋯π and C-H⋯π interactions in protein-ligand complexes: carbonic anhydrase II inhibition by carborane sulfonamides. Phys Chem Chem Phys 2023; 25:1728-1733. [PMID: 36594655 DOI: 10.1039/d2cp04673c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Among non-covalent interactions, B-H⋯π and C-H⋯π hydrogen bonding is rather weak and less studied. Nevertheless, since both can affect the energetics of protein-ligand binding, their understanding is an important prerequisite for reliable predictions of affinities. Through a combination of high-resolution X-ray crystallography and quantum-chemical calculations on carbonic anhydrase II/carborane-based inhibitor systems, this paper provides the first example of B-H⋯π hydrogen bonding in a protein-ligand complex. It shows that the B-H⋯π interaction is stabilized by dispersion, followed by electrostatics. Furthermore, it demonstrates that the similar C-H⋯π interaction is twice as strong, with a slightly smaller contribution of dispersion and a slightly higher contribution of electrostatics. Such a detailed insight will facilitate the rational design of future protein ligands, controlling these types of non-covalent interactions.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Michael Kugler
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Klára Pospíšilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jan Nekvinda
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.
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Keller W, Hofmann M, Sárosi MB, Fanfrlík J, Hnyk D. Reactivity of Perhalogenated Octahedral Phospha- and Arsaboranes toward THF: A Joint Experimental/Computational Study. Inorg Chem 2022; 61:16565-16572. [PMID: 36229410 DOI: 10.1021/acs.inorgchem.2c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of the perhalogenated polyhedral pnictogenaboranes closo-1,2-Pn2B4Hal4 (Pn = P, As; Hal = Cl, Br) with Lewis bases are presently being studied with a focus on rationalizing the sites of nucleophilic attacks on clusters bearing σ-holes. These σ-holes are localized both on pnictogens and, for Hal = Br, on bromine atoms, as revealed by electrostatic potential (ESP) and intrinsic bond orbital (IBO) analyses. Surprisingly, the attack of the cyclic ether THF on closo-1,2-Pn2B4Br4 does not occur on the site with the largest positive partial charge, centered in the middle of the pnictogen-pnictogen vector. Instead, presumably promoted by the positivated bromine substituents, THF inserts into the boron-bromine bonds of the negatively charged boron atoms opposite to the pnictogen atoms to form 4-(4-bromobut-1-oxy)-closo-1,2-Pn2B4Br3 (1-PB and 1-AsB) and 4,6-(4-bromobut-1-oxy)2-closo-1,2-Pn2B4Br2 (2-PB and 2-AsB). 11B and 31P chemical shift computations at various levels support the assignments of the signals, which reflect the correctness of the molecular geometries in solutions. The Lewis-acidic perchlorinated analogues closo-1,2-P2B4Cl4, closo-1,2-As2B4Cl4, and the mixed closo-1,2-AsPB4Cl4 bear negative charges. These negative charges are revealed by the Vs,max values when computing the electrostatic potentials both on the boron and the chlorine atoms. Due to this negative charge, the analogues do not react with THF unless they are heated above 66 °C, where they slowly decompose to borate esters B(OR)3 without the formation of concrete intermediates. The evaluation of 31P NMR data of 1-PB has allowed the experimental determination of the coupling constant 1J(31P(1), 31P(2)) = |143| Hz in a closo-diphosphaborane for the first time, which agrees well with the computed value of -178 Hz. The pioneering joint experimental vs computational interpretation of 31P NMR spectra in the area of boron cluster chemistry was decisive for the structural characterization of 1-PB and 2-PB.
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Affiliation(s)
- Willi Keller
- Institut für Chemie, Universität Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Menyhárt-Botond Sárosi
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, 04103 Leipzig, Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
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11
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Benýšek J, Buša M, Rubešová P, Fanfrlík J, Lepšík M, Brynda J, Matoušková Z, Bartz U, Horn M, Gütschow M, Mareš M. Highly potent inhibitors of cathepsin K with a differently positioned cyanohydrazide warhead: structural analysis of binding mode to mature and zymogen-like enzymes. J Enzyme Inhib Med Chem 2022; 37:515-526. [PMID: 35144520 PMCID: PMC8843313 DOI: 10.1080/14756366.2021.2024527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cathepsin K (CatK) is a target for the treatment of osteoporosis, arthritis, and bone metastasis. Peptidomimetics with a cyanohydrazide warhead represent a new class of highly potent CatK inhibitors; however, their binding mechanism is unknown. We investigated two model cyanohydrazide inhibitors with differently positioned warheads: an azadipeptide nitrile Gü1303 and a 3-cyano-3-aza-β-amino acid Gü2602. Crystal structures of their covalent complexes were determined with mature CatK as well as a zymogen-like activation intermediate of CatK. Binding mode analysis, together with quantum chemical calculations, revealed that the extraordinary picomolar potency of Gü2602 is entropically favoured by its conformational flexibility at the nonprimed-primed subsites boundary. Furthermore, we demonstrated by live cell imaging that cyanohydrazides effectively target mature CatK in osteosarcoma cells. Cyanohydrazides also suppressed the maturation of CatK by inhibiting the autoactivation of the CatK zymogen. Our results provide structural insights for the rational design of cyanohydrazide inhibitors of CatK as potential drugs.
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Affiliation(s)
- Jakub Benýšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michal Buša
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Matoušková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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12
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Bakardjiev M, Holub J, Růžičková Z, Růžička A, Fanfrlík J, Štíbr B, McKee ML, Hnyk D. Transformation of various multicenter bondings within bicapped-square antiprismatic motifs: Z-rearrangement. Dalton Trans 2021; 50:12098-12106. [PMID: 33656022 DOI: 10.1039/d0dt04225k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reported herein are mutual rearrangements in the whole series of seven bicapped-square antiprismatic closo-C2B8H10 by means of high-quality computations that disprove the earlier postulated dsd (diamond-square-diamond) scheme for these isomerizations. The experimentally existing closo-1,2-C2B8H10 was able to be converted to 1,6-, and 1,10-isomers by pyrolysis, and the dsd (diamond-square-diamond) mechanism was offered as an explanation of these processes. However, these computations disprove the postulated dsd scheme for these isomerizations that take place in the ten-vertex closo series. Experimentally observed thermal rearrangements, both in the parent and substituted closo-1,2-C2B8H10, closo-1-CB9H10-, and closo-B10H102-, indirectly support these refined computations. All these processes are based on the new concept of the so-called Z-mechanism, being consistent with a transition state of a boat shape with an open hexagonal belt that results from the initial breakage of three bonds. Such bond breakings and the consequent bond formations bring to mind the shape of the letter Z. In effect, the pattern of multicenter bonding shifts from reactant through a transition state to product. The molecular rearrangements that are available experimentally favour either the axial or equatorial isomers, and this ratio depends on temperature and the type of cluster and its substitution.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ - 250 68, Husinec-Řež, Czech Republic.
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ - 250 68, Husinec-Řež, Czech Republic.
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ - 166 10, Prague 6, Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ - 250 68, Husinec-Řež, Czech Republic.
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA.
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ - 250 68, Husinec-Řež, Czech Republic.
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13
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Vrána J, Holub J, Samsonov MA, Růžičková Z, Cvačka J, McKee ML, Fanfrlík J, Hnyk D, Růžička A. Access to cationic polyhedral carboranes via dynamic cage surgery with N-heterocyclic carbenes. Nat Commun 2021; 12:4971. [PMID: 34404809 PMCID: PMC8371172 DOI: 10.1038/s41467-021-25277-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/02/2021] [Indexed: 12/03/2022] Open
Abstract
Polyhedral boranes and heteroboranes appear almost exclusively as neutral or anionic species, while the cationic ones are protonated at exoskeletal heteroatoms or they are instable. Here we report the reactivity of 10-vertex closo-dicarbadecaboranes with one or two equivalents of N-heterocyclic carbene to 10-vertex nido mono- and/or bis-carbene adducts, respectively. These complexes easily undergo a reaction with HCl to give cages of stable and water soluble 10-vertex nido-type cations with protonation in the form of a BHB bridge or 10-vertex closo-type cations containing one carbene ligand when originating from closo-1,10-dicarbadecaborane. The reaction of a 10-vertex nido mono-carbene adduct with phosphorus trichloride gives nido-11-vertex 2-phospha-7,8-dicarbaundecaborane, which undergoes an oxidation of the phosphorus atom to P = O, while the product of a bis-carbene adduct reaction is best described as a distorted C2B6H8 fragment bridged by the (BH)2PCl2+ moiety. In comparison to their neutral or anionic counterparts, examples of cationic boron clusters remain scarce. Here, the authors prepare a variety of cationic polyhedral boranes by reacting closo-10-vertex carboranes with N-heterocyclic carbenes; the resulting open-cage cationic nido- arachno- or closo- derivatives are water soluble, which may enable unprecedented applications.
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Affiliation(s)
- Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Czech Academy of Sciences, Řež, Czech Republic
| | - Maksim A Samsonov
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Czech Academy of Sciences, Řež, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
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14
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Otava T, Šála M, Li F, Fanfrlík J, Devkota K, Perveen S, Chau I, Pakarian P, Hobza P, Vedadi M, Boura E, Nencka R. The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors. ACS Infect Dis 2021; 7:2214-2220. [PMID: 34152728 PMCID: PMC8265718 DOI: 10.1021/acsinfecdis.1c00131] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 12/23/2022]
Abstract
In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases (MTases), nsp14. This MTase catalyzes the transfer of the methyl group from S-adenosyl-l-methionine (SAM) to cap the guanosine triphosphate moiety of the newly synthesized viral RNA, yielding the methylated capped RNA and S-adenosyl-l-homocysteine (SAH). As the crystal structure of SARS-CoV-2 nsp14 is unknown, we have taken advantage of its high homology to SARS-CoV nsp14 and prepared its homology model, which has allowed us to identify novel SAH derivatives modified at the adenine nucleobase as inhibitors of this important viral target. We have synthesized and tested the designed compounds in vitro and shown that these derivatives exert unprecedented inhibitory activity against this crucial enzyme. The docking studies nicely explain the contribution of an aromatic part attached by a linker to the position 7 of the 7-deaza analogues of SAH.
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Affiliation(s)
- Tomáš Otava
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
- Faculty of Food and Biochemical Technology,
University of Chemistry and Technology, 166 28, Prague 6,
Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Fengling Li
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Kanchan Devkota
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Paknoosh Pakarian
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Masoud Vedadi
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
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15
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Bakardjiev M, Holub J, Bavol D, Vrána J, Samsonov MA, Růžička A, Růžičková Z, Fanfrlík J, Hnyk D. Thiaborane Icosahedral Barrier Increased by the Functionalization of all Terminal Hydrogens in closo-1-SB 11H 11. Inorg Chem 2021; 60:8428-8431. [PMID: 34101456 DOI: 10.1021/acs.inorgchem.1c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrophilic substitution of icosahedral closo-1-SB11H11 with methyl iodide has resulted in two B-functionalized thiaboranes, 7,12-I2-2,3,4,5,6,8,9,10,11-(CH3)9-1-closo-SB11 and 7,8,12-I3-2,3,4,5,6,9,10,11-(CH3)8-closo-1-SB11, with the former being significantly predominant. These two icosahedral thiaboranes are the first cases of polysubstituted polyhedral boron clusters with another vertex that differs from B and C. Such polyfunctionalizations have increased the earlier observed thiaborane icosahedral barrier, not exhibiting any reactivity toward bases, unlike the parent thiaborane. The search for methylation pathways has revealed that the complete B11-methylation is impossible, like in the case of decaborane(14), where this seems to be a result of the positively charged upper parts of these two molecules.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Dmytro Bavol
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Maksim A Samsonov
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
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16
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Jílková A, Rubešová P, Fanfrlík J, Fajtová P, Řezáčová P, Brynda J, Lepšík M, Mertlíková-Kaiserová H, Emal CD, Renslo AR, Roush WR, Horn M, Caffrey CR, Mareš M. Druggable Hot Spots in the Schistosomiasis Cathepsin B1 Target Identified by Functional and Binding Mode Analysis of Potent Vinyl Sulfone Inhibitors. ACS Infect Dis 2021; 7:1077-1088. [PMID: 33175511 PMCID: PMC8154419 DOI: 10.1021/acsinfecdis.0c00501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Schistosomiasis, a parasitic disease
caused by blood flukes of
the genus Schistosoma, is a global health problem
with over 200 million people infected. Treatment relies on just one
drug, and new chemotherapies are needed. Schistosoma mansoni cathepsin B1 (SmCB1) is a critical peptidase for the digestion of
host blood proteins and a validated drug target. We screened a library
of peptidomimetic vinyl sulfones against SmCB1 and identified the
most potent SmCB1 inhibitors reported to date that are active in the
subnanomolar range with second order rate constants (k2nd) of ∼2 × 105 M–1 s–1. High resolution crystal structures of the
two best inhibitors in complex with SmCB1 were determined. Quantum
chemical calculations of their respective binding modes identified
critical hot spot interactions in the S1′ and S2 subsites.
The most potent inhibitor targets the S1′ subsite with an N-hydroxysulfonic amide moiety and displays favorable functional
properties, including bioactivity against the pathogen, selectivity
for SmCB1 over human cathepsin B, and reasonable metabolic stability.
Our results provide structural insights for the rational design of
next-generation SmCB1 inhibitors as potential drugs to treat schistosomiasis.
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Affiliation(s)
- Adéla Jílková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Cory D. Emal
- Eastern Michigan University, 541 Mark Jefferson, Ypsilanti, Michigan 48197, United States
| | - Adam R. Renslo
- University of California San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - William R. Roush
- The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
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17
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Gregor J, Radilová K, Brynda J, Fanfrlík J, Konvalinka J, Kožíšek M. Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Molecules 2021; 26:molecules26041007. [PMID: 33673017 PMCID: PMC7917969 DOI: 10.3390/molecules26041007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 02/12/2021] [Indexed: 01/06/2023] Open
Abstract
Influenza A virus (IAV) encodes a polymerase composed of three subunits: PA, with endonuclease activity, PB1 with polymerase activity and PB2 with host RNA five-prime cap binding site. Their cooperation and stepwise activation include a process called cap-snatching, which is a crucial step in the IAV life cycle. Reproduction of IAV can be blocked by disrupting the interaction between the PB2 domain and the five-prime cap. An inhibitor of this interaction called pimodivir (VX-787) recently entered the third phase of clinical trial; however, several mutations in PB2 that cause resistance to pimodivir were observed. First major mutation, F404Y, causing resistance was identified during preclinical testing, next the mutation M431I was identified in patients during the second phase of clinical trials. The mutation H357N was identified during testing of IAV strains at Centers for Disease Control and Prevention. We set out to provide a structural and thermodynamic analysis of the interactions between cap-binding domain of PB2 wild-type and PB2 variants bearing these mutations and pimodivir. Here we present four crystal structures of PB2-WT, PB2-F404Y, PB2-M431I and PB2-H357N in complex with pimodivir. We have thermodynamically analysed all PB2 variants and proposed the effect of these mutations on thermodynamic parameters of these interactions and pimodivir resistance development. These data will contribute to understanding the effect of these missense mutations to the resistance development and help to design next generation inhibitors.
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Affiliation(s)
- Jiří Gregor
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
- First Faculty of Medicine, Charles University, Kateřinská 1660/32, 12108 Prague 2, Czech Republic
| | - Kateřina Radilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
- First Faculty of Medicine, Charles University, Kateřinská 1660/32, 12108 Prague 2, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 12800 Prague 2, Czech Republic
- Correspondence: (J.K.); (M.K.); Tel.: +420-220-183-218 (J.K.)
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 16610 Prague 6, Czech Republic; (J.G.); (K.R.); (J.B.); (J.F.)
- Correspondence: (J.K.); (M.K.); Tel.: +420-220-183-218 (J.K.)
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18
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Jílková A, Horn M, Fanfrlík J, Küppers J, Pachl P, Řezáčová P, Lepšík M, Fajtová P, Rubešová P, Chanová M, Caffrey CR, Gütschow M, Mareš M. Azanitrile Inhibitors of the SmCB1 Protease Target Are Lethal to Schistosoma mansoni: Structural and Mechanistic Insights into Chemotype Reactivity. ACS Infect Dis 2021; 7:189-201. [PMID: 33301315 PMCID: PMC7802074 DOI: 10.1021/acsinfecdis.0c00644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Azapeptide
nitriles are postulated to reversibly covalently react
with the active-site cysteine residue of cysteine proteases and form
isothiosemicarbazide adducts. We investigated the interaction of azadipeptide
nitriles with the cathepsin B1 drug target (SmCB1) from Schistosoma
mansoni, a pathogen that causes the global neglected disease
schistosomiasis. Azadipeptide nitriles were superior inhibitors of
SmCB1 over their parent carba analogs. We determined the crystal structure
of SmCB1 in complex with an azadipeptide nitrile and analyzed the
reaction mechanism using quantum chemical calculations. The data demonstrate
that azadipeptide nitriles, in contrast to their carba counterparts,
undergo a change from E- to Z-configuration
upon binding, which gives rise to a highly favorable energy profile
of noncovalent and covalent complex formation. Finally, azadipeptide
nitriles were considerably more lethal than their carba analogs against
the schistosome pathogen in culture, supporting the further development
of this chemotype as a treatment for schistosomiasis.
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Affiliation(s)
- Adéla Jílková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Jim Küppers
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
| | - Marta Chanová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 2028/7, 12800 Prague 2, Czech Republic
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases (CDIPD), Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague 6, Czech Republic
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19
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Fanfrlík J, Pecina A, Řezáč J, Lepšík M, Sárosi MB, Hnyk D, Hobza P. Benchmark Data Sets of Boron Cluster Dihydrogen Bonding for the Validation of Approximate Computational Methods. Chemphyschem 2020; 21:2599-2604. [PMID: 33179424 DOI: 10.1002/cphc.202000729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Indexed: 12/31/2022]
Abstract
The success of approximate computational methods, such as molecular mechanics, or dispersion-corrected density functional theory, in the description of non-covalent interactions relies on accurate parameterizations. Benchmark data sets are thus required. This area is well developed for organic molecules and biomolecules but practically non-existent for boron clusters, which have been gaining in importance in modern drug as well as material design. To fill this gap, we have introduced two data sets featuring the most common non-covalent interaction of boron clusters, the dihydrogen bond, and calculated reference interaction energies at the "golden standard" CCSD(T)/CBS level. The boron clusters studied interact with formamide, methanol, water and methane at various distances and in two geometrical arrangements. The performance of the tested approximate methods is variable and recommendations for further use are given.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Istituto Italiano di Tecnologia, Molecular Modeling and Drug Discovery, Via Morego 30, 161 63, Genoa, Italy
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Menyhárt B Sárosi
- Leipzig University, Faculty of Chemistry and Mineralogy, Institute of Inorganic Chemistry, Johannisallee 29, 04103, Leipzig, Germany
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 25068, Husinec-Řež, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 77146, Olomouc, Czech Republic
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20
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Holub J, Vishnevskiy YV, Fanfrlík J, Mitzel NW, Tikhonov D, Schwabedissen J, McKee ML, Hnyk D. Bromination Mechanism of closo-1,2-C 2 B 10 H 12 and the Structure of the Resulting 9-Br-closo-1,2-C 2 B 10 H 11 Determined by Gas Electron Diffraction. Chempluschem 2020; 85:2606-2610. [PMID: 33029907 DOI: 10.1002/cplu.202000543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/18/2020] [Indexed: 11/07/2022]
Abstract
9-Br-closo-1,2-C2 B10 H11 has been prepared and its gas-phase structure has been examined by means of gas electron diffraction. The structure of the carbaborane core is similar to the structure of the parent compound, which is of C2v symmetry. A DFT-based search for the corresponding reaction pathway of the bromination of closo-1,2-C2 B10 H12 revealed that the catalytic amount of aluminum reduces the barrier of the initial attack of the bromination agent toward the negatively charged part of the icosahedral carbaborane, i. e., the first transition state, from about 40 to about 27 kcalmol-1 . The Br-Br bond is weakened by an intermediate binding to the large π-hole on the aluminum atom of AlBr3 , which is the driving force for the AlBr3 -catalyzed bromination.
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Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68, Husinec - Řež, Czech Republic
| | - Yury V Vishnevskiy
- Universität Bielefeld, Fakultät für Chemie, Anorganische Chemie und Strukturchemie, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, CZ-16610, Praha 6, Czech Republic
| | - Norbert W Mitzel
- Universität Bielefeld, Fakultät für Chemie, Anorganische Chemie und Strukturchemie, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Denis Tikhonov
- Universität Bielefeld, Fakultät für Chemie, Anorganische Chemie und Strukturchemie, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jan Schwabedissen
- Universität Bielefeld, Fakultät für Chemie, Anorganische Chemie und Strukturchemie, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama, 36849, USA
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, CZ-250 68, Husinec - Řež, Czech Republic
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21
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2361. [PMID: 32986310 DOI: 10.1002/cplu.202000627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Invited for this month's cover is the group of Prof. Pavel Hobza, Czech Academy of Sciences, Prague. The cover picture shows a powerful automated quantum mechanics based SQM/COSMO approach to protein-ligand scoring. It comprises thorough preparation of ligand structures, extensive generation of binding complexes, fast geometry relaxation and reliable affinity prediction. Read the full text of the Minireview at 10.1002/cplu.202000120.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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22
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. Front Cover: SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design (ChemPlusChem 11/2020). Chempluschem 2020. [DOI: 10.1002/cplu.202000628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences Flemingovo namesti 2 166 10 Prague Czech Republic
- Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Palacky University 771 46 Olomouc Czech Republic
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23
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Zima V, Radilová K, Kožíšek M, Albiñana CB, Karlukova E, Brynda J, Fanfrlík J, Flieger M, Hodek J, Weber J, Majer P, Konvalinka J, Machara A. Unraveling the anti-influenza effect of flavonoids: Experimental validation of luteolin and its congeners as potent influenza endonuclease inhibitors. Eur J Med Chem 2020; 208:112754. [PMID: 32883638 DOI: 10.1016/j.ejmech.2020.112754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/09/2020] [Indexed: 01/27/2023]
Abstract
The biological effects of flavonoids on mammal cells are diverse, ranging from scavenging free radicals and anti-cancer activity to anti-influenza activity. Despite appreciable effort to understand the anti-influenza activity of flavonoids, there is no clear consensus about their precise mode-of-action at a cellular level. Here, we report the development and validation of a screening assay based on AlphaScreen technology and illustrate its application for determination of the inhibitory potency of a large set of polyols against PA N-terminal domain (PA-Nter) of influenza RNA-dependent RNA polymerase featuring endonuclease activity. The most potent inhibitors we identified were luteolin with an IC50 of 72 ± 2 nM and its 8-C-glucoside orientin with an IC50 of 43 ± 2 nM. Submicromolar inhibitors were also evaluated by an in vitro endonuclease activity assay using single-stranded DNA, and the results were in full agreement with data from the competitive AlphaScreen assay. Using X-ray crystallography, we analyzed structures of the PA-Nter in complex with luteolin at 2.0 Å resolution and quambalarine B at 2.5 Å resolution, which clearly revealed the binding pose of these polyols coordinated to two manganese ions in the endonuclease active site. Using two distinct assays along with the structural work, we have presumably identified and characterized the molecular mode-of-action of flavonoids in influenza-infected cells.
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Affiliation(s)
- Václav Zima
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Kateřina Radilová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 1660, 121 08, Prague 2, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic.
| | - Carlos Berenguer Albiñana
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Elena Karlukova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 140 00, Prague 4, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Miroslav Flieger
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 140 00, Prague 4, Czech Republic
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic
| | - Aleš Machara
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 00, Prague 2, Czech Republic; Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10, Prague 6, Czech Republic.
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24
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Holub J, Růžička A, Růžičková Z, Fanfrlík J, Hnyk D, Štíbr B. Electrophilic Methylation of Decaborane(14): Selective Synthesis of Tetramethylated and Heptamethylated Decaboranes and Their Conjugated Bases. Inorg Chem 2020; 59:10540-10547. [DOI: 10.1021/acs.inorgchem.0c00917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 250 68, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, Pardubice 532 10, Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, Pardubice 532 10, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, Praha 6 166 10, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 250 68, Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, Husinec-Řež 250 68, Czech Republic
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25
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Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P. SQM/COSMO Scoring Function: Reliable Quantum-Mechanical Tool for Sampling and Ranking in Structure-Based Drug Design. Chempluschem 2020; 85:2362-2371. [PMID: 32609421 DOI: 10.1002/cplu.202000120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Quantum mechanical (QM) methods have been gaining importance in structure-based drug design where a reliable description of protein-ligand interactions is of utmost significance. However, strategies i. e. QM/MM, fragmentation or semiempirical (SQM) methods had to be pursued to overcome the unfavorable scaling of QM methods. Various SQM-based approaches have significantly contributed to the accuracy of docking and improvement of lead compounds. Parametrizations of SQM and implicit solvent methods in our laboratory have been instrumental to obtain a reliable SQM-based scoring function. The experience gained in its application for activity ranking of ligands binding to tens of protein targets resulted in setting up a faster SQM/COSMO scoring approach, which outperforms standard scoring methods in native pose identification for two dozen protein targets with ten thousand poses. Recently, SQM/COSMO was effectively applied in a proof-of-concept study of enrichment in virtual screening. Due to its superior performance, feasibility and chemical generality, we propose the SQM/COSMO approach as an efficient tool in structure-based drug design.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Vijay Madhav Miriyala
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry, and Biochemistry of Czech Academy of Sciences, Flemingovo namesti 2, 166 10, Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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26
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Assaf KI, Holub J, Bernhardt E, Oliva‐Enrich JM, Fernández Pérez MI, Canle M, Santaballa JA, Fanfrlík J, Hnyk D, Nau WM. Face-Fusion of Icosahedral Boron Hydride Increases Affinity to γ-Cyclodextrin: closo,closo-[B 21 H 18 ] - as an Anion with Very Low Free Energy of Dehydration. Chemphyschem 2020; 21:971-976. [PMID: 32163219 PMCID: PMC7318346 DOI: 10.1002/cphc.201901225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/08/2020] [Indexed: 01/05/2023]
Abstract
The supramolecular recognition of closo,closo-[B21 H18 ]- by cyclodextrins (CDs) has been studied in aqueous solution by isothermal titration calorimetry and nuclear magnetic resonance spectroscopy. These solution studies follow up on previous mass-spectrometric measurements and computations, which indicated the formation and stability of CD ⋅ B21 H18- complexes in the gas phase. The thermodynamic signature of solution-phase binding is exceptional, the association constant for the γ-CD complex with B21 H18- reaches 1.8×106 M-1 , which is on the same order of magnitude as the so far highest observed value for the complex between γ-CD and a metallacarborane. The nature of the intermolecular interaction is also examined by quantum-mechanical computational protocols. These suggest that the desolvation penalty, which is particularly low for the B21 H18- anion, is the decisive factor for its high binding strength. The results further suggest that the elliptical macropolyhedral boron hydride is another example of a CD binder, whose extraordinary binding affinity is driven by the chaotropic effect, which describes the intrinsic affinity of large polarizable and weakly solvated chaotropic anions to hydrophobic cavities and surfaces in aqueous solution.
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Affiliation(s)
- Khaleel I. Assaf
- Department of Life Sciences and ChemistryJacobs University BremenCampus Ring 128759BremenGermany
- Department of ChemistryAl-Balqa Applied University19117Al-SaltJordan
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences25068Husinec-ŘežCzech Republic
| | - Eduard Bernhardt
- Bergische University WuppertalGaussstrasse 2042097WuppertalGermany
| | | | - M. Isabel Fernández Pérez
- Departamento de QuímicaFacultade de Ciencias and CICAZapateiraUniversidade da Coruña Grupo de Reactividade Química e Fotorreactividade (REACT!) ESP-15071CoruñaSpain
| | - Moisés Canle
- Departamento de QuímicaFacultade de Ciencias and CICAZapateiraUniversidade da Coruña Grupo de Reactividade Química e Fotorreactividade (REACT!) ESP-15071CoruñaSpain
| | - J. Arturo Santaballa
- Departamento de QuímicaFacultade de Ciencias and CICAZapateiraUniversidade da Coruña Grupo de Reactividade Química e Fotorreactividade (REACT!) ESP-15071CoruñaSpain
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo nam. 216610PragueCzech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences25068Husinec-ŘežCzech Republic
| | - Werner M. Nau
- Department of Life Sciences and ChemistryJacobs University BremenCampus Ring 128759BremenGermany
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27
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Kovač I, Jakl M, Fanfrlík J, Andrushchenko V, Jaklová Dytrtová J. Complexation and stability of the fungicide penconazole in the presence of zinc and copper ions. Rapid Commun Mass Spectrom 2020; 34:e8714. [PMID: 31880851 DOI: 10.1002/rcm.8714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE For the risk assessment of penconazole in the environment and the evaluation of the possible consequences of its use, it is important to determine how its reactivity and degradation are influenced by metals commonly found in nature, such as copper and zinc. METHODS Changes in the reactivity of penconazole in the presence of zinc/copper ions were studied using electrospray ionisation mass spectrometry and density functional theory calculations. RESULTS Many penconazole complexes with copper and zinc ions were created; a comparison of the elements showed that a few complexes were formed analogously (doubly charged complexes with four penconazole molecules, singly charged complexes with chlorine as a counterion and singly charged complexes with deprotonated penconazole as a counterion). The metal complexes with different structures indicated different reactivity of penconazole with copper and zinc. CONCLUSIONS The experimental and computational approaches have revealed different changes in the structure of penconazole. In the Zn(II) complex, penconazole deprotonated to stabilise the bond to Zn(II). In the Cu(II) complex, it loses one chlorine atom, creates an additional ring between the triazole ring and the phenyl ring, and/or creates a double bond in the short aliphatic chain.
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Affiliation(s)
- Ishak Kovač
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- UNESCO Laboratory of Environmental Electrochemistry, Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Jakl
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague - Suchdol, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Jaklová Dytrtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Physiology and Biochemistry, Faculty of Physical Education and Sport, Charles University, Prague, Czech Republic
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28
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Houštecká R, Hadzima M, Fanfrlík J, Brynda J, Pallová L, Hánová I, Mertlíková-Kaiserová H, Lepšík M, Horn M, Smrčina M, Majer P, Mareš M. Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis. J Med Chem 2020; 63:1576-1596. [PMID: 32003991 DOI: 10.1021/acs.jmedchem.9b01351] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human cathepsin D (CatD), a pepsin-family aspartic protease, plays an important role in tumor progression and metastasis. Here, we report the development of biomimetic inhibitors of CatD as novel tools for regulation of this therapeutic target. We designed a macrocyclic scaffold to mimic the spatial conformation of the minimal pseudo-dipeptide binding motif of pepstatin A, a microbial oligopeptide inhibitor, in the CatD active site. A library of more than 30 macrocyclic peptidomimetic inhibitors was employed for scaffold optimization, mapping of subsite interactions, and profiling of inhibitor selectivity. Furthermore, we solved high-resolution crystal structures of three macrocyclic inhibitors with low nanomolar or subnanomolar potency in complex with CatD and determined their binding mode using quantum chemical calculations. The study provides a new structural template and functional profile that can be exploited for design of potential chemotherapeutics that specifically inhibit CatD and related aspartic proteases.
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Affiliation(s)
- Radka Houštecká
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,First Faculty of Medicine , Charles University , Kateřinská 32 , 12108 Praha 2 , Czech Republic
| | - Martin Hadzima
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,Department of Organic Chemistry, Faculty of Science , Charles University , Albertov 6 , 12800 Praha 2 , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Lenka Pallová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Iva Hánová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic.,Department of Biochemistry, Faculty of Science , Charles University , Albertov 6 , 12800 Praha 2 , Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Martin Smrčina
- Tucson Research Center , Icagen Inc. , 2090 E. Innovation Park Drive , Oro Valley , Arizona 85755 , United States
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nám. 2 , 16610 Praha 6 , Czech Republic
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Holub J, Vrána J, Růžička A, Růžičková Z, Fanfrlík J, Hnyk D. Thiaboranes on Both Sides of the Icosahedral Barrier: Retaining and Breaking the Barrier with Carbon Functionalities. Chempluschem 2020; 84:822-827. [PMID: 31944001 DOI: 10.1002/cplu.201900115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/16/2019] [Indexed: 11/08/2022]
Abstract
The concept of icosahedral barrier has been expanded from the chemistry of carbaboranes to the area of thiaboranes. Both representatives of this barrier, i. e., closo-1,2-C2 B10 H12 and closo-1-SB11 H11 , are similar in their electron distribution, which is dominated by positive charge in the midpoint of the C-C vector and on the sulfur atom with experimentally determined dipole moments of 4.50 D and 3.64 D, respectively. This is a driving force for their reactivity as exemplified by their reactions with different carbon functionalities. Icosahedral closo-1-SB11 H11 reacts both with an electron sextet containing carbon (in the form of N-heterocyclic carbenes), reported earlier, and with methyl iodide with an electron octet on the carbon. The latter reaction provides hexamethylated thiaborane on the basis of methylation so far unknown in this area of heteroborane chemistry. The computations of the heat of formation (ΔHf 298 ) make it possible to estimate the height of the barrier as well as to propose closo-thiaboranes beyond the barrier. Eleven and twelve vertex thiaboranes with nido electron count are known experimentally for breaking the barrier. These computations also suggest that the larger nido-thiaboranes are promising candidates for the corresponding experimental availability, i. e., the ΔHf 298 of a 13-vertex nido-thiaborane cluster has been computed to be more negative than that of the well-known nido-SB10 H11 - cluster (-6.7 and -5.6 kcal mol-1 per vertex, respectively).
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Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry, of the Czech Academy of Sciences, 250 68, Husinec-Řež, Czech Republic
| | - Jan Vrána
- Department of General and Inorganic Chemistry Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences, 166 10, Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, of the Czech Academy of Sciences, 250 68, Husinec-Řež, Czech Republic
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Prudilová B, Otyepková E, Fanfrlík J, Hnyk D, Holub J, Petr M, Filip J, Čépe K, Lazar P, Otyepka M. Surface termination of MgB 2 unveiled by a combination of adsorption experiments and theoretical calculations. Phys Chem Chem Phys 2019; 21:7313-7320. [PMID: 30895998 DOI: 10.1039/c9cp00771g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Superconductivity in polycrystalline and thin-film MgB2 is strongly affected by the termination of its surface, but a reliable determination of the surface termination is still a challenging task of surface chemistry. Here, the surface properties of superconducting MgB2 were investigated using a combination of inverse gas chromatography and van der Waals corrected density functional theory calculations. The dispersive surface energy was measured as a function of the surface coverage and its value (58 mJ m-2 to 48 mJ m-2) was verified by high-level non-local EXX + RPA calculations, which predicted that the dispersive contribution to the cleavage energy was 56 mJ m-2. The isosteric adsorption enthalpies of cyclohexane, dioxane, acetone and acetonitrile molecules were measured on an MgB2 sample and compared to the DFT calculated enthalpies for the Mg-terminated MgB2, B-terminated MgB2 and MgO(001) surfaces. The close agreement between theory and experiment for the Mg-terminated surface suggested that the magnesium termination is the dominant surface phase of MgB2. Thus, combining inverse gas chromatography experiments with theoretical calculations may provide information about the surface termination.
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Affiliation(s)
- Barbora Prudilová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
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31
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Vrána J, Holub J, Samsonov MA, RůŽičková Z, Fanfrlík J, Hnyk D, RůŽička A. Thiaborane clusters with an exoskeletal B-H group. Chem Commun (Camb) 2019; 55:3375-3378. [PMID: 30816893 DOI: 10.1039/c9cc00952c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The thiaboranes closo-1-SB11H11 (1a) and 12-I-closo-1-SB11H10 (1b) react with 4-(dimethylamino)pyridine under inert conditions upon the formation of the nido-type thiaboranes 9-B{(4-Me2N)C5NH4}2(H)-7-SB10H11 and 9-B{(4-Me2N)C5NH4}2(H)-5-I-7-SB10H10 containing an exoskeletal B-H group. The same type of B-H moiety is also stabilised by one bipyridine molecule in a chelating fashion. These complexes are unstable in solution, and in air and hydrolyse to monodeboronated ionic compounds having [nido-7-SB10H11]- or [5-I-nido-7-SB10H10]- anions which are also products of the reactions of 1a and 1b with other N-bases such as pyridine, ammonia and DABCO. The extrusion of one boron and one sulphur atom takes place when 1a reacts with 2,6-di-tert-butylpyridine to yield decaborane.
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Affiliation(s)
- Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Studentská 573, CZ-532 10, Czech Republic.
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Vrána J, Holub J, Růžičková Z, Fanfrlík J, Hnyk D, Růžička A. Investigation of Thiaborane closo- nido Conversion Pathways Promoted by N-Heterocyclic Carbenes. Inorg Chem 2019; 58:2471-2482. [PMID: 30729783 DOI: 10.1021/acs.inorgchem.8b03037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 12-X- closo-SB11H10 (X = H or I) thiaboranes react with one or two molar equivalents of various N-heterocyclic carbenes (NHCs) to give the deprotonated 12-vertex species of [12-X-SB11H9·NHC]-[NHC-H]+composition as kinetic products. The use of one molar equivalent of a sterically more hindered NHC reactant leads to the formation of 12-X-SB11H10·NHC adducts with a heavily distorted cage and the nido electron count. Further reaction of 12-I-SB11H10·NHC to deboronated 12-X-SB10H9·NHC proceeds in acetone to complete the closo- nido reaction pathway under the thermodynamic control. The structures of all compounds have been investigated by NMR spectroscopy and diffraction techniques. The results are supported by theoretical methods.
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Affiliation(s)
- Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry , Czech Academy of Sciences , 250 68 Řež , Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry , Czech Academy of Sciences , 250 68 Řež , Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
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Bakardjiev M, Růžička A, Růžičková Z, Tok OL, Holub J, Hnyk D, Fanfrlík J, Štíbr B. Synthesis of closo-1,2-H 2C 2B 8Me 8 and 1,2-H 2C 2B 8Me 7X (X = I and OTf) Dicarbaboranes and Their Rearrangement Reactions. Inorg Chem 2019; 58:2865-2871. [PMID: 30730720 DOI: 10.1021/acs.inorgchem.8b03550] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methyl-camouflaged dicarbaboranes closo-1,2- and 1,10-H2C2B8Me8 have been prepared in high yields either from nido-5,6-H2C2B8H10 or closo-1,2-H2C2B8H8 via electrophilic methylation reactions and cluster-rearrangement methods. Prepared were also monosubstituted derivatives of general formulation closo-H2C2B8Me7-X (X = I or OTf). The permethylated compounds exhibit extreme air stability in comparison to unprotected counterparts as a consequence of rigid, egg-shaped hydrocarbon structures incorporating inner C2B8 carborane scaffolding. The structures of all compounds isolated were confirmed unambiguously by multinuclear (11B, 1H, 13C, and 19F) NMR measurements, supported by X-ray diffraction analyses and geometry optimization methods on several compounds.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemisty , of the Czech Academy of Sciences , Flemingovo nám, 5 , Prague 6 , Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry of the Czech Academy of Sciences , 250 68 Husinec-Řež , Czech Republic
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Baše T, Holub J, Fanfrlík J, Hnyk D, Lane PD, Wann DA, Vishnevskiy YV, Tikhonov D, Reuter CG, Mitzel NW. Icosahedral Carbaboranes with Peripheral Hydrogen-Chalcogenide Groups: Structures from Gas Electron Diffraction and Chemical Shielding in Solution. Chemistry 2019; 25:2313-2321. [DOI: 10.1002/chem.201805145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/27/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Tomáš Baše
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of, the Czech Academy of Sciences; 166 10 Praha 6 Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences; 250 68 Husinec-Řež Czech Republic
| | - Paul D. Lane
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
- Present address: School of Engineering and Physical Sciences; Heriot-Watt University; Edinburgh EH14 4AS UK
| | - Derek A. Wann
- Department of Chemistry; University of York; Heslington York YO10 5DD UK
| | - Yury V. Vishnevskiy
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Denis Tikhonov
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
- Present addresses: Department of Physical Chemistry; M. V. Lomonosov Moscow State University; GSP-1, 1-3 Leninskiye Gory 119991 Moscow Russian Federation
- FS-SMP Deutsches Elektronen-Synchrotron (DESY); Notkestrasse 85, Building 25f, Room 353 22607 Hamburg Germany
| | - Christian G. Reuter
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert W. Mitzel
- Fakultät für Chemie, Lehrstuhl für Anorganische Chemie, und Strukturchemie, Centrum für molekulare Materialien CM 2; Universität Bielefeld; Universitätsstrasse 25 33615 Bielefeld Germany
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Macháček J, Francés-Monerris A, Karmodak N, Roca-Sanjuán D, Fanfrlík J, Londesborough MGS, Hnyk D, Jemmis ED. A theoretical analysis of the structure and properties of B26H30 isomers. Consequences to the laser and semiconductor doping capabilities of large borane clusters. Phys Chem Chem Phys 2019; 21:12916-12923. [DOI: 10.1039/c9cp02371b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most stable isomer B26H30 with its predicted applications.
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Affiliation(s)
- Jan Macháček
- Institute of Inorganic Chemistry
- Czech Academy of Sciences
- CZ-250 68 Husinec-Řež
- Czech Republic
| | | | - Naiwrit Karmodak
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 56001
- India
| | | | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-166 10 Praha 6
- Czech Republic
| | | | - Drahommír Hnyk
- Institute of Inorganic Chemistry
- Czech Academy of Sciences
- CZ-250 68 Husinec-Řež
- Czech Republic
| | - Eluvathingal D. Jemmis
- Department of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bangalore 56001
- India
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36
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Bakardjiev M, Tok OL, Růžička A, Růžičková Z, Holub J, Hnyk D, Fanfrlík J, Štíbr B. Quantitative syntheses of permethylated closo-1,10-R 2C 2B 8Me 8 (R = H, Me) carboranes. Egg-shaped hydrocarbons on the Frontier between inorganic and organic chemistry. RSC Adv 2018; 8:38238-38244. [PMID: 35559069 PMCID: PMC9090134 DOI: 10.1039/c8ra06640j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/31/2018] [Indexed: 11/25/2022] Open
Abstract
Electrophilic methylation of the closo-1,10-R2C2B8H8 (1) (R = H or Me) dicarbaboranes at higher temperatures or thermal rearrangement of the 1,6-R2C2B8Me8 (3) compounds at 400-500 °C generated the B-permethylated derivatives closo-1,10-R2C2B8Me8 (2) in quantitative (>95%) yields. The compounds exhibit extreme air stability as a consequence of a rigid, egg shaped hydrocarbon structures incorporating inner 1,10-C2B8 carborane core.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice Studentská 573 532 10 Pardubice Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice Studentská 573 532 10 Pardubice Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2, 166 10 Prague 6 Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic Husinec-Řež 1001 Czech Republic
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Melánová K, Holub J, Hynek J, Fanfrlík J, Beneš L, Kutálek P, Krejčová A, Hnyk D, Zima V. Outerly functionalized and non-functionalized boron clusters intercalated into layered hydroxides with different modes of binding: materials for superacid storage. Dalton Trans 2018; 47:11669-11679. [PMID: 30101969 DOI: 10.1039/c8dt02251h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two binary boron hydrides (NH4)2B10H10 and Na2B12H12 and mono- and dicarboxy p- and m-carboranes (namely, 1-(COOH)-closo-1,7-C2B10H11, 1,12-(COOH)2-closo-1,12-C2B10H10 and 1,7-(COOH)2-closo-1,7-C2B10H10) were intercalated into ZnAl-layered double hydroxides (ZnAl-LDH) and into Zn5(OH)8(NO3)2·2H2O. The formed compounds were characterized using elemental analysis, thermogravimetry analysis, X-ray powder diffraction, infrared spectroscopy and solid state NMR. All the intercalated boron compounds are present in the interlayer space of the layered hosts as anions. It is presumed that in the case of B10H102-, B12H122- and 1,12-(COO)2-closo-1,12-C2B10H102-, the guest molecules form a monolayer, whereas in the case of 1-(COO)-closo-1,7-C2B10H111- and 1,7-(COO)2-closo-1,7-C2B10H102- a bilayer arrangement is more probable. In the case of 1,7-(COO)2-closo-1,7-C2B10H102-, the guest molecules are strongly interdigitated resulting in lowering of the interlayer distance. Two different modes of binding were found. Whereas the carboxylate derivatives of p- and m-carboranes are bonded through classical hydrogen bonds, the corresponding parent borane anions interact with the host structures by mainly dihydrogen bonding. In effect, both kinds of hydrogen bonding are mainly of an electrostatic nature. The dihydrogen bond is detected, e.g. in crystal engineering, and represents a driving force for interactions of boranes with biomolecules. Since the latter dicarboxylic acids were found to be superacids, their interactions with the host structures should be stronger than in the case of the benzoic and terephthalic acid intercalates.
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Affiliation(s)
- Klára Melánová
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic.
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec - ŘeŽ, Czech Republic.
| | - Jan Hynek
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec - ŘeŽ, Czech Republic.
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Ludvík Beneš
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 532 10 Pardubice, Czech Republic
| | - Petr Kutálek
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 532 10 Pardubice, Czech Republic
| | - Anna Krejčová
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 532 10 Pardubice, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec - ŘeŽ, Czech Republic.
| | - Vítězslav Zima
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czech Republic.
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Bakardjiev M, Tok OL, RůŽička A, RůŽičková Z, Holub J, Hnyk D, Špalt Z, Fanfrlík J, Štíbr B. Methyl camouflage in the ten-vertex closo-dicarbaborane(10) series. Isolation of closo-1,6-R 2C 2B 8Me 8 (R = H and Me) and their monosubstituted analogues. Dalton Trans 2018; 47:11070-11076. [PMID: 30033463 DOI: 10.1039/c8dt02586j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Reported are procedures leading to the first types of methyl camouflaged dicarbadecaboranes with fewer than eleven vertices. The compounds contain the closo-1,6-C2B8 scaffolding inside the egg-shaped hepta - decamethyl sheath, which imparts unusually high air and solvolytic stability to all of these compounds.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Oleg L Tok
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Aleš RůŽička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Zdeňka RůŽičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Zbyněk Špalt
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Bohumil Štíbr
- Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Husinec-ŘeŽ 1001, Czech Republic
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Kříž K, Fanfrlík J, Lepšík M. Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Chemphyschem 2018; 19:2540-2548. [PMID: 30003638 DOI: 10.1002/cphc.201800409] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 11/10/2022]
Abstract
A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry Faculty of Science, Charles University, Hlavova 8, 128 40, Praha 2, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
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40
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Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlík J. Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes. Chemphyschem 2018; 19:873-879. [PMID: 29316128 DOI: 10.1002/cphc.201701104] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/11/2022]
Abstract
Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by including quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function by using a challenging set of 10 inhibitors binding to carbonic anhydrase II through Zn2+ in the active site. This new dataset consists of the high-resolution (1.1-1.4 Å) crystal structures and experimentally determined inhibitory constant (Ki ) values. It allows for evaluation of the common approximations, such as representing the solvent implicitly or by using a single target conformation combined with a set of ligand docking poses. SQM/COSMO attained a good correlation of R2 of 0.56-0.77 with the experimental inhibitory activities, benefiting from careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.
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Affiliation(s)
- Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Vrzal
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Ramachandran Gnanasekaran
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Current address: Department of Chemistry, Pondicherry University, Puducherry, 605014, India
| | - Magdalena Hořejší
- Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Saltuk M Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Palacký University, 77146, Olomouc, Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Institute of Molecular Genetics of, Czech Academy of Sciences, Videnska 1083, 14220, Prague 4, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Palacký University, 77146, Olomouc, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
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41
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Abstract
A systematic revision of bonding types on a broad series of heteroboranes covering closo, nido, arachno and hypho architectures with incorporated tetrel, pnictogen or chalcogen heterovertices.
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Affiliation(s)
- Petr Melichar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i
- 250 68 Husinec-Řež
- Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
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42
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Holub J, Růžičková Z, Hobza P, Fanfrlík J, Hnyk D, Růžička A. Various types of non-covalent interactions contributing towards crystal packing of halogenated diphospha-dicarbaborane with an open pentagonal belt. NEW J CHEM 2018. [DOI: 10.1039/c8nj00450a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have synthesized and crystalized 3-Cl-10-I-nido-7,8,9,11-P2C2B7H7. Quantum chemical calculations have demonstrated that the obtained crystal structure is stabilized by hydrogen, dihydrogen and pnictogen bonds.
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Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- 250 68 Husinec-Řež
- Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- 53210 Pardubice
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- 250 68 Husinec-Řež
- Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- 53210 Pardubice
- Czech Republic
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43
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Jakl M, Fanfrlík J, Jaklová Dytrtová J. Mimicking of cyproconazole behavior in the presence of Cu and Zn. Rapid Commun Mass Spectrom 2017; 31:2043-2050. [PMID: 28901039 DOI: 10.1002/rcm.7988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 09/05/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE The frequently used pesticide cyproconazole (Cyp) interacts with the essential elements commonly present in soil which play important roles in various enzymatic processes. These interactions predetermine the Cyp degradation pathways. We suggest a simple experimental and theoretical approach for the prediction of pesticide behavior. METHODS Cu/Cyp complexes are explored because of the typical Cu(II) reduction in complexes. Its level and the stability of the Cu-ligand bond depend on the type and the number of the surrounding ligands. Zn/Cyp complexes were compared as it is not expected that Zn(II) will reduce. The complexations were studied by means of electrospray ionization ion trap mass spectrometry and MS/MS collision-induced dissociations with comparative and explicative density functional theory calculations. RESULTS The Cyp ligand allows both Cu(II) reduction as well as, in specific cases, it protects the higher Cu oxidation state. The reduction is observed in the complexes with solely neutral Cyp where the number of ligands is below 3; a higher number protects the Cu(II) state. The metal atom binds to Cyp via N2 of the triazole ring as well as via π-electrons of the benzene ring; additional stabilization brings an interaction with the deprotonated OH group. CONCLUSIONS The character of Cyp interactions with doubly charged metals (Cu(II), Zn(II)) clarified the creation of Cyp metabolites. The phenyl and triazole rings are bound to the metal cation and enable access for the isopropyl ring to be cleaved leaving the common metabolite (CAS Number: 58905-19-4).
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Affiliation(s)
- Michal Jakl
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague - Suchdol, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Jana Jaklová Dytrtová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
- Department of Physiology and Biochemistry, Faculty of Physical Education and Sport, Charles University, Prague 6, Czech Republic
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44
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Macháček J, Bühl M, Fanfrlík J, Hnyk D. Nuclear Magnetic Shielding of Monoboranes: Calculation and Assessment of 11B NMR Chemical Shifts in Planar BX3 and in Tetrahedral [BX4]− Systems. J Phys Chem A 2017; 121:9631-9637. [DOI: 10.1021/acs.jpca.7b09831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Macháček
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, v.v.i., 1001, CZ-250 68 Husinec-Řež, Czech Republic
| | - Michael Bühl
- School
of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-66 10 Prague 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, v.v.i., 1001, CZ-250 68 Husinec-Řež, Czech Republic
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45
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Holub J, Melichar P, Růžičková Z, Vrána J, Wann DA, Fanfrlík J, Hnyk D, Růžička A. A novel stibacarbaborane cluster with adjacent antimony atoms exhibiting unique pnictogen bond formation that dominates its crystal packing. Dalton Trans 2017; 46:13714-13719. [PMID: 28956033 DOI: 10.1039/c7dt02845h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have prepared nido-7,8,9,11-Sb2C2B7H9, the first cluster with simultaneous Sb-B, Sb-C and Sb-Sb atom pairs with interatomic separations with magnitudes that approach the respective sums of covalent radii. However, the length of the Sb-Sb separation in this cluster is slightly less than the sum of the covalent radii. Quantum chemical analysis has revealed that the crystal packing of nido-7,8,9,11-Sb2C2B7H9 is predominantly dictated by pnictogen (Pn) bonding, an unconventional σ-hole interaction. Indeed, the interaction energy of a very strong Sb2H-B Pn-bond in the nido-7,8,9,11-Sb2C2B7H9 dimer exceeds -6.0 kcal mol-1. This is a very large value and is comparable to the strengths of known Pn-bonds in Cl3Pnπ complexes (Pn = As, Sb).
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Affiliation(s)
- Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, v.v.i., 250 68 Husinec-Řež, Czech Republic.
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46
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Ajani H, Pecina A, Eyrilmez SM, Fanfrlík J, Haldar S, Řezáč J, Hobza P, Lepšík M. Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking. ACS Omega 2017; 2:4022-4029. [PMID: 30023710 PMCID: PMC6044937 DOI: 10.1021/acsomega.7b00503] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/18/2017] [Indexed: 06/08/2023]
Abstract
General and reliable description of structures and energetics in protein-ligand (PL) binding using the docking/scoring methodology has until now been elusive. We address this urgent deficiency of scoring functions (SFs) by the systematic development of corrected semiempirical quantum mechanical (SQM) methods, which correctly describe all types of noncovalent interactions and are fast enough to treat systems of thousands of atoms. Two most accurate SQM methods, PM6-D3H4X and SCC-DFTB3-D3H4X, are coupled with the conductor-like screening model (COSMO) implicit solvation model in so-called "SQM/COSMO" SFs and have shown unique recognition of native ligand poses in cognate docking in four challenging PL systems, including metalloprotein. Here, we apply the two SQM/COSMO SFs to 17 diverse PL complexes and compare their performance with four widely used classical SFs (Glide XP, AutoDock4, AutoDock Vina, and UCSF Dock). We observe superior performance of the SQM/COSMO SFs and identify challenging systems. This method, due to its generality, comparability across the chemical space, and lack of need for any system-specific parameters, gives promise of becoming, after comprehensive large-scale testing in the near future, a useful computational tool in structure-based drug design and serving as a reference method for the development of other SFs.
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Affiliation(s)
- Haresh Ajani
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Adam Pecina
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Saltuk M. Eyrilmez
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Palacký University, tř. 17. listopadu 1192/12, 77146 Olomouc, Czech Republic
| | - Jindřich Fanfrlík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Susanta Haldar
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Jan Řezáč
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
| | - Pavel Hobza
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacký University, 77146 Olomouc, Czech Republic
| | - Martin Lepšík
- Department
of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic
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47
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Nekardová M, Vymětalová L, Khirsariya P, Kováčová S, Hylsová M, Jorda R, Kryštof V, Fanfrlík J, Hobza P, Paruch K. Structural Basis of the Interaction of Cyclin-Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles. Chemphyschem 2017; 18:785-795. [DOI: 10.1002/cphc.201601319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Michaela Nekardová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Faculty of Mathematics and Physics; Charles University in Prague; Ke Karlovu 3 Prague 2 121 16 Czech Republic
| | - Ladislava Vymětalová
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
| | - Silvia Kováčová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Michaela Hylsová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
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48
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Pecina A, Haldar S, Fanfrlík J, Meier R, Řezáč J, Lepšík M, Hobza P. SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses. J Chem Inf Model 2017; 57:127-132. [DOI: 10.1021/acs.jcim.6b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Adam Pecina
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Susanta Haldar
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jindřich Fanfrlík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - René Meier
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Jan Řezáč
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Palacký University, 77146 Olomouc, Czech Republic
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49
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Fanfrlík J, Pecina A, Řezáč J, Sedlak R, Hnyk D, Lepšík M, Hobza P. B–H⋯π: a nonclassical hydrogen bond or dispersion contact? Phys Chem Chem Phys 2017; 19:18194-18200. [DOI: 10.1039/c7cp02762a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum mechanical calculations disprove the attractive electrostatic nature of B–H⋯π motif and define it as dispersion-driven contact.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Robert Sedlak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i., 250 68 Husinec-Řež
- Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials
- Department of Physical Chemistry
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50
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Eyrilmez SM, Bernhardt E, Dávalos JZ, Lepšík M, Hobza P, Assaf KI, Nau WM, Holub J, Oliva-Enrich JM, Fanfrlík J, Hnyk D. Binary twinned-icosahedral [B21H18]− interacts with cyclodextrins as a precedent for its complexation with other organic motifs. Phys Chem Chem Phys 2017; 19:11748-11752. [DOI: 10.1039/c7cp01074e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A macropolyhedral boron hydride anion with two counterions can form stable complexes with β- and γ-cyclodextrin in the gas phase.
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Affiliation(s)
- Saltuk M. Eyrilmez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
- Department of Physical Chemistry, Palacký University
| | - Eduard Bernhardt
- Bergische University Wuppertal, Gaussstrasse 20
- D-42097 Wuppertal
- Germany
| | - Juan Z. Dávalos
- Instituto de Química-Física “Rocasolano”, CSIC
- ES-28006 Madrid
- Spain
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University
| | - Khaleel I. Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1
- D-28759 Bremen
- Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1
- D-28759 Bremen
- Germany
| | - Josef Holub
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i. CZ-25068 Husinec-Řež
- Czech Republic
| | | | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- Flemingovo nam. 2
- CZ-16610 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i. CZ-25068 Husinec-Řež
- Czech Republic
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