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Oszajca M, Flejszar M, Szura A, Dróżdż P, Brindell M, Kurpiewska K. Exploring the coordination chemistry of ruthenium complexes with lysozymes: structural and in-solution studies. Front Chem 2024; 12:1371637. [PMID: 38638879 PMCID: PMC11024358 DOI: 10.3389/fchem.2024.1371637] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/06/2024] [Indexed: 04/20/2024] Open
Abstract
This study presents a comprehensive structural analysis of the adducts formed upon the reaction of two Ru(III) complexes [HIsq][trans-RuIIICl4(dmso)(Isq)] (1) and [H2Ind][trans-RuIIICl4(dmso)(HInd)] (2) (where HInd-indazole, Isq-isoquinoline, analogs of NAMI-A) and two Ru(II) complexes, cis-[RuCl2(dmso)4] (c) and trans-[RuCl2(dmso)4] (t), with hen-egg white lysozyme (HEWL). Additionally, the crystal structure of an adduct of human lysozyme (HL) with ruthenium complex, [H2Ind][trans-RuCl4(dmso)(HInd)] was solved. X-ray crystallographic data analysis revealed that all studied Ru complexes, regardless of coordination surroundings and metal center charge, coordinate to the same amino acids (His15, Arg14, and Asp101) of HEWL, losing most of their original ligands. In the case of the 2-HL adduct, two distinct metalation sites: (i) Arg107, Arg113 and (ii) Gln127, Gln129, were identified. Crystallographic data were supported by studies of the interaction of 1 and 2 with HEWL in an aqueous solution. Hydrolytic stability studies revealed that both complexes 1 and 2 liberate the N-heterocyclic ligand under crystallization-like conditions (pH 4.5) as well as under physiological pH conditions, and this process is not significantly affected by the presence of HEWL. A comparative examination of nine crystal structures of Ru complexes with lysozyme, obtained through soaking and co-crystallization experiments, together with in-solution studies of the interaction between 1 and 2 with HEWL, indicates that the hydrolytic release of the N-heterocyclic ligand is one of the critical factors in the interaction between Ru complexes and lysozyme. This understanding is crucial in shedding light on the tendency of Ru complexes to target diverse metalation sites during the formation and in the final forms of the adducts with proteins.
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Affiliation(s)
- Maria Oszajca
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Monika Flejszar
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
- Department of Physical Chemistry, Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Arkadiusz Szura
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Patrycja Dróżdż
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Małgorzata Brindell
- Department of Inorganic Chemistry, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Kraków, Poland
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2
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Patil P, Zheng Q, Kurpiewska K, Dömling A. Author Correction: The isocyanide S N2 reaction. Nat Commun 2023; 14:6239. [PMID: 37803066 PMCID: PMC10558445 DOI: 10.1038/s41467-023-42066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023] Open
Affiliation(s)
- Pravin Patil
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Qiang Zheng
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, 30-387, Kraków, Poland
| | - Alexander Dömling
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic.
- Department of Drug Design, University of Groningen, Groningen, The Netherlands.
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3
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Bonarek P, Mularczyk D, Loch JI, Kurpiewska K, Dziedzicka-Wasylewska M. β-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. J Mol Recognit 2023; 36:e3052. [PMID: 37610054 DOI: 10.1002/jmr.3052] [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: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
β-Lactoglobulin (BLG) is a member of the lipocalin family. As other proteins from this group, BLG can be modified to bind specifically compounds of medical interests. The aim of this study was to evaluate the role of two mutations, L39Y and L58F, in the binding of topical anesthetic pramoxine (PRM) to β-lactoglobulin. Circular dichroism spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography were used to understand the mechanisms of BLG-PRM interactions. Studies were performed for three new BLG mutants: L39Y, L58F, and L39Y/L58F. ITC measurements indicated a significant increase in the affinity to the PRM of variants L58F and L39Y. Measurements taken for the double mutant L39Y/L58F showed the additivity of two mutations leading to about 80-fold increase in the affinity to PRM in comparison to natural protein BLG from bovine milk. The determined crystal structures revealed that pramoxine is accommodated in the β-barrel interior of BLG mutants and stabilized by hydrophobic interactions. The observed additive effect of two mutations on drug binding opens the possibility for further designing of new BLG variants with high affinity to selected drugs.
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Affiliation(s)
- Piotr Bonarek
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Dorota Mularczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Joanna I Loch
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
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4
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Patil P, Zheng Q, Kurpiewska K, Dömling A. The isocyanide S N2 reaction. Nat Commun 2023; 14:5807. [PMID: 37726293 PMCID: PMC10509164 DOI: 10.1038/s41467-023-41253-2] [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: 03/25/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
The SN2 nucleophilic substitution reaction is a vital organic transformation used for drug and natural product synthesis. Nucleophiles like cyanide, oxygen, nitrogen, sulfur, or phosphorous replace halogens or sulfonyl esters, forming new bonds. Isocyanides exhibit unique C-centered lone pair σ and π* orbitals, enabling diverse radical and multicomponent reactions. Despite this, their nucleophilic potential in SN2 reactions remains unexplored. We have uncovered that isocyanides act as versatile nucleophiles in SN2 reactions with alkyl halides. This yields highly substituted secondary amides through in situ nitrilium ion hydrolysis introducing an alternative bond break compared to classical amide synthesis. This novel 3-component process accommodates various isocyanide and electrophile structures, functional groups, scalability, late-stage drug modifications, and complex compound synthesis. This reaction greatly expands chemical diversity, nearly doubling the classical amid coupling's chemical space. Notably, the isocyanide nucleophile presents an unconventional Umpolung amide carbanion synthon (R-NHC(-) = O), an alternative to classical amide couplings.
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Affiliation(s)
- Pravin Patil
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Qiang Zheng
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, 30-387, Kraków, Poland
| | - Alexander Dömling
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic.
- Department of Drug Design, University of Groningen, Groningen, The Netherlands.
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5
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Abstract
Guanine is one out of five endogenous nucleobases and of key interest in drug discovery and chemical biology. Hitherto, the synthesis of guanine derivatives involves lengthy multistep sequential synthesis of low overall diversity, resulting in the quest for innovation. Using a "single-atom skeletal editing" approach, we designed 2-aminoimidazo[2,1-f][1,2,4]triazin-4(3H)-one as a guanine isostere, conserving the biologically important HBA-HBD-HBD (HBA = hydrogen bond acceptor; HBD = hydrogen bond donor) substructure. We realized our design by a simple one-pot two-step method combining the Groebke-Blackburn-Bienaymé reaction (GBB-3CR) and a deprotection reaction to assemble the innovative guanine isosteres in moderate to good yields. Our innovative, diverse, short, and reliable multicomponent reaction synthesis will add to the toolbox of guanine isostere syntheses.
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Affiliation(s)
- Xin Li
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Marina Diguele Romero
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Sona Tcaturian
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Wójcik P, Glanowski M, Mrugała B, Procner M, Zastawny O, Flejszar M, Kurpiewska K, Niedziałkowska E, Minor W, Oszajca M, Bojarski AJ, Wojtkiewicz AM, Szaleniec M. Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Δ 1-Dehydrogenase from Sterolibacterium denitrificans─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis. Biochemistry 2023; 62:808-823. [PMID: 36625854 PMCID: PMC9960185 DOI: 10.1021/acs.biochem.2c00576] [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: 01/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenases (KstD) are important microbial flavin enzymes that initiate the metabolism of steroid ring A and find application in the synthesis of steroid drugs. We present a structure of the KstD from Sterolibacterium denitrificans (AcmB), which contains a previously uncharacterized putative membrane-associated domain and extended proton-relay system. The experimental and theoretical studies show that the steroid Δ1-dehydrogenation proceeds according to the Ping-Pong bi-bi kinetics and a two-step base-assisted elimination (E2cB) mechanism. The mechanism is validated by evaluating the experimental and theoretical kinetic isotope effect for deuterium-substituted substrates. The role of the active-site residues is quantitatively assessed by point mutations, experimental activity assays, and QM/MM MD modeling of the reductive half-reaction (RHR). The pre-steady-state kinetics also reveals that the low pH (6.5) optimum of AcmB is dictated by the oxidative half-reaction (OHR), while the RHR exhibits a slight optimum at the pH usual for the KstD family of 8.5. The modeling confirms the origin of the enantioselectivity of C2-H activation and substrate specificity for Δ4-3-ketosteroids. Finally, the cholest-4-en-3-one turns out to be the best substrate of AcmB in terms of ΔG of binding and predicted rate of dehydrogenation.
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Affiliation(s)
- Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Magdalena Procner
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Olga Zastawny
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Monika Flejszar
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland; Department of Physical Chemistry, Faculty of Chemistry, Rzeszow University of Technology, 35-959 Rzeszów, Poland
| | | | - Ewa Niedziałkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Maria Oszajca
- Faculty of Chemistry, Jagiellonian University,30-387 Kraków, Poland
| | - Andrzej J. Bojarski
- Jerzy Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Kraków, Poland
| | - Agnieszka M. Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Kraków, Poland
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Li X, Wang Q, Zheng Q, Kurpiewska K, Kalinowska-Tluscik J, Dömling A. Access to Isoquinolin-2(1 H)-yl-acetamides and Isoindolin-2-yl-acetamides from a Common MCR Precursor. J Org Chem 2022; 87:14463-14475. [PMID: 36282152 PMCID: PMC9639002 DOI: 10.1021/acs.joc.2c01905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Indexed: 01/07/2023]
Abstract
We achieved a divergent synthesis of isoquinolin-2(1H)-yl-acetamides (16 examples, up to 90% yields) and regioselective isoindolin-2-yl-acetamides (14 examples, up to 93% yields) in moderate to good yields by reacting various substituted ethanones or terminal alkynes with Ugi-4CR intermediates via an ammonia-Ugi-4CR/Copper(I)-catalyzed annulation sequence reaction. The same intermediate thus gives 2D distant but 3D closely related scaffolds, which can be of high interest in exploiting chemistry space on a receptor. The scopes and limitations of these efficient sequence reactions are described, as well as gram-scale synthesis.
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Affiliation(s)
- Xin Li
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qian Wang
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qiang Zheng
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty
of Chemistry, Department of Crystal Chemistry and Crystal, Physics,
Biocrystallography Group, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kalinowska-Tluscik
- Faculty
of Chemistry, Department of Crystal Chemistry and Crystal, Physics,
Biocrystallography Group, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands,
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8
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Rogacz K, Brzozowska M, Baś S, Kurpiewska K, Pinkowicz D. Low-Coordinate Erbium(III) Single-Molecule Magnets with Photochromic Behavior. Inorg Chem 2022; 61:16295-16306. [PMID: 36197744 PMCID: PMC9580000 DOI: 10.1021/acs.inorgchem.2c01999] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The structures and magnetic properties of photoresponsive
magnets
can be controlled or fine-tuned by visible light irradiation, which
makes them appealing as candidates for ternary memory devices: photochromic
and photomagnetic at the same time. One of the strategies for photoresponsive
magnetic systems is the use of photochromic/photoswitchable molecules
coordinated to paramagnetic metal centers to indirectly influence
their magnetic properties. Herein, we present two erbium(III)-based
coordination systems: a trinuclear molecule {[ErIII(BHT)3]3(dtepy)2}.4C5H12 (1) and a 1D coordination chain {[ErIII(BHT)3(azopy)}n·2C5H12 (2), where the bridging photochromic
ligands belong to the class of diarylethenes: 1,2-bis((2-methyl-5-pyridyl)thie-3-yl)perfluorocyclopentene
(dtepy) and 4,4′-azopyridine (azopy), respectively (BHT = 2,6-di-tert-butyl-4-methylphenolate). Both compounds show slow
dynamics of magnetization, typical for single-molecule magnets (SMMs)
as revealed by alternating current (AC) magnetic susceptibility measurements.
The trinuclear compound 1 also shows an immediate color
change from yellow to dark blue in response to near-UV irradiation.
Such behavior is typical for the photoisomerization of the open form
of the ligand into its closed form. The color change can be reversed
by exposing the closed form to visible light. The chain-like compound 2, on the other hand, does not show significant signs of the
expected trans–cis photoisomerization
of the azopyridine in response to UV irradiation and does not appear
to show photoswitching behavior. Three-coordinate
[ErIII(BHT)3] single
ion magnets undergo ligand addition reaction in pentane to form linear
trinuclear photochromic nanomagnets where both functionalities persist.
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Affiliation(s)
- Katarzyna Rogacz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Kraków, Poland
| | - Maria Brzozowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Kraków, Poland
| | - Sebastian Baś
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Kraków, Poland
| | - Dawid Pinkowicz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Kraków, Poland
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9
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Zheng Q, Li X, Kurpiewska K, Dömling A. Synthesis of Tunable Fluorescent Imidazole-Fused Heterocycle Dimers. Org Lett 2022; 24:5014-5017. [PMID: 35830622 PMCID: PMC9490819 DOI: 10.1021/acs.orglett.2c01642] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A short, concise, and one-pot synthesis of imidazo-fused
heterocycle
dimers with tunable fluorescent properties has been developed. By
the first time use of glyoxal dimethyl acetal in the Groebke–Blackburn–Bienaymé
(GBB) three-component reaction (3CR), the innovation features a new
series of fluorescence-tunable imidazo-fused heterocycle dimers exhibiting
a broad substrate scope with good yields. Luminescence studies demonstrate
that these GBB-dimers possess color-tunable properties, and their
emission colors can be successively changed from blue to green and
yellow by easy substituent control.
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Affiliation(s)
- Qiang Zheng
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xin Li
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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10
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Abstract
Discovering novel synthetic routes for rigid nitrogen-containing polyheterocycles using sustainable, atom-economical, and efficient (= short) synthetic pathways is of high interest in organic chemistry. Here, we describe an operationally simple and short synthesis of the privileged scaffold dihydropyrrolo[1,2-a]pyrazine-dione from readily accessible starting materials. The alkaloid-type polycyclic scaffold with potential bioactivity was achieved by a multicomponent reaction (MCR)-based protocol via a Ugi four-component reaction and Pictet-Spengler sequence under different conditions, yielding a diverse library of products.
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Affiliation(s)
- Bidong Zhang
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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11
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Impert O, Kozakiewicz-Piekarz A, Katafias A, Witwicki M, Komarnicka UK, Kurpiewska K, van Eldik R. Mixed-valence outer-sphere RuII/RuIII ion-pair complexes. Synthesis, experimental, and theoretical studies. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Affiliation(s)
- Qiang Zheng
- Department of Drug Design University of Groningen Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry Jagiellonian University 30-387 Kraków Poland
| | - Alexander Dömling
- Department of Drug Design University of Groningen Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
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13
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Kluza A, Mrugala B, Kurpiewska K, Porebski PJ, Niedzialkowska E, Minor W, Weiss MS, Chruszcz M, Borowski T. On substrate-binding cavity of hyoscyamine 6β-hydroxylase from devil's trumpet. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Kurpiewska K, Borowski T, Borowski T. Seven quick tips for beginners in protein crystallography. Acta Biochim Pol 2021; 68:535-546. [PMID: 34379378 DOI: 10.18388/abp.2020_5589] [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] [Received: 01/10/2021] [Accepted: 02/28/2021] [Indexed: 11/10/2022]
Abstract
The aim of this brief review is to provide a roadmap for beginning crystallographers who have little or no experience in structural biology and yet are keen to produce protein crystals and analyze their 3D structures to understand their biological roles. To achieve this goal it is crucial to perform crystallization, structure determination, visualization and analysis of the protein's structural features related to its biological function. Keeping that objective in mind, tips presented herein cover the most important steps in a crystallographic endeavor and present a selection of databases and software which can aid and accelerate the whole process. We hope that this short overview will help novices coming from different disciplines to navigate a protein crystallography project and, hopefully, allow avoiding some costly mistakes, even though being a crystallographer means learning by trial and error.
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Affiliation(s)
| | | | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences: Kraków, Poland
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15
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Sonani RR, Kurpiewska K, Lewiński K, Dubin G. Distinct sequence and structural feature of trypanosoma malate dehydrogenase. Biochem Biophys Res Commun 2021; 557:288-293. [PMID: 33894416 DOI: 10.1016/j.bbrc.2021.04.033] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Glycosomal malate dehydrogenase from Trypanosoma cruzi (tcgMDH) catalyzes the oxidation/reduction of malate/oxaloacetate, a crucial step of the glycolytic process occurring in the glycosome of the human parasite. Inhibition of tcgMDH is considered a druggable trait for the development of trypanocidal drugs. Sequence comparison of MDHs from different organisms revealed a distinct insertion of a prolin rich 9-mer (62-KLPPVPRDP-70) in tcgMDH as compared to other eukaryotic MDHs. Crystal structure of tcgMDH is solved here at 2.6 Å resolution with Rwork/Rfree values of 0.206/0.216. The tcgMDH forms homo-dimer with the solvation free energy (ΔGo) gain of -9.77 kcal/mol. The dimeric form is also confirmed in solution by biochemical assays, chemical-crosslinking and dynamic light scattering. The inserted 9-mer adopts a structure of a solvent accessible loop in the vicinity of NAD+ binding site. The distinct sequence and structural feature of tcgMDH, revealed in the present report, provides an anchor point for the development of inhibitors specific for tcgMDH, possible trypanocidal agents of the future.
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Affiliation(s)
- Ravi R Sonani
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Krzysztof Lewiński
- Department of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Krakow, Poland
| | - Grzegorz Dubin
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland.
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16
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Brzozowska M, Handzlik G, Kurpiewska K, Zychowicz M, Pinkowicz D. Pseudo-tetrahedral vs. pseudo-octahedral Er III single molecule magnets and the disruptive role of coordinated TEMPO radical. Inorg Chem Front 2021. [DOI: 10.1039/d1qi00262g] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tetrahedral ErIII complexes are potential candidates for high-performance single molecule magnets (SMMs).
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Affiliation(s)
| | | | | | | | - Dawid Pinkowicz
- Jagiellonian University
- Faculty of Chemistry
- 30-387 Kraków
- Poland
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17
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Kluza A, Wojdyla Z, Mrugala B, Kurpiewska K, Porebski PJ, Niedzialkowska E, Minor W, Weiss MS, Borowski T. Regioselectivity of hyoscyamine 6β-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations. Dalton Trans 2020; 49:4454-4469. [PMID: 32182320 DOI: 10.1039/d0dt00302f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional non-heme 2-oxoglutarate/Fe2+-dependent dioxygenase that catalyzes the two final steps in the biosynthesis of scopolamine. Based on high resolution crystal structures of H6H from Datura metel, detailed information on substrate binding was obtained that provided insights into the onset of the enzymatic process. In particular, the role of two prominent residues was revealed - Glu-116 that interacts with the tertiary amine located on the hyoscyamine tropane moiety and Tyr-326 that forms CH-π hydrogen bonds with the hyoscyamine phenyl ring. The structures were used as the basis for QM/MM calculations that provided an explanation for the regioselectivity of the hydroxylation reaction on the hyoscyamine tropane moiety (C6 vs. C7) and quantified contributions of active site residues to respective barrier heights.
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Affiliation(s)
- Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Beata Mrugala
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Katarzyna Kurpiewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL-30387 Krakow, Poland
| | - Przemyslaw J Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland. and Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue Pinn Hall, Charlottesville, VA 22908, USA
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, D-12489, Berlin, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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18
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Konstantinidou M, Boiarska Z, Butera R, Neochoritis CG, Kurpiewska K, Kalinowska‐Tłuscik J, Dömling A. Diaminoimidazopyrimidines: Access via the Groebke–Blackburn–Bienaymé Reaction and Structural Data Mining. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000933] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markella Konstantinidou
- Department of Pharmacy Group of Drug Design University of Groningen Antonius Deusinglaan 1 9713 AV Groningen the Netherlands
| | - Zlata Boiarska
- Department of Pharmacy Group of Drug Design University of Groningen Antonius Deusinglaan 1 9713 AV Groningen the Netherlands
| | - Roberto Butera
- Department of Pharmacy Group of Drug Design University of Groningen Antonius Deusinglaan 1 9713 AV Groningen the Netherlands
| | | | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry Jagiellonian University ul. Gronostajowa 2 30‐387 Krakow Poland
| | - Justyna Kalinowska‐Tłuscik
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry Jagiellonian University ul. Gronostajowa 2 30‐387 Krakow Poland
| | - Alexander Dömling
- Department of Pharmacy Group of Drug Design University of Groningen Antonius Deusinglaan 1 9713 AV Groningen the Netherlands
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19
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Li J, Di Lorenzo V, Patil P, Ruiz-Moreno AJ, Kurpiewska K, Kalinowska-Tłuścik J, Velasco-Velázquez MA, Dömling A. Scaffolding-Induced Property Modulation of Chemical Space. ACS Comb Sci 2020; 22:356-360. [PMID: 32441919 PMCID: PMC7362333 DOI: 10.1021/acscombsci.0c00072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/22/2020] [Indexed: 01/22/2023]
Abstract
Physicochemical property switching of chemical space is of great importance for optimization of compounds, for example, for biological activity. Cyclization is a key method to control 3D and other properties. A two-step approach, which involves a multicomponent reaction followed by cyclization, is reported to achieve the transition from basic moieties to charge neutral cyclic derivatives. A series of multisubstituted oxazolidinones, oxazinanones, and oxazepanones as well as their thio and sulfur derivatives are synthesized from readily available building blocks with mild conditions and high yields. Like a few other methods, MCR and cyclization allow for the collective transformation of a large chemical space into a related one with different properties.
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Affiliation(s)
- Jingyao Li
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Vincenzo Di Lorenzo
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Department of Pharmacy, Università degli studi di Napoli Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | - Pravin Patil
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Angel J. Ruiz-Moreno
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Departamento de Farmacología, Unidad Periférica
de Investigación en Biomedicina Traslacional, Facultad de Medicina
y Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Ciudad
de México, México
| | - Katarzyna Kurpiewska
- Faculty
of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Marco A. Velasco-Velázquez
- Departamento de Farmacología, Unidad Periférica
de Investigación en Biomedicina Traslacional, Facultad de Medicina
y Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, C.P. 04510, Ciudad
de México, México
| | - Alexander Dömling
- Department of Drug
Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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20
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Abstract
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Easy operation, readily
accessible starting materials, and short
syntheses of the privileged scaffold indeno[1,2-c]isoquinolinone were achieved by an multicomponent reaction (MCR)-based
protocol via an ammonia–Ugi-four component reaction (4CR)/copper-catalyzed
annulation sequence. The optimization and scope and limitations of
this short and general sequence are described. The methodology allows
an efficient construction of a wide variety of indenoisoquinolinones
in just two steps.
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Affiliation(s)
- Qian Wang
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Jesse Tuinhof
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Kumchok C Mgimpatsang
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
| | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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21
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Bonarek P, Loch JI, Tworzydło M, Cooper DR, Milto K, Wróbel P, Kurpiewska K, Lewiński K. Structure-based design approach to rational site-directed mutagenesis of β-lactoglobulin. J Struct Biol 2020; 210:107493. [PMID: 32169624 DOI: 10.1016/j.jsb.2020.107493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/19/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Recombinant proteins play an important role in medicine and have diverse applications in industrial biotechnology. Lactoglobulin has shown great potential for use in targeted drug delivery and body fluid detoxification because of its ability to bind a variety of molecules. In order to modify the biophysical properties of β-lactoglobulin, a series of single-site mutations were designed using a structure-based approach. A 3-dimensional structure alignment of homologous molecules led to the design of nine β-lactoglobulin variants with mutations introduced in the binding pocket region. Seven stable and correctly folded variants (L39Y, I56F, L58F, V92F, V92Y, F105L, M107L) were thoroughly characterized by fluorescence, circular dichroism, isothermal titration calorimetry, size-exclusion chromatography, and X-ray structural investigations. The effects of the amino acid substitutions were observed as slight rearrangements of the binding pocket geometry, but they also significantly influenced the global properties of the protein. Most of the mutations increased the thermal/chemical stability without altering the dimerization constant or pH-dependent conformational behavior. The crystal structures reveal that the I56F and F105L mutations reduced the depth of the binding pocket, which is advantageous since it can reduce the affinity to endogenous fatty acids. The F105L mutant created a unique binding mode for a fatty acid, supporting the idea that lactoglobulin can be altered to bind unique molecules. Selected variants possessing a unique combination of their individual properties can be used for further, more advanced mutagenesis, and the presented results support further research using β-lactoglobulin as a therapeutic delivery agent or a blood detoxifying molecule.
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Affiliation(s)
- Piotr Bonarek
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna I Loch
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Magdalena Tworzydło
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - David R Cooper
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Katažyna Milto
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Wróbel
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Krzysztof Lewiński
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland.
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22
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Abdelraheem EMM, Goodwin I, Shaabani S, de Haan MP, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. 'Atypical Ugi' tetrazoles. Chem Commun (Camb) 2020; 56:1799-1802. [PMID: 31950120 DOI: 10.1039/c9cc09194g] [Citation(s) in RCA: 4] [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: 11/21/2022]
Abstract
Amino acid-derived isocyano amides together with TMSN3, oxocomponents and 1° or 2° amines are common substrates in the Ugi tetrazole reaction. We surprisingly found that combining these substrates gives two different constitutional isomeric Ugi products A and B. A is the expected classical Ugi product whereas B is an isomeric product ('atypical Ugi') of the same molecular weight with the tetrazole heterocycle migrated to a different position. We synthesized, separated and characterized 22 different isomorphic examples of the two constitutional isomers of the Ugi reaction to unambiguously prove the formation of A and B. Mechanistic studies resulted in a proposed mechanism for the concomitant formation of A and B.
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Affiliation(s)
- Eman M M Abdelraheem
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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23
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Kurpiewska K, Miłaczewska A, Lewiński K. Insulin conformational changes under high pressure in structural studies and molecular dynamics simulations. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Butera R, Shrinidhi A, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Fourfold symmetric MCR's via the tetraisocyanide 1,3-diisocyano-2,2-bis(isocyanomethyl)propane. Chem Commun (Camb) 2020; 56:10662-10665. [DOI: 10.1039/d0cc04522e] [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: 11/21/2022]
Abstract
We developed a gram-scale synthesis of the novel tetraisocyanide 1,3-diisocyano-2,2-bis(isocyanomethyl)propane and applied this in unprecedented fourfold Ugi four-component and Passerini three-component reaction achieving unique symmetric structures.
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Affiliation(s)
- Roberto Butera
- University of Groningen
- Department of Drug Design
- A. Deusinglaan 1
- 9713 AV Groningen
- The Netherlands
| | - Annadka Shrinidhi
- University of California
- Department of Chemistry & Biochemistry
- San Diego
- USA
| | - Katarzyna Kurpiewska
- Department of Crystal Chemistry and Crystal Physics Faculty of Chemistry
- Jagiellonian University
- Poland
| | | | - Alexander Dömling
- University of Groningen
- Department of Drug Design
- A. Deusinglaan 1
- 9713 AV Groningen
- The Netherlands
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25
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Neochoritis CG, Zarganes-Tzitzikas T, Novotná M, Mitríková T, Wang Z, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Isocyanide-Based Multicomponent Reactions of Free Phenylboronic Acids. Eur J Chem 2019; 2019:6132-6137. [PMID: 33981465 PMCID: PMC8112803 DOI: 10.1002/ejoc.201901187] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Indexed: 12/14/2022]
Abstract
Boronic acids are amongst the most useful synthetic intermediates, frequently used by modern drug design. However, their access and fast synthesis of libraries are often problematic. We present a methodology on the synthesis of drug-like scaffolds via IMCRs with unprotected phenylboronic acids. To demonstrate an application of our approach, we also performed one-pot Suzuki couplings on the primary MCR scaffolds. Moreover, we performed a thorough data-mining of the Cambridge Structural Database, revealing interesting geometrical features.
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Affiliation(s)
- Constantinos G Neochoritis
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
- Department of Chemistry, University of Crete, Panepistimioupoli Vouton, T.K 70013 Iraklio, Crete, Greece
| | - Tryfon Zarganes-Tzitzikas
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
| | - Michaela Novotná
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
| | - Tatiana Mitríková
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
| | - Zefeng Wang
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Alexander Dömling
- Department of Pharmacy, Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, The Netherlands
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26
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Kot E, Kurpiewska K, Borowski T. The role of ODD in the biosynthesis of medically important alkaloids. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s2053273319094968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Gonchepour E, Neochoritis CG, Kurpiewska K, Kalinowska-Tłuścik J, Islami MR, Dömling A. Glycoconjugates via phosphorus ylides. European J Org Chem 2019; 2019:3632-3635. [PMID: 32863756 PMCID: PMC7451046 DOI: 10.1002/ejoc.201900434] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 01/30/2023]
Abstract
A facile, high yielding access to rare chimeric compounds combining phosphorus ylides with complex glycosyl formamides is described. We determined x-ray structures gaining structural insight into this compounds class. In addition, data mining of similar compounds deposited within the Cambridge Structural Database was performed. These derivatives could be used either as synthetic intermediates via the ylide functionalization and glyco chemical biology synthons or improving the pharmacokinetic properties of a potential bioactive molecule, exploiting the glycosyl moiety.
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Affiliation(s)
- Ehsan Gonchepour
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Ingardena Street 3, 30-060 Kraków, Poland
| | | | - Mohammad R Islami
- Department of Chemistry, Shahid Bahonar University of Kerman, 22 Bahman Avenue, 76169 Kerman, Iran
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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28
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Abstract
![]()
The Pomeranz–Fritsch reaction
and its Schlittler–Müller modification were successfully
applied in the Ugi postcyclization strategy by using orthogonally
protected aminoacetaldehyde diethyl acetal and complementary electron
rich building blocks. Several scaffolds, including isoquinolines,
carboline, alkaloid-like tetrazole-fused tetracyclic compounds, and
benzo[d]azepinone scaffolds, were synthesized in
generally moderate to good yield. All our syntheses provide a short
MCR-based sequence to novel or otherwise difficult to access scaffolds.
Hence, we foresee multiple applications of these synthesis technologies.
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Affiliation(s)
- Yuanze Wang
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Pravin Patil
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry , Jagiellonian University , 3 Ingardena Street , 30-060 Krakow , Poland
| | | | - Alexander Dömling
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
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29
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Wang Y, Shaabani S, Ahmadianmoghaddam M, Gao L, Xu R, Kurpiewska K, Kalinowska-Tluscik J, Olechno J, Ellson R, Kossenjans M, Helan V, Groves M, Dömling A. Acoustic Droplet Ejection Enabled Automated Reaction Scouting. ACS Cent Sci 2019; 5:451-457. [PMID: 30937372 PMCID: PMC6439453 DOI: 10.1021/acscentsci.8b00782] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Indexed: 05/28/2023]
Abstract
Miniaturization and acceleration of synthetic chemistry are critically important for rapid property optimization in pharmaceutical, agrochemical, and materials research and development. However, in most laboratories organic synthesis is still performed on a slow, sequential, and material-consuming scale and not validated for multiple substrate combinations. Herein, we introduce fast and touchless acoustic droplet ejection (ADE) technology into small-molecule chemistry to transfer building blocks by nL droplets and to scout a newly designed isoquinoline synthesis. With each compound in a discrete well, 384 random derivatives were synthesized in an automated fashion, and their quality was monitored by SFC-MS and TLC-UV-MS analysis. We exemplify a pipeline of fast and efficient nmol scouting to mmol- and mol-scale synthesis for the discovery of a useful novel reaction with great scope.
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Affiliation(s)
- Yuanze Wang
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Shabnam Shaabani
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Maryam Ahmadianmoghaddam
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Li Gao
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Ruixue Xu
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Department
of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Justyna Kalinowska-Tluscik
- Department
of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, ul. Gronostajowa 2, 30-387 Krakow, Poland
| | - Joe Olechno
- Labcyte
Inc., 170 Rose Orchard
Way, San Jose, California 95134, United States
| | - Richard Ellson
- Labcyte
Inc., 170 Rose Orchard
Way, San Jose, California 95134, United States
| | - Michael Kossenjans
- Hit
Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, SE-43183 Gothenburg, Sweden
| | - Victoria Helan
- Hit
Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Mölndal, SE-43183 Gothenburg, Sweden
| | - Matthew Groves
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, Deusinglaan 1, 7313 AV Groningen, The Netherlands
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30
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Kurhade S, Konstantinidou M, Sutanto F, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Sequential Multicomponent Synthesis of 2-(Imidazo[1,5-α]pyridin-1-yl)-1,3,4-Oxadiazoles. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Santosh Kurhade
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Markella Konstantinidou
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Fandi Sutanto
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; Gronostajowa 2 30-387 Krakow Poland
| | | | - Alexander Dömling
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
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31
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Neochoritis CG, Ghonchepour E, Miraki MK, Zarganes-Tzitzikas T, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Structure and Reactivity of Glycosyl Isocyanides. European J Org Chem 2019; 2019:50-55. [PMID: 33981183 DOI: 10.1002/ejoc.201801588] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
3D structural information was obtained from mono-, di- and trisaccharide formamide and isocyanide derivatives by analysis of their X-ray crystal structure and NMR spectroscopy. The isocyanide anomeric effect was observed. Data mining of the Cambridge Structural Database (CSD) was performed and statistically confirmed our findings. Application of the glycoside isocyanides in the synthesis of novel glycoconjugates as drug-like scaffolds by MCR chemistry underscores the usefulness of the novel building blocks.
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Affiliation(s)
- Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ehsan Ghonchepour
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Maryam Kazemi Miraki
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tryfon Zarganes-Tzitzikas
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, Ingardena Street 3, 30-060 Kraków, Poland
| | | | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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32
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Kurpiewska K, Biela A, Loch JI, Lipowska J, Siuda M, Lewiński K. Towards understanding the effect of high pressure on food protein allergenicity: β-lactoglobulin structural studies. Food Chem 2019; 270:315-321. [DOI: 10.1016/j.foodchem.2018.07.104] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/15/2018] [Accepted: 07/17/2018] [Indexed: 11/29/2022]
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33
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Affiliation(s)
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | | | - Alexander Dömling
- Drug Design; University of Groningen; A. Deusinglaan 1 9713 AV Groningen The Netherlands
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34
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Kurpiewska K, Biela A, Loch JI, Świątek S, Jachimska B, Lewiński K. Effect of pressure on the crystal structure and adsorption of β-lactoglobulin. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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35
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Kurhade S, Diekstra E, Sutanto F, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Multicomponent Reaction Based Synthesis of 1-Tetrazolylimidazo[1,5- a]pyridines. Org Lett 2018; 20:3871-3874. [PMID: 29943994 PMCID: PMC6038091 DOI: 10.1021/acs.orglett.8b01452] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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] [Indexed: 11/29/2022]
Abstract
![]()
A series
of unprecedented tetrazole-linked imidazo[1,5-a]pyridines
are synthesized from simple and readily available
building blocks. The reaction sequence involves an azido-Ugi-deprotection
reaction followed by an acetic anhydride-mediated N-acylation–cyclization process to afford the target heterocycle.
Furthermore, the scope of the methodology was extended to diverse
R3-substitutions by employing commercial anhydrides, acid
chlorides, and acids as an acyl component. The scope for the postmodification
reactions are explored and the usefulness of the synthesis is exemplified
by an improved three-step synthesis of a guanylate cyclase stimulator.
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Affiliation(s)
- Santosh Kurhade
- Department of Drug Design , University of Groningen , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Elmar Diekstra
- Department of Drug Design , University of Groningen , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Fandi Sutanto
- Department of Drug Design , University of Groningen , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University , Faculty of Chemistry , Gronostajowa 2 , 30-387 Krakow , Poland
| | | | - Alexander Dömling
- Department of Drug Design , University of Groningen , A. Deusinglaan 1 , 9713 AV Groningen , The Netherlands
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36
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Madhavachary R, Zarganes-Tzitzikas T, Patil P, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Synthesis of Highly Substituted Imidazole Uracil Containing Molecules via Ugi-4CR and Passerini-3CR. ACS Comb Sci 2018; 20:192-196. [PMID: 29457887 PMCID: PMC5894062 DOI: 10.1021/acscombsci.7b00145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
synthesis of uracil/thymine containing tetra/trisubstituted
imidazole derivatives was demonstrated using Ugi/Passerini-reaction
followed by a postcyclization reaction sequence. The approach enables
the one-pot facile construction of diverse compounds in moderate to
excellent yields (47–82%). The 5-fluorouracil and 5-methyluracil
moieties afford potentially bioactive molecules with drug-like properties.
These scaffolds are currently being utilized in the screening deck
of the European Lead Factory.
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Affiliation(s)
- Rudrakshula Madhavachary
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tryfon Zarganes-Tzitzikas
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pravin Patil
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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37
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Kluza A, Niedzialkowska E, Kurpiewska K, Wojdyla Z, Quesne M, Kot E, Porebski PJ, Borowski T. Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway. J Struct Biol 2018; 202:229-235. [PMID: 29408320 DOI: 10.1016/j.jsb.2018.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 11/17/2017] [Revised: 01/24/2018] [Accepted: 01/28/2018] [Indexed: 11/17/2022]
Abstract
Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and oripavine to morphinone. However, the substrate range of T6ODM was recently expanded to a number of various benzylisoquinoline alkaloids. Here, we present crystal structures of T6ODM in complexes with 2-oxoglutarate (T6ODM:2OG, PDB: 5O9W) and succinate (T6ODM:SIN, PDB: 5O7Y). Both metal and 2OG binding sites display similarity to other proteins from the ODD family, but T6ODM is characterized by an exceptionally large substrate binding cavity, whose volume can partially explain the promiscuity of this enzyme. Moreover, the size of the cavity allows for binding of multiple molecules at once, posing a question about the substrate-driven specificity of the enzyme.
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Affiliation(s)
- Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Katarzyna Kurpiewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland; Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, PL-30387 Krakow, Poland
| | - Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Matthew Quesne
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Ewa Kot
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Przemyslaw J Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, PL-30239 Krakow, Poland.
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38
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Patil P, Mishra B, Sheombarsing G, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Library-to-Library Synthesis of Highly Substituted α-Aminomethyl Tetrazoles via Ugi Reaction. ACS Comb Sci 2018; 20:70-74. [PMID: 29215263 PMCID: PMC5813278 DOI: 10.1021/acscombsci.7b00137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/21/2017] [Indexed: 12/26/2022]
Abstract
α-Aminomethyl tetrazoles, recently made accessible by an Ugi multicomponent reaction (MCR), were shown to be excellent starting materials for a further Ugi MCR, yielding substituted N-methyl-2-(((1-methyl-1H-tetrazol-5-yl)methyl)amino)acetamides having four points of diversity in a library-to-library approach. The scope and limitations of the two-step sequence was explored by conducting more than 50 reactions. Irrespective of electron-rich and electron-deficient oxo-components and the nature of the isocyanide component, the reactions give excellent yields. Sterically less hindered α-aminomethyl tetrazoles give better yields of in further Ugi MCR. The target scaffold has four points of diversity and is finding applications to fill screening decks for high-throughput screening (HTS) in the European Lead Factory and in structure-based drug design.
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Affiliation(s)
- Pravin Patil
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Bhupendra Mishra
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gitanjali Sheombarsing
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian
University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Kraków, Poland
| | - Alexander Dömling
- University
of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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39
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Abdelraheem EMM, Khaksar S, Kurpiewska K, Kalinowska-Tłuścik J, Shaabani S, Dömling A. Two-Step Macrocycle Synthesis by Classical Ugi Reaction. J Org Chem 2018. [PMID: 29327924 DOI: 10.1021/acs.joc.7b02984.] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The direct nonpeptidic macrocycle synthesis of α-isocyano-ω-amines via the classical Ugi four-component reaction (U-4CR) is introduced. Herein an efficient and flexible two-step procedure to complex macrocycles is reported. In the first step, the reaction between unprotected diamines and isocyanocarboxylic acids gives high diversity of unprecedented building blocks in high yield. In the next step, the α-isocyano-ω-amines undergo a U-4CR with high diversity of aldehydes and carboxylic acids in a one-pot procedure. This synthetic approach is short and efficient and leads to a wide range of macrocycles with different ring sizes.
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Affiliation(s)
- Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag, 82524, Egypt
| | - Samad Khaksar
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Shabnam Shaabani
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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40
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Abstract
![]()
The direct nonpeptidic
macrocycle synthesis of α-isocyano-ω-amines
via the classical Ugi four-component reaction (U-4CR) is introduced.
Herein an efficient and flexible two-step procedure to complex macrocycles
is reported. In the first step, the reaction between unprotected diamines
and isocyanocarboxylic acids gives high diversity of unprecedented
building blocks in high yield. In the next step, the α-isocyano-ω-amines
undergo a U-4CR with high diversity of aldehydes and carboxylic acids
in a one-pot procedure. This synthetic approach is short and efficient
and leads to a wide range of macrocycles with different ring sizes.
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Affiliation(s)
- Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag, 82524, Egypt
| | - Samad Khaksar
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Shabnam Shaabani
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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41
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Kurpiewska K, Biela A, Loch J, Świątek S, Jachimska B, Lewiński K. Investigation of high pressure effect on the structure and adsorption of β-lactoglobulin. Colloids Surf B Biointerfaces 2018; 161:387-393. [DOI: 10.1016/j.colsurfb.2017.10.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/03/2017] [Accepted: 10/30/2017] [Indexed: 11/17/2022]
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42
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Kok T, Wapenaar H, Wang K, Neochoritis CG, Zarganes-Tzitzikas T, Proietti G, Eleftheriadis N, Kurpiewska K, Kalinowska-Tłuścik J, Cool RH, Poelarends GJ, Dömling A, Dekker FJ. Discovery of chromenes as inhibitors of macrophage migration inhibitory factor. Bioorg Med Chem 2017; 26:999-1005. [PMID: 29428527 DOI: 10.1016/j.bmc.2017.12.032] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 11/27/2022]
Abstract
Macrophage migration inhibitory factor (MIF) is an essential signaling cytokine with a key role in the immune system. Binding of MIF to its molecular targets such as, among others, the cluster of differentiation 74 (CD74) receptor plays a key role in inflammatory diseases and cancer. Therefore, the identification of MIF binding compounds gained importance in drug discovery. In this study, we aimed to discover novel MIF binding compounds by screening of a focused compound collection for inhibition of its tautomerase enzyme activity. Inspired by the known chromen-4-one inhibitor Orita-13, a focused collection of compounds with a chromene scaffold was screened for MIF binding. The library was synthesized using versatile cyanoacetamide chemistry to provide diversely substituted chromenes. The screening provided inhibitors with IC50's in the low micromolar range. Kinetic evaluation suggested that the inhibitors were reversible and did not bind in the binding pocket of the substrate. Thus, we discovered novel inhibitors of the MIF tautomerase activity, which may ultimately support the development of novel therapeutic agents against diseases in which MIF is involved.
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Affiliation(s)
- Tjie Kok
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands; Faculty of Biotechnology, University of Surabaya, Jalan Raya Kalirungkut, Surabaya 60292, Indonesia
| | - Hannah Wapenaar
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Kan Wang
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | | | | | - Giordano Proietti
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Nikolaos Eleftheriadis
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Kraków, Poland
| | | | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Groningen, The Netherlands
| | - Frank J Dekker
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands.
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43
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Abdelraheem EM, Madhavachary R, Rossetti A, Kurpiewska K, Kalinowska-Tłuścik J, Shaabani S, Dömling A. Ugi Multicomponent Reaction Based Synthesis of Medium-Sized Rings. Org Lett 2017; 19:6176-6179. [PMID: 29083197 PMCID: PMC5698880 DOI: 10.1021/acs.orglett.7b03094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/30/2022]
Abstract
An Ugi multicomponent reaction based two-step strategy was applied to generate medium-sized rings. In the first linear expansion phase, a series of diamines reacted with cyclic anhydrides to produce different lengths of terminal synthetic amino acids as the starting material for the second phase. The Ugi-4-center 3-component reaction was utilized to construct complex medium-sized rings (8-11) by the addition of isocyanides and oxo components. This method features mild conditions and a broad substrate scope.
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Affiliation(s)
- Eman M.
M. Abdelraheem
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Rudrakshula Madhavachary
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Arianna Rossetti
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian
University, Faculty of Chemistry, Gronostajowa 2, 30-387 Krakow, Poland
| | | | - Shabnam Shaabani
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department
of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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44
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Chandgude AL, Narducci D, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Diastereoselective One Pot Five-Component Reaction toward 4-(Tetrazole)-1,3-Oxazinanes. RSC Adv 2017; 7:49995-49998. [PMID: 29430295 DOI: 10.1039/c7ra07392e] [Citation(s) in RCA: 10] [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: 11/21/2022] Open
Abstract
A diastereoselective one pot five-component reaction toward the synthesis of 4-(tetrazole)-1,3-oxazinanes has been reported. The sonication-accelerated, catalyst-free, simple, general and highly time efficient, Asinger-Ugi-tetrazole reaction was used for the synthesis of diverse 4-(tetrazole)-1,3-oxazinanes. The reaction exhibit excellent diastereoselectivity and broad substrate scope.
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Affiliation(s)
- Ajay L Chandgude
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Daniele Narducci
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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45
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Vishwanatha TM, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Cysteine Isocyanide in Multicomponent Reaction: Synthesis of Peptido-Mimetic 1,3-Azoles. J Org Chem 2017; 82:9585-9594. [PMID: 28817272 PMCID: PMC5603900 DOI: 10.1021/acs.joc.7b01615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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] [Indexed: 11/28/2022]
Abstract
![]()
An alternative approach toward the
simple and robust synthesis
of highly substituted peptidic thiazole derivatives using Ugi-multicomponent
reaction (U-MCR) is described. Thus, we introduced the enantiopure
(R)-2-methyl-2-isocyano-3-(tritylthio)propanoate
as a novel class of isocyanide in MCR. This bifunctional isocyanide
was found to undergo mild cyclodehydration to afford thiazole containing
peptidomimetics in a short synthetic sequence. Several examples of
bis-heterocyclic rings were also synthesized through the proper choice
of the aldehyde component in the U-4CR. The method opens a wide range
of applications toward the synthesis of nonribosomal natural products
and other bioactive compounds.
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Affiliation(s)
- Thimmalapura M Vishwanatha
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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46
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Abstract
![]()
A concise two step synthesis of tetrazole
containing macrocycles
from readily accessible starting materials is presented. The first
step comprises a chemoselective amidation of amino acid derived isocyanocarboxylicacid
esters with unprotected symmetrical diamines to afford diverse α-isocyano-ω-amines.
In the second step, the α-isocyano-ω-amines undergo an
Ugi tetrazole reaction to close the macrocycle. Advantageously, this
strategy allows short access to 11–19-membered macrocycles
in which substituents can be independently varied at three different
positions.
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Affiliation(s)
- Eman M M Abdelraheem
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University , Sohag 82524, Egypt
| | - Michel P de Haan
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pravin Patil
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University , 3 Ingardena Street, 30-060 Krakow, Poland
| | | | - Shabnam Shaabani
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Madhavachary R, Abdelraheem EMM, Rossetti A, Twarda-Clapa A, Musielak B, Kurpiewska K, Kalinowska-Tłuścik J, Holak TA, Dömling A. Two-Step Synthesis of Complex Artificial Macrocyclic Compounds. Angew Chem Int Ed Engl 2017; 56:10725-10729. [PMID: 28691783 DOI: 10.1002/anie.201704426] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 05/04/2017] [Revised: 06/23/2017] [Indexed: 11/08/2022]
Abstract
The design and synthesis of head-to-tail linked artificial macrocycles using the Ugi-reaction has been developed. This synthetic approach of just two steps is unprecedented, short, efficient and works over a wide range of medium (8-11) and macrocyclic (≥12) loop sizes. The substrate scope and functional group tolerance is exceptional. Using this approach, we have synthesized 39 novel macrocycles by two or even one single synthetic operation. The properties of our macrocycles are discussed with respect to their potential to bind to biological targets that are not druggable by conventional, drug-like compounds. As an application of these artificial macrocycles we highlight potent p53-MDM2 antagonism.
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Affiliation(s)
- Rudrakshula Madhavachary
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Eman M M Abdelraheem
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Arianna Rossetti
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | | | - Bogdan Musielak
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | | | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland
| | - Alexander Dömling
- Drug Design, University of Groningen, Address Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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48
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Madhavachary R, Abdelraheem EMM, Rossetti A, Twarda-Clapa A, Musielak B, Kurpiewska K, Kalinowska-Tłuścik J, Holak TA, Dömling A. Two-Step Synthesis of Complex Artificial Macrocyclic Compounds. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Eman M. M. Abdelraheem
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
- Chemistry Department; Faculty of Science; Sohag University; Sohag 82524 Egypt
| | - Arianna Rossetti
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
| | | | - Bogdan Musielak
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | | | - Tad A. Holak
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | - Alexander Dömling
- Drug Design; University of Groningen; Address Deusinglaan 1 9713 AV Groningen The Netherlands
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49
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Abstract
Ammonia in the tetrazole Ugi variation together with α-amino acid methyl ester-derived isocyanides provides tetrazolopiperidinones in good to high yields in one pot. The scope and limitations of this reaction were investigated by performing >70 reactions. The scaffold is useful to fill high-throughput screening decks and in structure-based drug design.
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Affiliation(s)
- Pravin Patil
- Drug
Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Biocrystallography
Group, Department of Crystal Chemistry and Crystal Physics, Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Justyna Kalinowska-Tłuścik
- Biocrystallography
Group, Department of Crystal Chemistry and Crystal Physics, Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Alexander Dömling
- Drug
Design Group, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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50
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Abstract
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Isocyanide-based
multicomponent reactions (IMCR) are by far the
most versatile reactions that can construct relatively complex molecules
by one-pot synthesis. More importantly, the development of post IMCR
modifications significantly improves the scaffold’s diversity.
Here, we describe the use of N-Boc protected hydrazine
together with α-amino acid derived isocyanides in the Ugi tetrazole
reaction and its post cyclization under both acidic and basic conditions.
The cyclization in acidic conditions was conducted in a one pot fashion,
which give 7-aminotetrazolopyrazinone (6) and tetrazolotriazepinone
(7) cyclic products. The post cyclization under basic
condition could selectively afford Boc-protected 7-aminotetrazolopyrazinone
(8) products in yield of 38–87%.
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Affiliation(s)
- Yuanze Wang
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pravin Patil
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tluscik
- Jagiellonian University, Faculty of Chemistry, Department
of Crystal Chemistry and Crystal Physics, Biocrystallography Group, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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