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Klein P, Barthels F, Johe P, Wagner A, Tenzer S, Distler U, Le TA, Schmid P, Engel V, Engels B, Hellmich UA, Opatz T, Schirmeister T. Naphthoquinones as Covalent Reversible Inhibitors of Cysteine Proteases-Studies on Inhibition Mechanism and Kinetics. Molecules 2020; 25:molecules25092064. [PMID: 32354191 PMCID: PMC7248907 DOI: 10.3390/molecules25092064] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
The facile synthesis and detailed investigation of a class of highly potent protease inhibitors based on 1,4-naphthoquinones with a dipeptidic recognition motif (HN-l-Phe-l-Leu-OR) in the 2-position and an electron-withdrawing group (EWG) in the 3-position is presented. One of the compound representatives, namely the acid with EWG = CN and with R = H proved to be a highly potent rhodesain inhibitor with nanomolar affinity. The respective benzyl ester (R = Bn) was found to be hydrolyzed by the target enzyme itself yielding the free acid. Detailed kinetic and mass spectrometry studies revealed a reversible covalent binding mode. Theoretical calculations with different density functionals (DFT) as well as wavefunction-based approaches were performed to elucidate the mode of action.
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Affiliation(s)
- Philipp Klein
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany;
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
| | - Annika Wagner
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität, Johann-Joachim Becherweg 30, 55128 Mainz, Germany; (A.W.); (U.A.H.)
| | - Stefan Tenzer
- Institute of Immunology, University Medical Center, Johannes Gutenberg-Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (S.T.); (U.D.)
| | - Ute Distler
- Institute of Immunology, University Medical Center, Johannes Gutenberg-Universität Mainz, Langenbeckstr. 1, 55131 Mainz, Germany; (S.T.); (U.D.)
| | - Thien Anh Le
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Paul Schmid
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Volker Engel
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany; (T.A.L.); (P.S.); (V.E.); (B.E.)
| | - Ute A. Hellmich
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität, Johann-Joachim Becherweg 30, 55128 Mainz, Germany; (A.W.); (U.A.H.)
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60323 Frankfurt, Germany
| | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany;
- Correspondence: (T.O.); (T.S.); Tel.: +49-(0)6131-39-22272 (T.O.); +49-(0)6131-39-25742 (T.S.)
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, 55128 Mainz, Germany; (F.B.); (P.J.)
- Correspondence: (T.O.); (T.S.); Tel.: +49-(0)6131-39-22272 (T.O.); +49-(0)6131-39-25742 (T.S.)
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New Cysteine Protease Inhibitors: Electrophilic (Het)arenes and Unexpected Prodrug Identification for the Trypanosoma Protease Rhodesain. Molecules 2020; 25:molecules25061451. [PMID: 32210166 PMCID: PMC7145299 DOI: 10.3390/molecules25061451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/07/2020] [Accepted: 03/13/2020] [Indexed: 01/05/2023] Open
Abstract
Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the SNAr addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (Ki = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the SNAr reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation.
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Kaiser D, Winne JM, Ortiz-Soto ME, Seibel J, Le TA, Engels B. Mechanistical Insights into the Bioconjugation Reaction of Triazolinediones with Tyrosine. J Org Chem 2018; 83:10248-10260. [PMID: 30005167 DOI: 10.1021/acs.joc.8b01445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bioconjugation at tyrosine residues using cyclic diazodicarboxamides, especially 4-substituted 3 H-1,2,4-triazole-3,5(4 H)-dione (PTAD), is a highly enabling synthetic reaction because it can be employed for orthogonal and site-selective (multi)functionalizations of native peptides and proteins. Despite its importance, the underlying mechanisms have not been thoroughly investigated. The reaction can proceed along four distinctive pathways: (i) the SEAr path, (ii) along a pericyclic group transfer pathway (a classical ene reaction), (iii) along a stepwise reaction path, or (iv) along an unusual higher order concerted pericyclic mechanism. The product mixtures obtained from reactions of PTAD with 2,4-unsubstituted phenolate support the SEAr mechanism, but it remains unclear if other mechanisms also take place. In the present work, the various mechanisms are compared using high-level quantum chemistry approaches for the model reaction of 4 H,3 H-1,2,4-triazole-3,5(4 H)-dione (HTAD) with p-cresol and p-cresolate. In a protic solvent (water), the barriers of the SEAr mechanism and the ene reaction are similar but still too high to explain the available experimental observations. This is only possible if the SEAr reaction of cresolate with HTAD is taken into account for which nearly vanishing barriers are computed. This satisfactorily explains measured conversion rates in buffered aqueous solutions and the strong activation effects observed upon addition of bases.
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Affiliation(s)
- Dustin Kaiser
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
| | - Johan M Winne
- Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281-S4 , B-9000 Ghent , Germany
| | - Maria Elena Ortiz-Soto
- Institute of Organic Chemistry , Julius-Maximilians Universität Würzburg , Am Hubland , Würzburg 97074 , Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry , Julius-Maximilians Universität Würzburg , Am Hubland , Würzburg 97074 , Germany
| | - Thien A Le
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry , Julius-Maximilians Universität Würzburg , Emil-Fischer-Str. 42 , Würzburg 97074 , Germany
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Arafet K, Ferrer S, González FV, Moliner V. Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones. Phys Chem Chem Phys 2018; 19:12740-12748. [PMID: 28480929 DOI: 10.1039/c7cp01726j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cysteine proteases are the most abundant proteases in parasitic protozoa and they are essential enzymes to the life cycle of several of them, thus becoming attractive therapeutic targets for the development of new inhibitors. In this paper, a computational study of the inhibition mechanism of cysteine protease by dipeptidyl-2,3-epoxyketone Cbz-Phe-Hph-(S), a recently proposed inhibitor, has been carried out by means of molecular dynamics (MD) simulations with hybrid QM/MM potentials. The computed free energy surfaces of the inhibition mechanism of cysteine proteases by peptidyl epoxyketones showing how the activation of the epoxide ring and the attack of Cys25 on either C2 or C3 atoms take place in a concerted manner. According to our results, the acid species responsible for the protonation of the oxygen atom of the ring would be able to conserve His159, in contrast to previous studies that proposed a water molecule as the activating species. The low activation free energies for the reaction where Cys25 attacks the C2 atom of the epoxide ring (12.1 kcal mol-1) or to the C3 atom (15.4 kcal mol-1), together with the high negative reaction energies suggest that the derivatives of peptidyl-2,3-epoxyketones can be used to develop new potent inhibitors for the treatment of Chagas disease.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain.
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Schneider TH, Rieger M, Ansorg K, Sobolev AN, Schirmeister T, Engels B, Grabowsky S. Vinyl sulfone building blocks in covalently reversible reactions with thiols. NEW J CHEM 2015. [DOI: 10.1039/c5nj00368g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of quantum-chemical calculations, Hirshfeld surface analyses and reactivity studies predicts how to turn vinyl sulfones into electrophiles that react covalently but reversibly with thiols.
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Affiliation(s)
| | - Max Rieger
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Kay Ansorg
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Alexandre N. Sobolev
- The University of Western Australia
- School of Chemistry and Biochemistry
- Perth
- Australia
| | - Tanja Schirmeister
- University of Mainz
- Institute of Pharmacy and Biochemistry
- 55128 Mainz
- Germany
| | - Bernd Engels
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Simon Grabowsky
- The University of Western Australia
- School of Chemistry and Biochemistry
- Perth
- Australia
- Universität Bremen
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6
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Callebaut G, Meiresonne T, De Kimpe N, Mangelinckx S. Synthesis and Reactivity of 2-(Carboxymethyl)aziridine Derivatives. Chem Rev 2014; 114:7954-8015. [DOI: 10.1021/cr400582d] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gert Callebaut
- Department of Sustainable
Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tamara Meiresonne
- Department of Sustainable
Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Norbert De Kimpe
- Department of Sustainable
Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Sven Mangelinckx
- Department of Sustainable
Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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Fanfrlík J, Brahmkshatriya PS, Řezáč J, Jílková A, Horn M, Mareš M, Hobza P, Lepšík M. Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors. J Phys Chem B 2013; 117:14973-82. [PMID: 24195769 DOI: 10.1021/jp409604n] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The quantum mechanics (QM)-based scoring function that we previously developed for the description of noncovalent binding in protein-ligand complexes has been modified and extended to treat covalent binding of inhibitory ligands. The enhancements are (i) the description of the covalent bond breakage and formation using hybrid QM/semiempirical QM (QM/SQM) restrained optimizations and (ii) the addition of the new ΔG(cov)' term to the noncovalent score, describing the "free" energy difference between the covalent and noncovalent complexes. This enhanced QM-based scoring function is applied to a series of 20 vinyl sulfone-based inhibitory compounds inactivating the cysteine peptidase cathepsin B1 of the Schistosoma mansoni parasite (SmCB1). The available X-ray structure of the SmCB1 in complex with a potent vinyl sulfone inhibitor K11017 is used as a template to build the other covalently bound complexes and to model the derived noncovalent complexes. We present the correlation of the covalent score and its constituents with the experimental binding data. Four outliers are identified. They contain bulky R1' substituents structurally divergent from the template, which might induce larger protein rearrangements than could be accurately modeled. In summary, we propose a new computational approach and an optimal protocol for the rapid evaluation and prospective design of covalent inhibitors with a conserved binding mode.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, v.v.i., and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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Conformational mobility of active and E-64-inhibited actinidin. Biochim Biophys Acta Gen Subj 2013; 1830:4790-9. [DOI: 10.1016/j.bbagen.2013.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 11/22/2022]
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10
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Grabowsky S, Jayatilaka D, Fink RF, Schirmeister T, Engels B. Can Experimental Electron-Density Studies be Used as a Tool to Predict Biologically Relevant Properties of Low-Molecular Weight Enzyme Ligands? Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201200518] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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Kim J, Yoo E, Chang S, Lee YS. Electronic and chelation effects on the unusual C2-methylation of N-(para-substituted)phenylaziridines with lithium organocuprates. J Comput Chem 2011; 32:1859-68. [PMID: 21455961 DOI: 10.1002/jcc.21768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 01/10/2011] [Accepted: 01/14/2011] [Indexed: 11/09/2022]
Abstract
Density functional theory calculations with the B3LYP functional were performed for the title ring-opening reaction to understand the intrinsic activating and directing effects of the N-substituents, as well as the electron donating effect of the para-substituted (Y = Cl, H, Me) phenyl group at the more hindered benzylic C2 atom. The N-tosyl group (i.e., N-Tos) or the N-(2-pyridyl)sulfonyl group (i.e., N-Py) was introduced to activate the ring nitrogen atom (N1) and the para-substituted (Y = Cl, H, Me) phenyl group for the activation of the C2 atom. Conformational searches and geometry optimizations were performed for the N-(para-substituted)phenylaziridines (1∼6). Calculations indicate that the aziridine 6 (i.e., Py/Me) has the most elongated C2-N1 bond intrinsically due to the electronic activating effects, implying the aziridine 6 to be the most potent candidate for the more-hindered C2 opening. Transition states (TSs) were investigated for the prospective ring-opening paths (I∼IV), considering the types of intermolecular push-pull interactions between the N-activated phenylaziridines and the cuprate. The N-Py group provides an unique C2-favored TS along the path IV, which the N-Tos group cannot afford, due to the less charge transfer from the nucleophilic CH 3δ- of the cuprate into the electrophilic C2 atom. Furthermore, the e-donating effect of the para-substituents (Y = Cl, H, Me) enhances the C2 opening for the path IV. This study enables us to understand the unusual ring-opening phenomena in terms of electronic and directing effects and hence may serve as a tool to design substrates for highly regioselective ring openings.
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Affiliation(s)
- Jongtaek Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
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Pérez JM, Helten H, Schnakenburg G, Streubel R. An Approach to 1,3,4-Dioxaphospholane Complexes through an Acid-Induced Ring Expansion of an Oxaphosphirane Complex: The Problem of Construction and Deconstruction of O,P-Heterocycles. Chem Asian J 2011; 6:1539-45. [DOI: 10.1002/asia.201000861] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 11/06/2022]
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Engels B, Schmidt TC, Gatti C, Schirmeister T, Fink RF. Challenging Problems in Charge Density Determination: Polar Bonds and Influence of the Environment. ELECTRON DENSITY AND CHEMICAL BONDING II 2011. [DOI: 10.1007/430_2010_36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Helten H, Schnakenburg G, Daniels J, Arduengo AJ, Streubel R. When Sterics Overcome Electronics: An Unusual Haptotropic P→N Pentacarbonyltungsten Shift. Organometallics 2010. [DOI: 10.1021/om1007709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Holger Helten
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Gregor Schnakenburg
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Jörg Daniels
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Anthony J. Arduengo
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Rainer Streubel
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
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Aziridine-2,3-dicarboxylate-based cysteine cathepsin inhibitors induce cell death in Leishmania major associated with accumulation of debris in autophagy-related lysosome-like vacuoles. Antimicrob Agents Chemother 2010; 54:5028-41. [PMID: 20855728 DOI: 10.1128/aac.00327-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The papain-like cysteine cathepsins expressed by Leishmania play a key role in the life cycle of these parasites, turning them into attractive targets for the development of new drugs. We previously demonstrated that two compounds of a series of peptidomimetic aziridine-2,3-dicarboxylate [Azi(OBn)(2)]-based inhibitors, Boc-(S)-Leu-(R)-Pro-(S,S)-Azi(OBn)(2) (compound 13b) and Boc-(R)-Leu-(S)-Pro-(S,S)-Azi(OBn)(2) (compound 13e), reduced the growth and viability of Leishmania major and the infection rate of macrophages while not showing cytotoxicity against host cells. In the present study, we characterized the mode of action of inhibitors 13b and 13e in L. major. Both compounds targeted leishmanial cathepsin B-like cysteine cathepsin cysteine proteinase C, as shown by fluorescence proteinase activity assays and active-site labeling with biotin-tagged inhibitors. Furthermore, compounds 13b and 13e were potent inducers of cell death in promastigotes, characterized by cell shrinkage, reduction of mitochondrial transmembrane potential, and increased DNA fragmentation. Transmission electron microscopic studies revealed the enrichment of undigested debris in lysosome-like organelles participating in micro- and macroautophagy-like processes. The release of digestive enzymes into the cytoplasm after rupture of membranes of lysosome-like vacuoles resulted in the significant digestion of intracellular compartments. However, the plasma membrane integrity of compound-treated promastigotes was maintained for several hours. Taken together, our results suggest that the induction of cell death in Leishmania by cysteine cathepsin inhibitors 13b and 13e is different from mammalian apoptosis and is caused by incomplete digestion in autophagy-related lysosome-like vacuoles.
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Paasche A, Schiller M, Schirmeister T, Engels B. Mechanistic study of the reaction of thiol-containing enzymes with alpha,beta-unsaturated carbonyl substrates by computation and chemoassays. ChemMedChem 2010; 5:869-80. [PMID: 20401893 PMCID: PMC7162195 DOI: 10.1002/cmdc.201000020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We investigated the reactions between substituted α,β‐unsaturated carbonyl compounds (Michael systems) and thiols by computations as well as chemoassays. The results give insight into variations in the underlying mechanisms as a function of the substitution pattern. This is of interest for the mechanisms of inhibition of the SARS coronavirus main protease (SARS‐CoV Mpro) by etacrynic acid derivatives as well as for the excess toxicity of substituted α,β‐unsaturated carbonyl compounds. This study compares possible reaction courses including 1,4‐addition followed by a ketonization step, and underscores the importance of a base‐catalyzed step for the reactivity of thiol groups in enzymes. Phenyl and methyl substituents at the Michael system decrease the reactivity of the electrophilic compound, but chlorophenyl substituents partly recover the reactivity. Computations also indicate that electron‐pushing substituents lead to a change in the reaction mechanism. The conformation of the Michael system is also found to significantly influence reactivity: the s‐cis conformation leads to higher reactivity than the s‐trans conformation. The computed data explain the trends in measured inhibition potencies of substituted α,β‐unsaturated carbonyl compounds and of reaction rates in chemical assays. They also indicate that the reversibility of inhibition does not stand in contrast to the formation of a new covalent bond between inhibitor and protease.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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Schlund S, Basílio Janke EM, Weisz K, Engels B. Predicting the tautomeric equilibrium of acetylacetone in solution. I. The right answer for the wrong reason? J Comput Chem 2010; 31:665-70. [PMID: 19557765 DOI: 10.1002/jcc.21354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study investigates how the various components (method, basis set, and treatment of solvent effects) of a theoretical approach influence the relative energies between keto and enol forms of acetylacetone, which is an important model system to study the solvent effects on chemical equilibria from experiment and theory. The computations show that the most popular density functional theory (DFT) approaches, such as B3LYP overestimate the stability of the enol form with respect to the keto form by approximately 10 kJ mol(-1), whereas the very promising SCS-MP2 approach is underestimating it. MP2 calculations indicate that in particular the basis set size is crucial. The Dunning Huzinaga double zeta basis (D95z(d,p)) used in previous studies overestimates the stability of the keto form considerably as does the popular split-valence plus polarization (SVP) basis. Bulk properties of the solvent included by continuum approaches strongly stabilize the keto form, but they are not sufficient to reproduce the reversal in stabilities measured by low-temperature nuclear magnetic resonance experiments in freonic solvents. Enthalpic and entropic effects further stabilize the keto form, however, the reversal is only obtained if also molecular effects are taken into account. Such molecular effects seem to influence only the energy difference between the keto and the enol forms. Trends arising due to variation in the dielectric constant of the solvent result from bulk properties of the solvent, i.e., are already nicely described by continuum approaches. As such this study delivers a deep insight into the abilities of various approaches to describe solvent effects on chemical equilibria.
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Affiliation(s)
- Sebastian Schlund
- Institute for Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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Marinas Pérez J, Helten H, Donnadieu B, Reed C, Streubel R. Protonation-Induced Rearrangement of an Oxaphosphirane Complex. Angew Chem Int Ed Engl 2010; 49:2615-8. [DOI: 10.1002/anie.200906825] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Marinas Pérez J, Helten H, Donnadieu B, Reed C, Streubel R. Protonen-induzierte Umlagerung eines Oxaphosphirankomplexes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906825] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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21
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Vektariene A, Vektaris G. Theoretical studies on the methylsulfenyl chloride addition to propene. HETEROATOM CHEMISTRY 2010. [DOI: 10.1002/hc.20571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Fankel S, Helten H, von Frantzius G, Schnakenburg G, Daniels J, Chu V, Müller C, Streubel R. Novel access to azaphosphiridine complexes and first applications using Brønsted acid-induced ring expansion reactions. Dalton Trans 2010; 39:3472-81. [DOI: 10.1039/b922166b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paasche A, Arnone M, Fink RF, Schirmeister T, Engels B. Origin of the reactivity differences of substituted aziridines: CN vs CC bond breakages. J Org Chem 2009; 74:5244-9. [PMID: 19719251 DOI: 10.1021/jo900505q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Aziridines are broadly used as starting materials for various chemical syntheses, and the underlying reactions (CN vs CC bond breaking accompanied by an attack of a nucleophile or a dipolarophile) are strongly influenced by the substitution pattern. The present study investigates reaction courses of possible ring-opening reactions accompanied by the attack of a nucleophile for different substitution patterns of the aziridine. Information is obtained through the computation of the underlying potential energy surfaces and reaction paths. The results provide insight into the mechanisms of different ring-opening reactions and explain how the kinetics and thermodynamics of the reaction are influenced by substituents. This allows predicting substitution patterns that steer the reaction course to either CN or CC bond cleavage.
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Affiliation(s)
- Alexander Paasche
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, Würzburg D-97074, Germany
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24
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Janke EMB, Schlund S, Paasche A, Engels B, Dede R, Hussain I, Langer P, Rettig M, Weisz K. Tautomeric equilibria of 3-formylacetylacetone: low-temperature NMR spectroscopy and ab initio calculations. J Org Chem 2009; 74:4878-81. [PMID: 19485345 DOI: 10.1021/jo9004475] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Keto-enol tautomerization of 3-formylacetylacetone has been studied by NMR spectroscopy, ab initio, and DFT calculations in the gas phase and continuum solvation. By employing very low temperatures in a freonic solvent, tautomeric and conformational equilibria in the slow exchange regime were analyzed in detail. The beta-tricarbonyl compound always adopts a structure with an enolized keto group irrespective of an increasing dielectric constant of the solvent when lowering the temperature of the Freon mixture. This experimentally observed tautomeric distribution of 3-formylacetylacetone is correctly reproduced by continuum solvated DFT calculations.
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Affiliation(s)
- Eline M. Basílio Janke
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Sebastian Schlund
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Alexander Paasche
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Bernd Engels
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Rüdiger Dede
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Ibrar Hussain
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Peter Langer
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Michael Rettig
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institut für Chemie, Freie Universität Berlin, Takustrasse 3, D-14195 Berlin, Germany, Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany, Institut für Chemie, Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany, and Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17489 Greifswald, Germany
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Ismail FMD, Levitsky DO, Dembitsky VM. Aziridine alkaloids as potential therapeutic agents. Eur J Med Chem 2009; 44:3373-87. [PMID: 19540628 DOI: 10.1016/j.ejmech.2009.05.013] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2008] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 10/20/2022]
Abstract
The present review describes research on natural aziridine alkaloids isolated from both terrestrial and marine species, as well as their lipophilic semi-synthetic, and/or synthetic analogs. Over 130 biologically active aziridine-containing compounds demonstrate confirmed pharmacological activity including antitumor, antimicrobial, antibacterial effects. The structures, origin, and biological activities of aziridine alkaloids are reviewed. Consequently this review emphasizes the role of aziridine alkaloids as an important source of drug prototypes and leads for drug discovery.
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Affiliation(s)
- Fyaz M D Ismail
- Medicinal Chemistry Research Group, Department of Pharmacy and Chemistry, Liverpool John Moores University, 221C Phase 1, Byrom Street, Liverpool, Merseyside L3 3AF, UK
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26
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Buback V, Mladenovic M, Engels B, Schirmeister T. Rational Design of Improved Aziridine-Based Inhibitors of Cysteine Proteases. J Phys Chem B 2009; 113:5282-9. [DOI: 10.1021/jp810549n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Verena Buback
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Milena Mladenovic
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie and Lebensmittelchemie, Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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27
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Helten H, Engeser M, Gudat D, Schilling R, Schnakenburg G, Nieger M, Streubel R. Protonation of 2H-Azaphosphirene Complexes: PN Bond Activation and Ring-Expansion Reactions. Chemistry 2009; 15:2602-16. [DOI: 10.1002/chem.200802003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Helten H, Pérez JM, Daniels J, Streubel R. First Brønsted Acid-Induced Ring Expansion of an Oxaphosphirane Complex: A Combined Experimental and DFT Study. Organometallics 2009. [DOI: 10.1021/om8010245] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Holger Helten
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Janaina Marinas Pérez
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Jörg Daniels
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Rainer Streubel
- Institut für Anorganische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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29
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Mladenovic M, Ansorg K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the stereoselectivity of epoxide-based inhibitors. J Phys Chem B 2008; 112:11798-808. [PMID: 18712902 DOI: 10.1021/jp803895f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to their important role in many diseases, cysteine proteases represent new promising drug targets. An important class of cysteine-protease inhibitors is derived from the naturally occurring compound E64, possessing an epoxysuccinyl moiety as warhead. Experimental studies show stereoselectivity concerning the inhibition potency, e.g., a trans-configured epoxide ring is essential for inhibition, and furthermore, in most cases, the ( S, S)-configured inhibitors have a higher inhibition potency than their ( R, R)-counterparts. However, the underlying effects are not fully understood. In this work, such effects are investigated by classical molecular dynamics simulations and combined quantum mechanics/molecular modeling (QM/MM) calculations for the E64c-cathepsin B complex. Our computations reveal that the hydrogen bonding network between the enzyme and the E64c (or its derivatives) determines the stereoselectivity of the subsequent ring opening reaction by governing the distance between the attacking thiolate and the attacked C2 atom of the epoxide ring. For the ( S, S)-configuration, a strong network can be realized which enables a close contact between the reacting centers, so that the irreversible step becomes very efficient. The ( R, S)-configuration ( cis-configuration) can only form networks in which the two reacting centers are so far away from each other that the irreversible step can hardly happen. The ( R, R)-configuration is in between, less optimal than the ( S, S)-configuration but much better than the ( R, S)-configuration. Exceptions where the ( R, R)-configurations shows higher potency than the ( S, S) ones are also explained.
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Affiliation(s)
- Milena Mladenovic
- Institut fur Organische Chemie, Universitat Wurzburg, Am Hubland, Wurzburg, Germany
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30
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Mladenovic M, Schirmeister T, Thiel S, Thiel W, Engels B. The importance of the active site histidine for the activity of epoxide- or aziridine-based inhibitors of cysteine proteases. ChemMedChem 2008; 2:120-8. [PMID: 17066390 DOI: 10.1002/cmdc.200600159] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In the present study the importance of the active site histidine residue (His) for the activity of epoxide- or aziridine-based cysteine protease inhibitors is examined theoretically. To account for all important effects, QM/MM hybrid approaches are employed which combine quantum mechanical (QM) methods that are necessary to describe bond-breaking and formation processes, with molecular mechanics (MM) methods that incorporate the influence of the protein environment. Using various model systems, the computations exclude a direct proton shift from the active site His residue to the inhibitor, but show that one water molecule is sufficient to establish a very efficient relay system. This relay system allows an easy proton transfer from the active site His residue to the inhibitor and is thus essential for the activity of both types of inhibitors. Differences between the epoxides and the aziridines are discussed, along with some implications for the rational design of optimized inhibitors. The work presented herein represents the first QM/MM study into the mode of action of these important inhibitor classes.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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31
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Mladenovic M, Fink RF, Thiel W, Schirmeister T, Engels B. On the origin of the stabilization of the zwitterionic resting state of cysteine proteases: a theoretical study. J Am Chem Soc 2008; 130:8696-705. [PMID: 18557615 DOI: 10.1021/ja711043x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Papain-like cysteine proteases are ubiquitous proteolytic enzymes. The protonated His199/deprotonated Cys29 ion pair (cathepsin B numbering) in the active site is essential for their proper functioning. The presence of this ion pair stands in contrast to the corresponding intrinsic residue p K a values, indicating a strong influence of the enzyme environment. In the present work we show by molecular dynamics simulations on quantum mechanical/molecular mechanical (QM/MM) potentials that the ion pair is stabilized by a complex hydrogen bond network which comprises several amino acids situated in the active site of the enzyme and 2-4 water molecules. QM/MM reaction path computations for the proton transfer from His199 to the thiolate of the Cys29 moiety indicate that the ion pair is about 32-36 kJ mol (-1) more stable than the neutral form if the whole hydrogen bonding network is active. Without any hydrogen bonding network the ion pair is predicted to be significantly less stable than the neutral form. QM/MM charge deletion analysis and QM model calculations are used to quantify the stabilizing effect of the active-site residues and the L1 helix in favor of the zwitterionic form. The active-site water molecules contribute about 30 kJ mol (-1) to the overall stabilization. Disruption of the hydrogen bonding network upon substrate binding is expected to enhance the nucleophilic reactivity of the thiolate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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32
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Mladenovic M, Junold K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors. J Phys Chem B 2008; 112:5458-69. [PMID: 18393547 DOI: 10.1021/jp711287c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epoxides and aziridines are important building blocks for inhibitors of cysteine proteases which are promising drug targets for many diseases. In spite of the large amount of experimental data concerning inhibition potency, structure-activity relationships, and structural arrangements of enzyme-inhibitor complexes, little is known about the basic principles which connect the substitution pattern with the resulting activities. To shed some light on this issue which is essential for the rational design of improved compounds, we have studied the inhibition processes theoretically for various inhibitors using quantum mechanical/molecular mechanical hybrid approaches and classical molecular dynamics simulations. The careful analysis of the computational results allows insight into the interactions which govern the regio- and stereospecificity of the interactions. Known structure-activity relationships are rationalized in terms of the same interactions that determine the measured pH dependencies. Inconsistencies in existing X-ray structures are resolved through comparison with the computed structures, which leads to a reassessment of the factors that control the inhibition potency. Similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated. Finally the small reaction barriers computed for the irreversible step in E64 analogues call into question the commonly accepted two-step model of inhibition since the second, irreversible step is predicted to be so fast that suitably oriented enzyme-inhibitor complexes will react rather than dissociate and equilibrate.
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Affiliation(s)
- Milena Mladenovic
- Institut für Organische Chemie, and Institut für Pharmazie und Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Degel B, Staib P, Rohrer S, Scheiber J, Martina E, Büchold C, Baumann K, Morschhäuser J, Schirmeister T. Cis-Configured Aziridines Are New Pseudo-Irreversible Dual-Mode Inhibitors ofCandida albicans Secreted Aspartic Protease 2. ChemMedChem 2008; 3:302-15. [DOI: 10.1002/cmdc.200700101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Kóňa J. Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease. Org Biomol Chem 2008; 6:359-65. [DOI: 10.1039/b715828a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Helten H, Neumann C, Espinosa A, Jones PG, Nieger M, Streubel R. Evidence for Ligand-Centered Reactivity of a 17e Radical Cationic 2H-Azaphosphirene Complex. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200700658] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Schlund S, Müller R, Grassmann C, Engels B. Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively. J Comput Chem 2007; 29:407-15. [PMID: 17631648 DOI: 10.1002/jcc.20798] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The determination of all possible low-lying energy conformers of flexible molecules is of fundamental interest for various applications. It necessitates a reliable conformational search that is able to detect all important minimum structures and calculates the energies on an adequate level of theory. This work presents a strategy to identify low-energy conformers using arginine as an example by means of a force-field based conformational search in combination with high-level geometry optimizations (RI-MP2/TZVPP+). The methods used for various stages in the conformational search strategy are shown and various pitfalls are discussed. We can show that electronic energies calculated on a DFT level of theory with standard exchange-correlation functionals strongly underestimate the intramolecular stabilization resulting from stacked orientations of the guanidine and carbonyl moiety of arginine due to the deficiency of DFT to describe dispersion effects. In this case by usage of electron correlation methods, low energy conformers comprising stacked arrangements that are counterintuitive become favorable.
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Affiliation(s)
- Sebastian Schlund
- Institute for Organic Chemistry, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
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37
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Namuangruk S, Khongpracha P, Pantu P, Limtrakul J. Structures and Reaction Mechanisms of Propene Oxide Isomerization on H-ZSM-5: An ONIOM Study. J Phys Chem B 2006; 110:25950-7. [PMID: 17181244 DOI: 10.1021/jp065266s] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isomerization mechanisms of propene oxide over H-ZSM-5 zeolite have been investigated via the utilization of 5T and 46T cluster models calculated by the B3LYP/6-31G(d,p) and the ONIOM(B3LYP/6-31G(d,p):UFF) methods, respectively. The reactions are considered to proceed through a stepwise mechanism: (1) the epoxide ring protonation, and concurrently the ring-opening, and (2) the 1,2-hydride shift forming the adsorbed carbonyl compound. Because of the asymmetric structure of propene oxide, two different C-O bonds (more or less substituted carbon atom sides) can be broken leading to two different types of products, propanal and propanone. The ring-opening step of these mechanisms is found to be the rate-determining step with an activation barrier of 38.5 kcal/mol for the propanal and of 42.4 kcal/mol for the propanone. Therefore, the propanal is predicted to be the main product for this reaction.
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Affiliation(s)
- Supawadee Namuangruk
- Laboratory for Computational and Applied Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Zhao Y, Truhlar DG. How Well Can New-Generation Density Functionals Describe Protonated Epoxides Where Older Functionals Fail? J Org Chem 2006; 72:295-8. [PMID: 17194116 DOI: 10.1021/jo061863z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a recent article, Carlier et al. (J. Org. Chem. 2006, 71, 1592) examined the prediction of several DFT functionals and showed that the most popular density functional, B3LYP, and 15 others fail badly for the prediction of the structure of protonated 2-methyl-1,2-epoxypropane. In this note, we compare the performance of several recently developed density functionals for the calculation of structures and energetics of protonated cyclic ethers, including epoxides. We found that several of the newly developed DFT methods perform better than B3LYP or any of the other 17 functionals examined by Carlier. We conclude that a recently published functional, M05-2X, has greatly improved performance for an unsymmetrical protonated epoxide, and we recommend this functional for studies that involve protonated epoxides and protonated ethers.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
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Vicik R, Helten H, Schirmeister T, Engels B. Rational design of aziridine-containing cysteine protease inhibitors with improved potency: studies on inhibition mechanism. ChemMedChem 2006; 1:1021-8. [PMID: 16933238 DOI: 10.1002/cmdc.200600081] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To enable a rational design of improved cysteine protease inhibitors, the present work investigates trends in the inhibition potency of aziridine derivatives with a substituted nitrogen center. To predict the influence of electron-withdrawing substituents, quantum chemical computations of the ring opening of N-formylated, N-methylated, and N-unsubstituted aziridines with thiolate were performed. They revealed that the N-formyl group leads to a strong decrease of the reaction barrier and a considerable increase in exothermicity due to stabilization of the transition state. In contrast, a nucleophilic attack at the carbonyl carbon atom is characterized by very low reaction barriers, suggesting a reversible reaction, thus providing the theoretical background for the reversible inhibition of cysteine proteases by peptidyl aldehydes. Reactions of aziridine building blocks (diethyl aziridine-2,3-dicarboxylate 1, diethyl 1-formyl aziridine-2,3-dicarboxylate 2) with a model thiolate in aqueous solution which were followed by NMR spectroscopy and mass spectrometry, showed the N-formylated compound 2 to readily undergo a ring-opening reaction. In contrast, the reaction of 1 with the thiolate is much slower. Enzyme assays with the cysteine protease cathepsin L showed 2 to be a 5000-fold better enzyme inhibitor than 1. Dialysis assays clearly proved irreversible inhibition. These experiments, together with the results obtained with the model thiolate, indicate that the main inhibition mechanism of the N-formylated aziridine 2 is the ring-opening reaction rather than the reversible attack of the active site cysteine residue at the carbonyl carbon atom.
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Affiliation(s)
- Radim Vicik
- Institute of Pharmacy and Food Chemistry, University of Würzburg Am Hubland, 97074 Würzburg, Germany
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Vicik R, Busemann M, Gelhaus C, Stiefl N, Scheiber J, Schmitz W, Schulz F, Mladenovic M, Engels B, Leippe M, Baumann K, Schirmeister T. Aziridide-Based Inhibitors of Cathepsin L: Synthesis, Inhibition Activity, and Docking Studies. ChemMedChem 2006; 1:1126-41. [PMID: 16933358 DOI: 10.1002/cmdc.200600106] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A comprehensive screening of N-acylated aziridine (aziridide) based cysteine protease inhibitors containing either Boc-Leu-Caa (Caa=cyclic amino acid), Boc-Gly-Caa, or Boc-Phe-Ala attached to the aziridine nitrogen atom revealed Boc-(S)-Leu-(S)-Azy-(S,S)-Azi(OBn)(2) (18 a) as a highly potent cathepsin L (CL) inhibitor (K(i)=13 nM) (Azy=aziridine-2-carboxylate, Azi=aziridine-2,3-dicarboxylate). Docking studies, which also accounted for the unusual bonding situations (the flexibility and hybridization of the aziridides) predict that the inhibitor adopts a Y shape and spans across the entire active site cleft, binding into both the nonprimed and primed sites of CL.
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Affiliation(s)
- Radim Vicik
- Institute of Pharmacy and Food Chemistry, Department of Pharmaceutical/Medicinal Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
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Vicik R, Hoerr V, Glaser M, Schultheis M, Hansell E, McKerrow JH, Holzgrabe U, Caffrey CR, Ponte-Sucre A, Moll H, Stich A, Schirmeister T. Aziridine-2,3-dicarboxylate inhibitors targeting the major cysteine protease of Trypanosoma brucei as lead trypanocidal agents. Bioorg Med Chem Lett 2006; 16:2753-7. [PMID: 16516467 DOI: 10.1016/j.bmcl.2006.02.026] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 02/02/2006] [Accepted: 02/03/2006] [Indexed: 11/18/2022]
Abstract
The protozoan parasite Trypanosoma brucei causes Human African trypanosomiasis, which is fatal if left untreated. Due to the toxicity of currently used drugs and emerging drug resistance, there is an urgent need for novel therapies. The major trypanosome papain-like cysteine protease expressed by the parasite (e.g., rhodesain in T. b. rhodesiense) is considered an important target for the development of new trypanocidal drugs. Series of aziridine-2,3-dicarboxylate-based cysteine protease inhibitors have been tested, most of them inhibiting rhodesain in the low micromolar range. Among these, only dibenzyl aziridine-2,3-dicarboxylates display trypanocidal activity being equipotent to the drug eflornithine. The Leu-Pro-containing aziridinyl tripeptides 13a-f are the most promising as they are not cytotoxic to macrophages up to concentrations of 125microM.
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Affiliation(s)
- Radim Vicik
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
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Carlier PR, Deora N, Crawford TD. Protonated 2-Methyl-1,2-epoxypropane: A Challenging Problem for Density Functional Theory. J Org Chem 2006; 71:1592-7. [PMID: 16468811 DOI: 10.1021/jo052303n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protonated epoxides feature prominently in organic chemistry as reactive intermediates. Herein, we describe 10 protonated epoxides using B3LYP, MP2, and CCSD/6-311++G calculations. Relative to CCSD, B3LYP consistently overestimates the C2-O bond length. Protonated 2-methyl-1,2-epoxypropane is the most problematic species studied, where B3LYP overestimates the C2-O bond length by 0.191 angstroms. Seventeen other density functional methods were applied to this protonated epoxide; on average, they overestimated the CCSD bond length by 0.2 angstroms. We present a range of data that suggest the difficulty for DFT methods in modeling the structure of the titled protonated epoxide lies in the extremely weak C2-O bond, which is reflected in the highly asymmetric charge distribution between the two ring carbons. Protonated epoxides featuring more symmetrical charge distribution and cyclic homologues featuring less ring strain are treated with greater accuracy by B3LYP. Finally, MP2 performed very well against CCSD, deviating in the C2-O bond length at most by 0.009 angstroms; it is, therefore, recommended when computational resources prove insufficient for coupled cluster methods.
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Affiliation(s)
- Paul R Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA.
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Schlund S, Schmuck C, Engels B. “Knock-Out” Analogues as a Tool to Quantify Supramolecular Processes: A Theoretical Study of Molecular Interactions in Guanidiniocarbonyl Pyrrole Carboxylate Dimers. J Am Chem Soc 2005; 127:11115-24. [PMID: 16076219 DOI: 10.1021/ja052536w] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was recently shown experimentally that 5-(guanidiniocarbonyl)-1H-pyrrole-2-carboxylate 1, a self-complementary zwitterion, dimerizes even in water with an unprecedented high association constant of K = 170 M(-1) (J. Am. Chem. Soc. 2003, 125, 452-459). To get an insight into the importance of the various noncovalent binding interactions and of their interplay (electrostatic interactions, hydrogen binding, cooperative effects), we employ density functional theory to study the stability of several "knock-out" analogues in which single hydrogen bonds within these multiple point binding motif are switched off by replacing N-H hydrogen-donor groups with either methylene groups or an oxygen ether bridge. The influence of a highly polar solvent on the dimer stabilities is also examined. These calculations reproduce the experimental data for zwitterion 1. A comparison of 1 with the arginine dimer shows that the energy contents of the monomers also significantly influence the dimer stabilities. The analysis of the various "knock-out" analogues reveals as a main conclusion that simple models either based just on hydrogen-bond counting or on the assumption that the charge interaction by itself is the main and dominant factor fail to explain the stability of such self-assembled dimers. Our computations show that the hydrogen-bond network, the electrostatic attraction, and also their mutual interactions are responsible for the high stability of zwitterion 1.
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Affiliation(s)
- Sebastian Schlund
- University of Wuerzburg, Institute for Organic Chemistry, Am Hubland, 97074 Wuerzburg, Germany
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Helten H, Schirmeister T, Engels B. Theoretical Studies about the Influence of Different Ring Substituents on the Nucleophilic Ring Opening of Three-Membered Heterocycles and Possible Implications for the Mechanisms of Cysteine Protease Inhibitors. J Org Chem 2004; 70:233-7. [PMID: 15624927 DOI: 10.1021/jo048373w] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Epoxides, aziridines, and thiiranes are electrophilic building blocks that are widely used in synthetic organic chemistry. As a result of their reactivity against nucleophiles they are also used as electrophilic "warheads" for irreversible peptidic or peptidomimetic cysteine protease inhibitors. A general feature of these inhibitors is the remarkable higher inhibition potency of derivatives containing a free carboxylic acid in comparison to corresponding esters. In contrast, experimental investigations about the reaction of methyl thiolate with substituted epoxides revealed a contrary reactivity pattern. These studies also gave information about the regioselectivity of such reactions; however, mechanistic studies were not performed. By analyzing the computed energy profiles of the corresponding reactions we investigate the substituent effects (H vs ester vs carboxylic acid) on the kinetics and thermodynamics of the ring opening by the nucleophile methyl thiolate. Our model computations nicely explain experimental results concerning variations in the reactivities and the regioselectivities and indicate different reasons for the increased inhibition potency of three-membered heterocycles containing an acidic substituent. For aziridines an intramolecular water-mediated acid catalysis seems to be the main reason for the high activity of these inhibitors in acidic media. For epoxides and thiiranes this catalysis is not found, confirming the hypothesis that an ionic interaction between negatively charged carboxylate and the histidinium ion of the active site of the proteases mainly causes the high inhibitory activity of the acids compared to the esters.
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Affiliation(s)
- Holger Helten
- Institut für Organische Chemie and Institut für Pharmazie und Lebensmittelchemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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