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Potowski M, Kunig VBK, Eberlein L, Škopić MK, Vakalopoulos A, Kast SM, Brunschweiger A. Investigations Into Chemically Stabilized Four-Letter DNA for DNA-Encoded Chemistry. Front Chem 2022; 10:894563. [PMID: 35755251 PMCID: PMC9218945 DOI: 10.3389/fchem.2022.894563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
DNA-encoded libraries are a prime technology for target-based small molecule screening. Native DNA used as genetic compound barcode is chemically vulnerable under many reaction conditions. DNA barcodes that are composed of pyrimidine nucleobases, 7-deazaadenine, and 7-deaza-8-azaguanine have been investigated for their suitability for encoded chemistry both experimentally and computationally. These four-letter barcodes were readily ligated by T4 ligation, amplifiable by Taq polymerase, and the resultant amplicons were correctly sequenced. Chemical stability profiling showed a superior chemical stability compared to native DNA, though higher susceptibility to depurination than a three-letter code based on pyrimidine DNA and 7-deazaadenine.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Lukas Eberlein
- Department of Chemistry and Chemical Biology, Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Mateja Klika Škopić
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Alexandros Vakalopoulos
- Bayer AG, Pharmaceuticals, Research and Development, Synthetic Modalities, Wuppertal, Germany
| | - Stefan M Kast
- Department of Chemistry and Chemical Biology, Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemisch stabilisierte DNA‐Codes für DNA‐kodierte Chemie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Potowski
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Verena B. K. Kunig
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Lukas Eberlein
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Stefan M. Kast
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Andreas Brunschweiger
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry. Angew Chem Int Ed Engl 2021; 60:19744-19749. [PMID: 34153170 PMCID: PMC8456907 DOI: 10.1002/anie.202104348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Indexed: 12/18/2022]
Abstract
DNA‐encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7‐deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson–Crick pairs, yielded ligation‐competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid‐ and metal ion‐promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid‐promoted Pictet–Spengler and Biginelli reactions, and metal‐promoted pyrazole syntheses on controlled pore glass‐coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification.
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Affiliation(s)
- Marco Potowski
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Verena B K Kunig
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lukas Eberlein
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | | | - Stefan M Kast
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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Tielker N, Eberlein L, Hessler G, Schmidt KF, Güssregen S, Kast SM. Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges? J Comput Aided Mol Des 2021; 35:453-472. [PMID: 33079358 PMCID: PMC8018924 DOI: 10.1007/s10822-020-00347-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/26/2020] [Indexed: 01/26/2023]
Abstract
Joint academic-industrial projects supporting drug discovery are frequently pursued to deploy and benchmark cutting-edge methodical developments from academia in a real-world industrial environment at different scales. The dimensionality of tasks ranges from small molecule physicochemical property assessment over protein-ligand interaction up to statistical analyses of biological data. This way, method development and usability both benefit from insights gained at both ends, when predictiveness and readiness of novel approaches are confirmed, but the pharmaceutical drug makers get early access to novel tools for the quality of drug products and benefit of patients. Quantum-mechanical and simulation methods particularly fall into this group of methods, as they require skills and expense in their development but also significant resources in their application, thus are comparatively slowly dripping into the realm of industrial use. Nevertheless, these physics-based methods are becoming more and more useful. Starting with a general overview of these and in particular quantum-mechanical methods for drug discovery we review a decade-long and ongoing collaboration between Sanofi and the Kast group focused on the application of the embedded cluster reference interaction site model (EC-RISM), a solvation model for quantum chemistry, to study small molecule chemistry in the context of joint participation in several SAMPL (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenges. Starting with early application to tautomer equilibria in water (SAMPL2) the methodology was further developed to allow for challenge contributions related to predictions of distribution coefficients (SAMPL5) and acidity constants (SAMPL6) over the years. Particular emphasis is put on a frequently overlooked aspect of measuring the quality of models, namely the retrospective analysis of earlier datasets and predictions in light of more recent and advanced developments. We therefore demonstrate the performance of the current methodical state of the art as developed and optimized for the SAMPL6 pKa and octanol-water log P challenges when re-applied to the earlier SAMPL5 cyclohexane-water log D and SAMPL2 tautomer equilibria datasets. Systematic improvement is not consistently found throughout despite the similarity of the problem class, i.e. protonation reactions and phase distribution. Hence, it is possible to learn about hidden bias in model assessment, as results derived from more elaborate methods do not necessarily improve quantitative agreement. This indicates the role of chance or coincidence for model development on the one hand which allows for the identification of systematic error and opportunities toward improvement and reveals possible sources of experimental uncertainty on the other. These insights are particularly useful for further academia-industry collaborations, as both partners are then enabled to optimize both the computational and experimental settings for data generation.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Gerhard Hessler
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany
| | - K Friedemann Schmidt
- R&D Preclinical Safety, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany
| | - Stefan Güssregen
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany.
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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Munte CE, Karl M, Kauter W, Eberlein L, Pham TV, Beck Erlach M, Kast SM, Kremer W, Kalbitzer HR. Erratum: High pressure response of 1H NMR chemical shifts of purine nucleotides. Biophys Chem 2020; 265:106408. [PMID: 32513595 DOI: 10.1016/j.bpc.2020.106408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Claudia E Munte
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Matthias Karl
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Waldemar Kauter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Lukas Eberlein
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Thuy-Vy Pham
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Stefan M Kast
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Werner Kremer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Hans Robert Kalbitzer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Centre of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany.
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Eberlein L, Beierlein FR, van Eikema Hommes NJR, Radadiya A, Heil J, Benner SA, Clark T, Kast SM, Richards NGJ. Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet. J Chem Theory Comput 2020; 16:2766-2777. [PMID: 32125859 DOI: 10.1021/acs.jctc.9b01079] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.
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Affiliation(s)
- Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Frank R Beierlein
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Nico J R van Eikema Hommes
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Timothy Clark
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
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Pongratz T, Kibies P, Eberlein L, Tielker N, Hölzl C, Imoto S, Beck Erlach M, Kurrmann S, Schummel PH, Hofmann M, Reiser O, Winter R, Kremer W, Kalbitzer HR, Marx D, Horinek D, Kast SM. Pressure-dependent electronic structure calculations using integral equation-based solvation models. Biophys Chem 2020; 257:106258. [DOI: 10.1016/j.bpc.2019.106258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/25/2019] [Indexed: 12/18/2022]
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Tielker N, Tomazic D, Eberlein L, Güssregen S, Kast SM. The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory. J Comput Aided Mol Des 2020; 34:453-461. [PMID: 31981015 PMCID: PMC7125249 DOI: 10.1007/s10822-020-00283-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022]
Abstract
Results are reported for octanol–water partition coefficients (log P) of the neutral states of drug-like molecules provided during the SAMPL6 (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenge from applying the “embedded cluster reference interaction site model” (EC-RISM) as a solvation model for quantum-chemical calculations. Following the strategy outlined during earlier SAMPL challenges we first train 1- and 2-parameter water-free (“dry”) and water-saturated (“wet”) models for n-octanol solvation Gibbs energies with respect to experimental values from the “Minnesota Solvation Database” (MNSOL), yielding a root mean square error (RMSE) of 1.5 kcal mol−1 for the best-performing 2-parameter wet model, while the optimal water model developed for the pKa part of the SAMPL6 challenge is kept unchanged (RMSE 1.6 kcal mol−1 for neutral compounds from a model trained on both neutral and ionic species). Applying these models to the blind prediction set yields a log P RMSE of less than 0.5 for our best model (2-parameters, wet). Further analysis of our results reveals that a single compound is responsible for most of the error, SM15, without which the RMSE drops to 0.2. Since this is the only compound in the challenge dataset with a hydroxyl group we investigate other alcohols for which Gibbs energy of solvation data for both water and n-octanol are available in the MNSOL database to demonstrate a systematic cause of error and to discuss strategies for improvement.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Tomazic
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, 65926, Frankfurt am Main, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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Munte CE, Karl M, Kauter W, Eberlein L, Pham TV, Erlach MB, Kast SM, Kremer W, Kalbitzer HR. High pressure response of 1H NMR chemical shifts of purine nucleotides. Biophys Chem 2019; 254:106261. [PMID: 31522070 DOI: 10.1016/j.bpc.2019.106261] [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: 08/03/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 11/25/2022]
Abstract
The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5'-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5' carbon are non-equivalent and can be observed separately. The gg-rotamer at C4'- C5' bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged.
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Affiliation(s)
- Claudia E Munte
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Matthias Karl
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Waldemar Kauter
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Lukas Eberlein
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Thuy-Vy Pham
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Stefan M Kast
- TU Dortmund University, Physical Chemistry III, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Werner Kremer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Hans Robert Kalbitzer
- University of Regensburg, Institute of Biophysics and Physical Biochemistry, Center of Magnetic Resonance in Chemistry and Biomedicine, Universitätsstraße 31, 93053 Regensburg, Germany.
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Tielker N, Eberlein L, Chodun C, Güssregen S, Kast SM. pK a calculations for tautomerizable and conformationally flexible molecules: partition function vs. state transition approach. J Mol Model 2019; 25:139. [PMID: 31041535 DOI: 10.1007/s00894-019-4033-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/07/2019] [Indexed: 11/26/2022]
Abstract
Calculations of acidities of molecules with multiple tautomeric and/or conformational states require adequate treatment of the relative energetics of accessible states accompanied by a statistical-mechanical formulation of their contribution to the macroscopic pKa value. Here, we demonstrate rigorously the formal equivalence of two such approaches: a partition function treatment and statistics over transitions between molecular tautomeric and conformational states in the limit of a theory that does not require adjustment by empirical parameters correcting energetic values. However, for a frequently employed correction scheme, linear scaling of (free) energies and regression with respect to reference data taking an additive constant into account, this equivalence breaks down if more than one acid or base state is involved. The consequences of the resulting inconsistency are discussed on our datasets developed for aqueous pKa predictions during the recent SAMPL6 challenge, where molecular state energetics were computed based on the "embedded cluster reference interaction site model" (EC-RISM). This method couples integral equation theory as a solvation model to quantum-chemical calculations and yielded a test set root mean square error of 1.1 pK units from a partition function ansatz. For all practical purposes, the present results indicate that a state transition approach yields comparable accuracy despite the formal theoretical inconsistency, and that an additive regression intercept, which is strictly constant in the limit of large compound mass only, is a valid approximation. Graphical abstract Embedded cluster reference interaction site model-derived vs. experimental pKa for the test set calculated with either the partition function (blue) or the state transition approach (red), using m as a free parameter.
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Affiliation(s)
- Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Christian Chodun
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Stefan Güssregen
- R&D Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, 65926, Frankfurt am Main, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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Tielker N, Eberlein L, Güssregen S, Kast SM. The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory. J Comput Aided Mol Des 2018; 32:1151-1163. [DOI: 10.1007/s10822-018-0140-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/28/2018] [Indexed: 12/15/2022]
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Deck KA, Buschtöns P, Eberlein L. [Effect of metopirone and physical exertion on adrenal cortes function during the influence of 6-methylprednisolone acetate]. Med Welt 1979; 30:1190-2. [PMID: 491913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Dericks-Tan JS, Eberlein L, Streb C, Taubert HD. The effect of oral contraceptives and of bromocriptine upon pituitary stimulation by LH-RH and TRH. Contraception 1978; 17:79-86. [PMID: 414880 DOI: 10.1016/0010-7824(78)90063-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Radio-immunological estimation of free cortisol in urine in a group of normal persons showed a median daily excretion of 42,5 +/- 22,8 mug (n = 31) using radio-loss-labelling, extraction, and thin layer chromatography. After simple extraction the median value was 54.1 +/- 15.3 mug/d (n = 10). Radioimmunological estimation in simple urine extract seems to be sufficient for routine clinical purposes. The estimation of free cortisol in urine permits a better differentiation between normal adrenal function and adrenal hyperactivity than the determination of 17-hydroxycorticosteroids (17-OHCS). This is shown by comparison of 1) the frequency distribution of the basal values of 17-OHCS and free cortisol in normal persons and in Cushing's disease, 2) the suppression effect of dexamethasone on 17-OHCS and free cortisol in Cushing patients, and 3) the stimulatory effect of ACTH on 17-OHCS and free cortisol in normal persons.
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Deck KA, Luedtke A, Eberlein L. [Diurnal variation in the urinary excretion of vanilmandelic acid and aldosterone in normal and hypertensive persons (author's transl)]. Klin Wochenschr 1976; 54:131-5. [PMID: 1256000 DOI: 10.1007/bf01468790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The excretion of creatinine, VMA, and aldosterone was measured in the urine of 14 normal and 25 persons with stable essential hypertension during a day time (7.00-23.00 hrs) and a night time (23.00-7.00 hrs) period. Excretion of VMA and aldosterone per hour in the two groups was lower during the night period than during the day. No significant difference existed between the excretion values of both groups. Night/day rations for the excretion of VMA and of aldosterone respectively, per mg of creatinine excreted were calculated for each subject. In the normal group the night/day ratios of aldosterone excretion showed a significant correlation to the corresponding ratios of VMA excretion; such correlation was not found in the hypertensive group. The fact that a correlation was observed in the normal group is compatible with the hypothesis that catecholamines are involved in the regulation of the renin-angiotensin-aldosterone system. Lack of correlation in the group of hypertensive does not as yet allow any conclusions. In two patients with primary hyperaldosteronism, the aldosterone excretion during the night was relatively more elevated than in the day.
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Deck KA, Eberlein L. [A simple routine method for the radioimmunological determination of urinary aldosterone (author's transl)]. Z Klin Chem Klin Biochem 1974; 12:504-7. [PMID: 4440090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Eberlein L. Neuere Milchuntersuchungsmethoden und ihre Bedeutungen für die Milchwirtschaft. Angew Chem Int Ed Engl 1929. [DOI: 10.1002/ange.19290421602] [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: 11/05/2022]
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Eberlein L. Fortschritte auf dem Gebiete der Milchindustrien. Angew Chem Int Ed Engl 1928. [DOI: 10.1002/ange.19280414805] [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: 11/12/2022]
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Eberlein L. Fortschritte auf dem Gebiete der Milchindustrien. Angew Chem Int Ed Engl 1928. [DOI: 10.1002/ange.19280414703] [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]
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