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Levina EO, Khrenova MG, Astakhov AA, Tsirelson VG. Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase. RSC Adv 2020; 10:8664-8676. [PMID: 35496524 PMCID: PMC9050041 DOI: 10.1039/c9ra10649a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/14/2020] [Indexed: 11/21/2022] Open
Abstract
The QM/MM simulations followed by electron density feature analysis are carried out to deepen the understanding of the reaction mechanism of cephalosporin hydrolysis in the active site of the L1 metallo-β-lactamase. The differences in reactivity of ten similar cephalosporin compounds are explained by using an extended set of bonding descriptors. The limiting step of the reaction is characterized by the proton transfer to the nitrogen atom of the cephalosporin thiazine ring accompanied with formation of the C4
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C3 double bond in its N–C4–C3 fragment. The temporary N⋯H–Ow hydrogen bond, which is formed in the transition state of the limiting step of the reaction was recognized as a key atomic interaction governing the reactivity of various cephalosporins. Non-local real-space bonding descriptors show that different extent of localization of electron lone pair at N atom in the transition state affect the reactivity of compounds: smaller electron localization is typical for the less reactive species. In particular, the Fermi hole analysis shows how exchange electron correlation in the N⋯H–Ow fragment control electron lone pair localization. Delocalization tensor, linear response kernel and source function indicate that features of electron delocalization in the N–C4–C3 fragment of cephalosporins in the transition state complexes determine the differences in C4–C3 bond for substrates with high and low rate constants. The C4–C3 bond of the N–C4–C3 fragment at the transition state is similar to that of the preceding intermediate for the less reactive species and resembles the features of the enzyme–product complex for more reactive compounds. The power and limitations of the descriptors applied for solving the problem are discussed and the generality of approach is stressed. Combination of QM/MM and modern bonding descriptors explains different reactivity of cephalosporins in the active site of the L1 metallo-β-lactamase.![]()
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Affiliation(s)
- Elena O. Levina
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Moscow Institute of Physics and Technology
- Dolgoprudny
| | - Maria G. Khrenova
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Lomonosov Moscow State University
- Moscow
| | - Andrey A. Astakhov
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Joint Institute for Nuclear Research
- Dubna
| | - Vladimir G. Tsirelson
- Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences
- Moscow
- Russia
- Mendeleev University of Chemical Technology of Russia
- Moscow
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Kwiatkowski A, Kolehmainen E, Ośmiałowski B. Conformational and Tautomeric Control by Supramolecular Approach in Ureido- N- iso-propyl, N'-4-(3-pyridin-2-one) pyrimidine. Molecules 2019; 24:molecules24132491. [PMID: 31288375 PMCID: PMC6651695 DOI: 10.3390/molecules24132491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/29/2019] [Accepted: 07/05/2019] [Indexed: 11/17/2022] Open
Abstract
Ureido-N-iso-propyl,N’-4-(3-pyridin-2-one)pyrimidine (1) and its 2-methoxy pyridine derivative (1Me) has been designed and prepared. The conformational equilibrium in urea moiety and tautomerism in the pyrimidine part have been investigated by variable temperature and 1H NMR titrations as well as DFT quantum chemical calculations. The studied compounds readily associate by triple hydrogen bonding with 2-aminonaphthyridine (A) and/or 2,6-bis(acetylamino)pyridine (B). In 1, the proton is forced to 1,3-tautomeric shift upon stimuli and keeps it position, even when one of the partners in the complex was replaced by another molecule. The observed tautomerism controlled by conformational state (kinetic trapping effect) opens new possibilities in molecular sensing that are based on the fact that reverse reaction is not preferred.
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Affiliation(s)
- Adam Kwiatkowski
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Street, 87-100 Toruń, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7 Gagarin Street, 87-100 Toruń, Poland.
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Ośmiałowski B, Kolehmainen E, Ejsmont K, Ikonen S, Valkonen A, Rissanen K, Nonappa. Association of 2-acylaminopyridines and benzoic acids. Steric and electronic substituent effect studied by XRD, solution and solid-state NMR and calculations. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.09.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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JIMÉNEZ-PULIDO SONIAB, ILLÁN-CABEZA NURIAA, HUESO-UREÑA FRANCISCO, MORENO-CARRETERO MIGUELN. TAUTOMERISM IN NEUTRAL AND DEPROTONATED 6-AMINO-5-FORMYLURACILS: A PM3-COSMO APPROACH. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to identify the structure of the most stable tautomers of 6-amino-5-formyluracil and its N-methylated derivatives in different pH conditions, relative stabilities of potential tautomers in aqueous phase have been calculated taking into account the entropy effects over the tautomeric equilibria. In each medium, the tautomer with lower energy must be the most representative form at the corresponding pH and the knowledge of the effect of the medium in the tautomerization energies allows evaluating the possible effect of the medium over the molecular stability. The results show that, in aqueous phase, the order of basicity of protonation sites in the 6-amino-5-formyluracil derivatives is N 9 > ( N 3 > N 1) > ( O 8 > O 4 > O 2). The 6-amino-5-formyluracil derivatives act as an amino-formyl-keto tautomer with a strong imino character, although, upon successive deprotonations, a growing contribution of enolyzed forms which explain the increasing labilization of carbonyl bonds must be pointed out.
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Affiliation(s)
| | - NURIA A. ILLÁN-CABEZA
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071-Jaén, Spain
| | - FRANCISCO HUESO-UREÑA
- Department of Inorganic and Organic Chemistry, University of Jaén, 23071-Jaén, Spain
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Ośmiałowski B, Mroczyńska K, Kolehmainen E, Kowalska M, Valkonen A, Pietrzak M, Rissanen K. Association of N-(Pyridin-2-yl),N′-substituted Ureas with 2-Amino-1,8-naphthyridines and Benzoates: NMR and Quantum Chemical Studies of the Substituent Effect on Complexation. J Org Chem 2013; 78:7582-93. [PMID: 23845101 DOI: 10.1021/jo4011393] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Karina Mroczyńska
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014, Finland
| | - Magdalena Kowalska
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Arto Valkonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014, Finland
| | - Marek Pietrzak
- Faculty of Chemical Technology
and Engineering, University of Technology and Life Sciences, Seminaryjna 3, PL-85-326 Bydgoszcz, Poland
| | - Kari Rissanen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35,
FI-40014, Finland
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Oliveira BGD. Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds. Phys Chem Chem Phys 2013; 15:37-79. [DOI: 10.1039/c2cp41749a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Kazemi SH, Eshtiagh-Hosseini H, Mirzaei M. Computational study of the intramolecular proton transfer reactions of dipicolinic acid (pyridine-2,6-dicarboxylic acid) and its dimers. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ośmiałowski B, Kolehmainen E, Ikonen S, Valkonen A, Kwiatkowski A, Grela I, Haapaniemi E. 2-Acylamino- and 2,4-Bis(acylamino)pyrimidines as Supramolecular Synthons Analyzed by Multiple Noncovalent Interactions. DFT, X-ray Diffraction, and NMR Spectral Studies. J Org Chem 2012; 77:9609-19. [PMID: 23020688 DOI: 10.1021/jo301643z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Borys Ośmiałowski
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Erkki Kolehmainen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Satu Ikonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Arto Valkonen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
| | - Adam Kwiatkowski
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Izabela Grela
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna
3, PL-85-326 Bydgoszcz, Poland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Finland
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