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Vermeyen T, Cunha A, Bultinck P, Herrebout W. Impact of conformation and intramolecular interactions on vibrational circular dichroism spectra identified with machine learning. Commun Chem 2023; 6:148. [PMID: 37438485 DOI: 10.1038/s42004-023-00944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Vibrational Circular Dichroism (VCD) spectra often differ strongly from one conformer to another, even within the same absolute configuration of a molecule. Simulated molecular VCD spectra typically require expensive quantum chemical calculations for all conformers to generate a Boltzmann averaged total spectrum. This paper reports whether machine learning (ML) can partly replace these quantum chemical calculations by capturing the intricate connection between a conformer geometry and its VCD spectrum. Three hypotheses concerning the added value of ML are tested. First, it is shown that for a single stereoisomer, ML can predict the VCD spectrum of a conformer from solely the conformer geometry. Second, it is found that the ML approach results in important time savings. Third, the ML model produced is unfortunately hardly transferable from one stereoisomer to another.
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Affiliation(s)
- Tom Vermeyen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium.
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Ana Cunha
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281, Gent, 9000, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerpen, 2020, Belgium
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2
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Lam J, Lewis RJ, Goodman JM. Interpreting vibrational circular dichroism spectra: the Cai•factor for absolute configuration with confidence. J Cheminform 2023; 15:36. [PMID: 36945031 PMCID: PMC10031863 DOI: 10.1186/s13321-023-00706-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/26/2023] [Indexed: 03/23/2023] Open
Abstract
Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect. The majority of molecules tested have a high confidence score and all of these have the correct assignment.
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Affiliation(s)
- Jonathan Lam
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Richard J Lewis
- Department of Medicinal Chemistry, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Jonathan M Goodman
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK.
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3
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Böselt L, Aerts R, Herrebout W, Riniker S. Improving the IR spectra alignment algorithm with spectra deconvolution and combination with Raman or VCD spectroscopy. Phys Chem Chem Phys 2023; 25:2063-2074. [PMID: 36546852 PMCID: PMC9847344 DOI: 10.1039/d2cp04907d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The relative stereochemistry of organic molecules can be determined by comparing theoretical and experimental infrared (IR) spectra of all isomers and assessing the best match. For this purpose, we have recently developed the IR spectra alignment (IRSA) algorithm for automated optimal alignment. IRSA provides a set of quantitative metrics to identify the candidate structure that agrees best with the experimental spectrum. While the correct diastereomer could be determined for the tested sets of rigid and flexible molecules, two issues were identified with more complex compounds that triggered further development. First, strongly overlapping peaks in the IR spectrum are not treated adequately in the current IRSA implementation. Second, the alignment of multiple spectra from different sources (e.g. IR and VCD or Raman) can be improved. In this study, we present an in-depth discussion of these points, followed by the description of modifications to the IRSA algorithm to address them. In particular, we introduce the concept of deconvolution of the experimental and theoretical spectra with a set of pseudo-Voigt bands. The pseudo-Voigt bands have a set of parameters, which can be employed in the alignment algorithm, leading to improved scoring functions. We test the modified algorithm on two data sets. The first set contains compounds with IR and Raman spectra measured in this study, and the second set contains compounds with IR and VCD spectra available in the literature. We show that the algorithm is able to determine the correct diastereomer in all cases. The results highlight that vibrational spectroscopy can be a valuable alternative or complementary method to inform about the stereochemistry of compounds, and the performance of the updated IRSA algorithm suggests that it is a powerful tool for quantitative-based spectral assignments in academia and industry.
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Affiliation(s)
- Lennard Böselt
- Laboratory of Physical Chemistry, ETH ZürichVladimir-Prelog-Weg 28093 ZürichSwitzerland
| | - Roy Aerts
- Department of Chemistry, University of AntwerpGroenenborgerlaan 171B-2020 AntwerpBelgium
| | - Wouter Herrebout
- Department of Chemistry, University of AntwerpGroenenborgerlaan 171B-2020 AntwerpBelgium
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH ZürichVladimir-Prelog-Weg 28093 ZürichSwitzerland
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4
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Yao H, Sherer EC, Lu M, Small J, Martin GE, Lam YH, Chen Q, Helmy R, Liu Y, Chen H. One-Step Regio- and Stereoselective Electrochemical Synthesis of Orexin Receptor Antagonist Oxidative Metabolites. J Org Chem 2022; 87:15011-15021. [PMID: 36322780 PMCID: PMC10512451 DOI: 10.1021/acs.joc.2c01311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Synthesis of drug metabolites, which often have complex structures, is an integral step in the evaluation of drug candidate metabolism, pharmacokinetic (PK) properties, and safety profiles. Frequently, such synthetic endeavors entail arduous, multiple-step de novo synthetic routes. Herein, we present the one-step Shono-type electrochemical synthesis of milligrams of chiral α-hydroxyl amide metabolites of two orexin receptor antagonists, MK-8133 and MK-6096, as revealed by a small-scale (pico- to nano-mole level) reaction screening using a lab-built online electrochemistry (EC)/mass spectrometry (MS) (EC/MS) platform. The electrochemical oxidation of MK-8133 and MK-6096 was conducted in aqueous media and found to produce the corresponding α-piperidinols with exclusive regio- and stereoselectivity, as confirmed by high-resolution nuclear magnetic resonance (NMR) characterization of products. Based on density functional theory (DFT) calculations, the exceptional regio- and stereoselectivity for this electrochemical oxidation are governed by more favorable energetics of the transition state, leading to the preferred secondary carbon radical α to the amide group and subsequent steric hindrance associated with the U-shaped conformation of the cation derived from the secondary α-carbon radical, respectively.
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Affiliation(s)
- Huifang Yao
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Edward C. Sherer
- Analytical Research and Development, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Mei Lu
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH 45701, USA
| | - James Small
- Analytical Research and Development, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Gary E. Martin
- Analytical Research and Development, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Yu-hong Lam
- Computational and Structural Chemistry, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Qinghao Chen
- Process Research and Development, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Roy Helmy
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Yong Liu
- Analytical Research and Development, MRL, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA
| | - Hao Chen
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH 45701, USA
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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5
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Rode JE, Lyczko K, Kosińska K, Matalińska J, Dyniewicz J, Misicka A, Dobrowolski JC, Lipiński PFJ. The solid state VCD of a novel N-acylhydrazone trifluoroacetate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120761. [PMID: 34954483 DOI: 10.1016/j.saa.2021.120761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
A novel N-acylhydrazone with pharmaceutical importance was subject of structural and IR/VCD investigations in the solid state. In the crystal structure, dimers of anion-cation pairs are stabilized by H-bonding and ionic interactions. Some less common interaction types, like C=N···C-NH3+ (σ-hole) interactions, hydrazone-aromatic interactions and dispersive contacts of the CF3 groups are also present in the crystal. Satisfactory reproduction of the solid state IR and VCD spectra required that quantum-chemical calculations be done on a tetramer (four cation-anion pairs) cut out from the crystal structure, exhibiting key intermolecular interactions. Ten DFT functionals were assessed as to the agreement between the calculated and experimental spectra. Various approaches to scaling of the calculated frequencies were applied. The best results were yielded with individual (optimized) frequency scaling factors (FSFs) and band half-widths at half maximum-(HWHM) for four separate spectral subregions. The best matching between the experimental and theoretical spectra (according to SimIR, SimVCD and SimVDF indices) was found for the B3PW91 functional, however, a few other functionals follow closely in the ranking. Based on the quantum chemical calculations, spectral assignments have been made.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, PL 03-195 Warsaw, Poland
| | - Katarzyna Kosińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland
| | - Jan Cz Dobrowolski
- Department for Medicines Biotechnology and Bioinformatics, National Medicines Institute, 30/34 Chełmska Street, PL 00-725 Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106 Warsaw, Poland.
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6
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Buelna-García CE, Robles-Chaparro E, Parra-Arellano T, Quiroz-Castillo JM, del-Castillo-Castro T, Martínez-Guajardo G, Castillo-Quevedo C, de-León-Flores A, Anzueto-Sánchez G, Martin-del-Campo-Solis MF, Mendoza-Wilson AM, Vásquez-Espinal A, Cabellos JL. Theoretical Prediction of Structures, Vibrational Circular Dichroism, and Infrared Spectra of Chiral Be 4B 8 Cluster at Different Temperatures. Molecules 2021; 26:3953. [PMID: 34203563 PMCID: PMC8271876 DOI: 10.3390/molecules26133953] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 11/16/2022] Open
Abstract
Lowest-energy structures, the distribution of isomers, and their molecular properties depend significantly on geometry and temperature. Total energy computations using DFT methodology are typically carried out at a temperature of zero K; thereby, entropic contributions to the total energy are neglected, even though functional materials work at finite temperatures. In the present study, the probability of the occurrence of one particular Be4B8 isomer at temperature T is estimated by employing Gibbs free energy computed within the framework of quantum statistical mechanics and nanothermodynamics. To identify a list of all possible low-energy chiral and achiral structures, an exhaustive and efficient exploration of the potential/free energy surfaces is carried out using a multi-level multistep global genetic algorithm search coupled with DFT. In addition, we discuss the energetic ordering of structures computed at the DFT level against single-point energy calculations at the CCSD(T) level of theory. The total VCD/IR spectra as a function of temperature are computed using each isomer's probability of occurrence in a Boltzmann-weighted superposition of each isomer's spectrum. Additionally, we present chemical bonding analysis using the adaptive natural density partitioning method in the chiral putative global minimum. The transition state structures and the enantiomer-enantiomer and enantiomer-achiral activation energies as a function of temperature evidence that a change from an endergonic to an exergonic type of reaction occurs at a temperature of 739 K.
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Affiliation(s)
- Carlos Emiliano Buelna-García
- Departamento de Investigación en Polímeros y Materiales, Edificio 3G, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (C.E.B.-G.); (J.M.Q.-C.); (T.d.-C.-C.)
- Organización Científica y Tecnológica del Desierto, Hermosillo 83150, Sonora, Mexico
| | - Eduardo Robles-Chaparro
- Departamento de Ciencias Químico Biologicas, Edificio 5A, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (E.R.-C.); (T.P.-A.); (A.d.-L.-F.)
| | - Tristan Parra-Arellano
- Departamento de Ciencias Químico Biologicas, Edificio 5A, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (E.R.-C.); (T.P.-A.); (A.d.-L.-F.)
| | - Jesus Manuel Quiroz-Castillo
- Departamento de Investigación en Polímeros y Materiales, Edificio 3G, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (C.E.B.-G.); (J.M.Q.-C.); (T.d.-C.-C.)
| | - Teresa del-Castillo-Castro
- Departamento de Investigación en Polímeros y Materiales, Edificio 3G, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (C.E.B.-G.); (J.M.Q.-C.); (T.d.-C.-C.)
| | - Gerardo Martínez-Guajardo
- Unidad Académica de Ciencias Químicas, Área de Ciencias de la Salud, Universidad Autónomade Zacatecas, Km. 6 Carretera Zacatecas-Guadalajara s/n, Ejido La Escondida C.P., Zacatecas 98160, Zac, Mexico;
| | - Cesar Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Carretera Federal No. 23, Km. 191, C.P., Colotlán 46200, Jalisco, Mexico; (C.C.-Q.); (M.F.M.-d.-C.-S.)
| | - Aned de-León-Flores
- Departamento de Ciencias Químico Biologicas, Edificio 5A, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico; (E.R.-C.); (T.P.-A.); (A.d.-L.-F.)
| | | | - Martha Fabiola Martin-del-Campo-Solis
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Carretera Federal No. 23, Km. 191, C.P., Colotlán 46200, Jalisco, Mexico; (C.C.-Q.); (M.F.M.-d.-C.-S.)
| | - Ana Maria Mendoza-Wilson
- Coordinación de Tecnología de Alimentos de Origen Vegetal, CIAD, A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Hermosillo 83304, Sonora, Mexico;
| | - Alejandro Vásquez-Espinal
- Computational and Theoretical Chemistry Group Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Republica 498, Santiago 8370035, Chile;
| | - Jose Luis Cabellos
- Departamento de Investigación en Física, Edificio 3M, Universidad de Sonora, Hermosillo 83000, Sonora, Mexico
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7
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Saito F, Gerbig D, Becker J, Schreiner PR. Breaking the Symmetry of a Meso Compound by Isotopic Substitution: Synthesis and Stereochemical Assignment of Monodeuterated cis-Perhydroazulene. Org Lett 2021; 23:113-117. [PMID: 33306399 DOI: 10.1021/acs.orglett.0c03795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the synthesis and absolute configuration of monodeuterated cis-perhydroazulene (d1-1), which is a rare example of an isotopically chiral hydrocarbon whose synthesis and stereochemical analysis are known to be particularly difficult. The synthesis features nickel-boride-catalyzed deuteration that allowed formation of the diastereomerically pure cis-fused bicyclic system in d1-1. The vibrational circular dichroism results are in excellent agreement with the computed spectrum at ωB97XD/aug-cc-pVTZ, allowing unambiguous assignment of the absolute configuration of d1-1.
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Affiliation(s)
- Fumito Saito
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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8
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Joyce LA, Schultz DM, Sherer EC, Neill JL, Sonstrom RE, Pate BH. Direct regioisomer analysis of crude reaction mixtures via molecular rotational resonance (MRR) spectroscopy. Chem Sci 2020; 11:6332-6338. [PMID: 32953028 PMCID: PMC7472927 DOI: 10.1039/d0sc01853h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/30/2020] [Indexed: 01/05/2023] Open
Abstract
Direct analyses of crude reaction mixtures have been carried out using molecular rotational resonance (MRR) spectroscopy. Two examples are presented, a demonstration application in photocatalytic CH-arylation as well as generation of an intermediate in a natural product synthesis. In both cases, the reaction can proceed at more than one site, leading to a mixture of regioisomers that can be challenging to distinguish. MRR structural parameters were calculated for the low lying conformers for the desired compounds, and then compared to the experimental spectra of the crude mixtures to confirm the presence of these species. Next, quantitation was performed by comparing experimentally measured line intensities with simulations based on computed values for the magnitude and direction of the molecular dipole moment of each species. This identification and quantification was performed without sample purification and without isolated standards of the compounds of interest. The values obtained for MRR quantitation were in good agreement with the chromatographic values. Finally, previously unknown impurities were discovered within the photocatalytic CH-arylation work. This paper demonstrates the utility of MRR as a reaction characterization tool to simplify analytical workflows.
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Affiliation(s)
- Leo A Joyce
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Danielle M Schultz
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA .
| | - Edward C Sherer
- Department of Computational and Structural Chemistry , Merck & Co., Inc. , Rahway , NJ 07065 , USA
| | - Justin L Neill
- BrightSpec, Inc. , 770 Harris St., Suite 104b , Charlottesville , VA 22904 , USA .
| | - Reilly E Sonstrom
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
| | - Brooks H Pate
- Department of Chemistry , University of Virginia , McCormick Road , Charlottesville , VA 22904 , USA
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9
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Böselt L, Dötzer R, Steiner S, Stritzinger M, Salzmann S, Riniker S. Determining the Regiochemistry and Relative Stereochemistry of Small and Druglike Molecules Using an Alignment Algorithm for Infrared Spectra. Anal Chem 2020; 92:9124-9131. [DOI: 10.1021/acs.analchem.0c01399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Reinhard Dötzer
- Competence Center Analytics, BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Sandra Steiner
- Competence Center Analytics, BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Michaela Stritzinger
- Competence Center Analytics, BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Susanne Salzmann
- Digitalization of R&D, BASF SE, Carl-Bosch-Strasse 38, 67056 Ludwigshafen, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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10
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Biegasiewicz KF, Cooper SJ, Gao X, Oblinsky DG, Kim JH, Garfinkle SE, Joyce LA, Sandoval BA, Scholes GD, Hyster TK. Photoexcitation of flavoenzymes enables a stereoselective radical cyclization. Science 2020; 364:1166-1169. [PMID: 31221855 DOI: 10.1126/science.aaw1143] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Photoexcitation is a common strategy for initiating radical reactions in chemical synthesis. We found that photoexcitation of flavin-dependent "ene"-reductases changes their catalytic function, enabling these enzymes to promote an asymmetric radical cyclization. This reactivity enables the construction of five-, six-, seven-, and eight-membered lactams with stereochemical preference conferred by the enzyme active site. After formation of a prochiral radical, the enzyme guides the delivery of a hydrogen atom from flavin-a challenging feat for small-molecule chemical reagents. The initial electron transfer occurs through direct excitation of an electron donor-acceptor complex that forms between the substrate and the reduced flavin cofactor within the enzyme active site. Photoexcitation of promiscuous flavoenzymes has thus furnished a previously unknown biocatalytic reaction.
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Affiliation(s)
| | - Simon J Cooper
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Xin Gao
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ji Hye Kim
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | | | - Leo A Joyce
- Department of Process Research and Development, Merck, Rahway, NJ 07065, USA
| | | | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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11
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Lu X, Tsutsumi Y, Huang C, Xu W, Byrn SR, Templeton AC, Buevich AV, Amoureux JP, Su Y. Molecular packing of pharmaceuticals analyzed with paramagnetic relaxation enhancement and ultrafast magic angle pinning NMR. Phys Chem Chem Phys 2020; 22:13160-13170. [DOI: 10.1039/d0cp02049d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Probing molecular details of fluorinated pharmaceutical compounds at a faster acquisition utilizing paramagnetic relaxation enhancement and better resolution from ultrafast magic angle spinning (νrot = 110 kHz) and high magnetic field (B0 = 18.8 T).
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Affiliation(s)
| | | | | | - Wei Xu
- MRL, Merck & Co., Inc
- Kenilworth
- USA
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
- Purdue University
- Indiana 47907
- USA
| | | | | | | | - Yongchao Su
- MRL, Merck & Co., Inc
- Kenilworth
- USA
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
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12
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Herrera BT, Moor SR, McVeigh M, Roesner EK, Marini F, Anslyn EV. Rapid Optical Determination of Enantiomeric Excess, Diastereomeric Excess, and Total Concentration Using Dynamic-Covalent Assemblies: A Demonstration Using 2-Aminocyclohexanol and Chemometrics. J Am Chem Soc 2019; 141:11151-11160. [PMID: 31251589 DOI: 10.1021/jacs.9b03844] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical analysis of reaction parameters such as enantiomeric excess (ee), diastereomeric excess (de), and yield are becoming increasingly useful as assays for differing functional groups become available. These assays typically exploit reversible covalent or noncovalent assemblies that impart optical signals, commonly circular dichroism (CD), that are indicative of the stereochemistry and ee at a stereocenter proximal to the functional group of interest. Very few assays have been reported that determine ee and de when two stereocenters are present, and none have targeted two different functional groups that are vicinal and lack chromophores entirely. Using a CD assay that targets chiral secondary alcohols, a separate CD assay for chiral primary amines, a UV-vis assay for de, and a fluorescence assay for concentration, we demonstrate a work-flow for speciation of the enantiomers and diastereomers of 2-aminocyclohexanol as a test-bed analyte. Because of the fact the functional groups are vicinal, we found that the ee determination at the two stereocenters is influenced by the adjacent center, and this led us to implement a chemometric patterning approach, resulting in a 4% absolute error in full speciation of the four stereoisomers. The procedure presented herein would allow for the total speciation of around 96 reactions in 27 min using a high-throughput experimentation routine. While 2-aminocyclohexanol is used to demonstrate the methods, the general workflow should be amenable to analysis of other stereoisomers when two stereocenters are present.
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Affiliation(s)
- Brenden T Herrera
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Sarah R Moor
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Matthew McVeigh
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Emily K Roesner
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Federico Marini
- Department of Chemistry , University of Rome "La Sapienza" , P.le Aldo Moro 5 , Rome I-00185 , Italy
| | - Eric V Anslyn
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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13
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Merten C, Golub TP, Kreienborg NM. Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy. J Org Chem 2019; 84:8797-8814. [PMID: 31046276 DOI: 10.1021/acs.joc.9b00466] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.
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Affiliation(s)
- Christian Merten
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Tino P Golub
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Nora M Kreienborg
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
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14
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Böselt L, Sidler D, Kittelmann T, Stohner J, Zindel D, Wagner T, Riniker S. Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. J Chem Inf Model 2019; 59:1826-1838. [DOI: 10.1021/acs.jcim.8b00789] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Dominik Sidler
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Tobias Kittelmann
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Jürgen Stohner
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Daniel Zindel
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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15
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Abbate S, Longhi G, Mazzeo G, Villani C, Petković S, Ruzziconi R. CF3: an overlooked chromophore in VCD spectra. A review of recent applications in structural determination. RSC Adv 2019; 9:11781-11796. [PMID: 35517012 PMCID: PMC9063343 DOI: 10.1039/c9ra01358j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/03/2019] [Indexed: 12/03/2022] Open
Abstract
The VCD spectra of several chiral compounds containing the CF3 group are reviewed and analyzed. The list of compounds contains pharmaceutically relevant molecules as well as simple model molecules, having the value of case studies. In particular we point out the importance of the sign of the VCD band relative to some stretching normal mode of CF3 in the region 1110–1150 cm−1, as diagnostic of the configuration of stereogenic carbons C* to which the CF3 group is bound: the correspondence (−) ↔ (R) and (+) ↔ (S) holds for 100% of 1-aryl-2,2,2-trifluoroethanols. DFT calculations confirm these conclusions, but for the rule established here they serve just as a check. This rule is tested on two new compounds, namely N-tert-butanesulfinyl-1-(quinoline-4-yl)-2,2,2-trifluoroethylamine, 8, and 4-[2-(2,2,2-trifluoro-1-hydroxyethyl)pyrrolidin-1-yl]-2-(trifluoromethyl)benzonitrile, 10, both containing two stereogenic elements, one of them being an asymmetric carbon C* of unknown configuration binding a CF3 group. Discussion of the general validity of the rule is provided and some further tests are run on compounds in well-established drugs. VCD allows one to investigate the configuration of stereogenic centers bearing a CF3-group and to define its interactions with nearby chemical groups.![]()
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Affiliation(s)
- Sergio Abbate
- DMMT (Dipartimento di Medicina Molecolare e Traslazionale)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Giovanna Longhi
- DMMT (Dipartimento di Medicina Molecolare e Traslazionale)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Giuseppe Mazzeo
- DMMT (Dipartimento di Medicina Molecolare e Traslazionale)
- Università di Brescia
- 25123 Brescia
- Italy
| | - Claudio Villani
- Dipartimento di Chimica e Tecnologie del Farmaco
- Università di Roma “La Sapienza”
- 00185 Roma
- Italy
| | - Silvija Petković
- Dipartimento di Chimica, Biologia e Biotecnologie
- Università di Perugia
- 06123 Perugia
- Italy
| | - Renzo Ruzziconi
- Dipartimento di Chimica, Biologia e Biotecnologie
- Università di Perugia
- 06123 Perugia
- Italy
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16
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Zhong YL, Cleator E, Liu Z, Yin J, Morris WJ, Alam M, Bishop B, Dumas AM, Edwards J, Goodyear A, Mullens P, Song ZJ, Shevlin M, Thaisrivongs DA, Li H, Sherer EC, Cohen RD, Yin J, Tan L, Yasuda N, Limanto J, Davies A, Campos KR. Highly Diastereoselective Synthesis of a HCV NS5B Nucleoside Polymerase Inhibitor. J Org Chem 2018; 84:4780-4795. [PMID: 30475616 DOI: 10.1021/acs.joc.8b02500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An asymmetric synthesis of HCV NS5B nucleoside polymerase inhibitor (1) is described. This novel route features several remarkably diastereoselective and high-yielding transformations, including construction of the all-carbon quaternary stereogenic center at C-2 via a thermodynamic aldol reaction. A subsequent glycosylation reaction with activated uracil via C-1 phosphate and installation of the cyclic phosphate group using an achiral phosphorus(III) reagent followed by oxidation provides 1.
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Affiliation(s)
- Yong-Li Zhong
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Ed Cleator
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Zhijian Liu
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Jianguo Yin
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - William J Morris
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Mahbub Alam
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Brian Bishop
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Aaron M Dumas
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - John Edwards
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Adrian Goodyear
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Peter Mullens
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Zhiguo Jake Song
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Michael Shevlin
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - David A Thaisrivongs
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Hongming Li
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Edward C Sherer
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Ryan D Cohen
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Jingjun Yin
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Lushi Tan
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Nobuyoshi Yasuda
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - John Limanto
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Antony Davies
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
| | - Kevin R Campos
- Process Research and Development , Merck & Co., Inc. , P.O. Box 2000, Rahway , New Jersey 07065 , United States
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17
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Bertin MJ, Saurí J, Liu Y, Via CW, Roduit AF, Williamson RT. Trichophycins B-F, Chlorovinylidene-Containing Polyketides Isolated from a Cyanobacterial Bloom. J Org Chem 2018; 83:13256-13266. [PMID: 30280904 DOI: 10.1021/acs.joc.8b02070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR-guided isolation (based on 1D 1H and 13C NMR resonances consistent with a chlorovinylidene moiety) resulted in the characterization of five new highly functionalized polyketides, trichophycins B-F (1-5), and one nonchlorinated metabolite tricholactone (6) from a collection of Trichodesmium bloom material from the Gulf of Mexico. The planar structures of 1-6 were determined using 1D and 2D NMR spectroscopy, mass spectrometry, and complementary spectroscopic procedures. Absolute configuration analysis of 1 and 2 were carried out by 1H NMR analysis of diastereomeric Mosher esters in addition to ECD spectroscopy, J-based configuration analysis, and DFT calculations. The absolute configurations of 3-6 were proposed on the basis of comparative analysis of 13C NMR chemical shifts, relative configurations, and optical rotation values to compounds 1 and 2. Compounds 1-5 represent new additions to the trichophycin family and are hallmarked by a chlorovinylidene moiety. These new trichophycins and tricholactone (1-6) feature intriguing variations with respect to putative biosynthetic starting units, halogenation, and terminations, and trichophycin E (4) features a rare alkynyl bromide functionality. The phenyl-containing trichophycins showed low cytotoxicity to neuro-2A cells, while the alkyne-containing trichophycins showed no toxicity.
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Affiliation(s)
- Matthew J Bertin
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , 7 Greenhouse Road , Kingston , Rhode Island 02881 , United States
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development , Merck and Co. Inc , 33 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - Yizhou Liu
- Structure Elucidation Group, Process and Analytical Research and Development , Merck and Co. Inc , 126 East Lincoln Avenue , Rahway , New Jersey 07065 , United States
| | - Christopher W Via
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , 7 Greenhouse Road , Kingston , Rhode Island 02881 , United States
| | - Alexandre F Roduit
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy , University of Rhode Island , 7 Greenhouse Road , Kingston , Rhode Island 02881 , United States
| | - R Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development , Merck and Co. Inc , 126 East Lincoln Avenue , Rahway , New Jersey 07065 , United States
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18
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Buevich AV, Elyashberg ME. Towards unbiased and more versatile NMR-based structure elucidation: A powerful combination of CASE algorithms and DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:493-504. [PMID: 28833470 DOI: 10.1002/mrc.4645] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
Computer-assisted structure elucidation (CASE) is composed of two steps: (a) generation of all possible structural isomers for a given molecular formula and 2D NMR data (COSY, HSQC, and HMBC) and (b) selection of the correct isomer based on empirical chemical shift predictions. This method has been very successful in solving structural problems of small organic molecules and natural products. However, CASE applications are generally limited to structural isomer problems and can sometimes be inconclusive due to insufficient accuracy of empirical shift predictions. Here, we report a synergistic combination of a CASE algorithm and density functional theory calculations that broadens the range of amenable structural problems to encompass proton-deficient molecules, molecules with heavy elements (e.g., halogens), conformationally flexible molecules, and configurational isomers.
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Affiliation(s)
- Alexei V Buevich
- Discovery and Preclinical Sciences, Process and Analytical Chemistry, NMR Structure Elucidation, Merck & Co., Inc., Kenilworth, NJ, 07033, USA
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19
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Shen J, Magesh S, Chen L, Hu L, He Y. Enantiomeric characterization and structure elucidation of LH601A using vibrational circular dichroism spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:312-317. [PMID: 29172127 PMCID: PMC10544735 DOI: 10.1016/j.saa.2017.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/23/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
LH601A is a novel non-reactive chiral molecule inhibiting Keap1-Nrf2 protein-protein interaction. The absolute configuration (AC) was independently determined in this study using vibrational circular dichroism (VCD) spectroscopy. Because of band overlapping and broadening in the IR spectrum, a direct VCD spectrum comparison method is devised without the conventional IR band alignment. Being an unbiased AC inquiry, all possible chiralities are evaluated based on the statistical analysis of VCD similarity, Sv. The AC of three-center stereoisomer LH601A is unambiguously assigned to (S,R,S). A comparative study was also carried out to investigate the structural and energy differences of calculated conformers using the polarized continuum model of dimethyl sulfoxide.
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Affiliation(s)
- Jian Shen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; S&M Systems, P.O.Box 6583, Bridgewater, NJ 08807, USA.
| | - Sadagopan Magesh
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Lin Chen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Longqin Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; The Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Yanan He
- Biotools, Inc., 17546 Beeline Hwy, Jupiter, FL 33458, USA
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20
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Engkvist O, Norrby PO, Selmi N, Lam YH, Peng Z, Sherer EC, Amberg W, Erhard T, Smyth LA. Computational prediction of chemical reactions: current status and outlook. Drug Discov Today 2018; 23:1203-1218. [PMID: 29510217 DOI: 10.1016/j.drudis.2018.02.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/31/2018] [Accepted: 02/26/2018] [Indexed: 01/05/2023]
Abstract
Over the past few decades, various computational methods have become increasingly important for discovering and developing novel drugs. Computational prediction of chemical reactions is a key part of an efficient drug discovery process. In this review, we discuss important parts of this field, with a focus on utilizing reaction data to build predictive models, the existing programs for synthesis prediction, and usage of quantum mechanics and molecular mechanics (QM/MM) to explore chemical reactions. We also outline potential future developments with an emphasis on pre-competitive collaboration opportunities.
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Affiliation(s)
- Ola Engkvist
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden.
| | - Per-Ola Norrby
- Pharmaceutical Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden
| | - Nidhal Selmi
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, SE-43183 Mölndal, Sweden
| | - Yu-Hong Lam
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Zhengwei Peng
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Modeling and Informatics, MRL, Merck & Co., Rahway, NJ 07065, USA
| | - Willi Amberg
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Thomas Erhard
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Lynette A Smyth
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Discovery, Medicinal Chemistry, Knollstrasse, 67061 Ludwigshafen, Germany
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21
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Welch CJ, Zawatzky K, Makarov AA, Fujiwara S, Matsumoto A, Soai K. Can the analyte-triggered asymmetric autocatalytic Soai reaction serve as a universal analytical tool for measuring enantiopurity and assigning absolute configuration? Org Biomol Chem 2018; 15:96-101. [PMID: 27714244 DOI: 10.1039/c6ob01939k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An investigation is reported on the use of the autocatalytic enantioselective Soai reaction, known to be influenced by the presence of a wide variety of chiral materials, as a generic tool for measuring the enantiopurity and absolute configuration of any substance. Good generality for the reaction across a small group of test analytes was observed, consistent with literature reports suggesting a diversity of compound types that can influence the stereochemical outcome of this reaction. Some trends in the absolute sense of stereochemical enrichment were noted, suggesting the possible utility of the approach for assigning absolute configuration to unknown compounds, by analogy to closely related species with known outcomes. Considerable variation was observed in the triggering strength of different enantiopure materials, an undesirable characteristic when dealing with mixtures containing minor impurities with strong triggering strength in the presence of major components with weak triggering strength. A strong tendency of the reaction toward an 'all or none' type of behavior makes the reaction most sensitive for detecting enantioenrichment close to zero. Consequently, the ability to discern modest from excellent enantioselectivity was relatively poor. While these properties limit the ability to obtain precise enantiopurity measurements in a simple single addition experiment, prospects may exist for more complex experimental setups that may potentially offer improved performance.
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Affiliation(s)
- Christopher J Welch
- Department of Process Research & Development, Merck Research Laboratories, Rahway, NJ, USA.
| | - Kerstin Zawatzky
- Department of Process Research & Development, Merck Research Laboratories, Rahway, NJ, USA.
| | - Alexey A Makarov
- Department of Process Research & Development, Merck Research Laboratories, Rahway, NJ, USA.
| | - Satoshi Fujiwara
- Department of Applied Chemistry, Tokyo University of Science Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Arimasa Matsumoto
- Research Center for Chirality, Research Institute for Science and Technology, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Kenso Soai
- Research Center for Chirality, Research Institute for Science and Technology, Tokyo University of Science, Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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22
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Joyce LA, Nawrat CC, Sherer EC, Biba M, Brunskill A, Martin GE, Cohen RD, Davies IW. Beyond optical rotation: what's left is not always right in total synthesis. Chem Sci 2018; 9:415-424. [PMID: 29629112 PMCID: PMC5868320 DOI: 10.1039/c7sc04249c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/27/2017] [Indexed: 12/02/2022] Open
Abstract
This work describes the application of vibrational (VCD) and electronic (ECD) circular dichroism spectroscopy to solve the longstanding debate around the absolute configuration of (+)-frondosin B (1). The absolute configuration of (+)-1 could confidently be assigned as (R) using these spectroscopic techniques. The discrepancy in the optical rotation (OR) values obtained in previous studies can be attributed to an undetected minor impurity (ca. 7%) that arose unexpectedly in a key step late in the synthesis. Additionally, the conditions used in the final step of the previous reports for demethylation to form the natural product proceeded with significant loss of enantiopurity. The large OR measured for the impurity at its observed level, when compared to the small rotation for the less enantiopure natural product 1, led to a measured OR value for the synthetic material that had the opposite sign of the natural product.
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Affiliation(s)
- Leo A Joyce
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Christopher C Nawrat
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Edward C Sherer
- Department of Modeling and Informatics , Merck & Co., Inc. , Rahway , NJ 07065 , USA
| | - Mirlinda Biba
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Andrew Brunskill
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Gary E Martin
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Ryan D Cohen
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
| | - Ian W Davies
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , NJ 07065 , USA . ;
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23
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DiRocco DA, Ji Y, Sherer EC, Klapars A, Reibarkh M, Dropinski J, Mathew R, Maligres P, Hyde AM, Limanto J, Brunskill A, Ruck RT, Campeau LC, Davies IW. A multifunctional catalyst that stereoselectively assembles prodrugs. Science 2017; 356:426-430. [PMID: 28450641 DOI: 10.1126/science.aam7936] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/09/2017] [Indexed: 12/12/2022]
Abstract
The catalytic stereoselective synthesis of compounds with chiral phosphorus centers remains an unsolved problem. State-of-the-art methods rely on resolution or stoichiometric chiral auxiliaries. Phosphoramidate prodrugs are a critical component of pronucleotide (ProTide) therapies used in the treatment of viral disease and cancer. Here we describe the development of a catalytic stereoselective method for the installation of phosphorus-stereogenic phosphoramidates to nucleosides through a dynamic stereoselective process. Detailed mechanistic studies and computational modeling led to the rational design of a multifunctional catalyst that enables stereoselectivity as high as 99:1.
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Affiliation(s)
- Daniel A DiRocco
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | - Yining Ji
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Artis Klapars
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - James Dropinski
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rose Mathew
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Peter Maligres
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alan M Hyde
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - John Limanto
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Andrew Brunskill
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Rebecca T Ruck
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Ian W Davies
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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24
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Kong J, Joyce LA, Liu J, Jarrell TM, Culberson JC, Sherer EC. Absolute configuration assignment of (+)-fluralaner using vibrational circular dichroism. Chirality 2017; 29:854-864. [PMID: 28981965 DOI: 10.1002/chir.22770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 01/01/2023]
Abstract
The absolute configurations of the separated enantiomers of fluralaner, a racemic animal health product used to prevent fleas and ticks, have been assigned using vibrational circular dichroism (VCD). The crystallographic structure of the active enantiomer (+)-fluralaner has previously been shown to have the (S) configuration using small molecule crystallography. We sought a faster analytical method to determine the absolute configuration of the separated enantiomers. When comparing the measured IR (infrared) and VCD spectra, it is apparent that the amide carbonyl groups appear in the IR but are nearly absent in the VCD. Computational work to calculate the VCD and IR using in vacuo models, implicit solvation, and explicitly solvated complexes has implicated conformational averaging of the carbonyl VCD intensities.
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Affiliation(s)
- John Kong
- Animal Health, Intervet, Inc., Rahway, New Jersey
| | - Leo A Joyce
- Process Research & Development, MRL, Rahway, New Jersey
| | - Jinchu Liu
- Process Research & Development, MRL, Rahway, New Jersey
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25
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Abstract
The generation of conformations for small molecules is a problem of continuing interest in cheminformatics and computational drug discovery. This review will present an overview of methods used to sample conformational space, focusing on those methods designed for organic molecules commonly of interest in drug discovery. Different approaches to both the sampling of conformational space and the scoring of conformational stability will be compared and contrasted, with an emphasis on those methods suitable for conformer sampling of large numbers of drug-like molecules. Particular attention will be devoted to the appropriate utilization of information from experimental solid-state structures in validating and evaluating the performance of these tools. The review will conclude with some areas worthy of further investigation.
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Affiliation(s)
- Paul C D Hawkins
- OpenEye Scientific , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States
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26
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Lodola A, Bertolini S, Biagetti M, Capacchi S, Facchinetti F, Gallo PM, Pappani A, Mor M, Pala D, Rivara S, Visentini F, Corsi M, Capelli AM. Atropisomerism and Conformational Equilibria: Impact on PI3Kδ Inhibition of 2-((6-Amino-9H-purin-9-yl)methyl)-5-methyl-3-(o-tolyl)quinazolin-4(3H)-one (IC87114) and Its Conformationally Restricted Analogs. J Med Chem 2017; 60:4304-4315. [DOI: 10.1021/acs.jmedchem.7b00247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Serena Bertolini
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Matteo Biagetti
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Silvia Capacchi
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Fabrizio Facchinetti
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Paola Maria Gallo
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Alice Pappani
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Daniele Pala
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze 27/A, 43124 Parma, Italy
| | | | - Mauro Corsi
- Aptuit s.r.l., Via Fleming 4, 37135 Verona, Italy
| | - Anna Maria Capelli
- Chemistry
Research and Drug Design Department, Chiesi Farmaceutici S.p.A., Largo F. Belloli 11/A, 43122 Parma, Italy
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27
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Burgueño-Tapia E, Joseph-Nathan P. Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products. Nat Prod Commun 2017. [DOI: 10.1177/1934578x1701200501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013–2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.
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Affiliation(s)
- Eleuterio Burgueño-Tapia
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Santo Tomás, México D.F., 11340 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14–740, México D.F., 07000 Mexico
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28
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Aliagas I, Berger R, Goldberg K, Nishimura RT, Reilly J, Richardson P, Richter D, Sherer EC, Sparling BA, Bryan MC. Sustainable Practices in Medicinal Chemistry Part 2: Green by Design. J Med Chem 2017; 60:5955-5968. [DOI: 10.1021/acs.jmedchem.6b01837] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ignacio Aliagas
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Raphaëlle Berger
- MRL, Merck & Co., Inc., 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kristin Goldberg
- Innovative Medicines Unit, AstraZeneca, Building 310, Milton Science Park, Cambridge, CB4 0FZ, U.K
| | - Rachel T. Nishimura
- Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California 92121, United States
| | - John Reilly
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paul Richardson
- Pfizer Global Research and Development, 10777 Science Center Drive (CB2), San Diego, California 92121, United States
| | - Daniel Richter
- Pfizer Global Research and Development, 10777 Science Center Drive (CB2), San Diego, California 92121, United States
| | - Edward C. Sherer
- MRL, Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065, United States
| | - Brian A. Sparling
- Amgen, Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marian C. Bryan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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29
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Buevich AV, Elyashberg ME. Synergistic Combination of CASE Algorithms and DFT Chemical Shift Predictions: A Powerful Approach for Structure Elucidation, Verification, and Revision. JOURNAL OF NATURAL PRODUCTS 2016; 79:3105-3116. [PMID: 28006916 DOI: 10.1021/acs.jnatprod.6b00799] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structure elucidation of complex natural products and new organic compounds remains a challenging problem. To support this endeavor, CASE (computer-assisted structure elucidation) expert systems were developed. These systems are capable of generating a set of all possible structures consistent with an ensemble of 2D NMR data followed by selection of the most probable structure on the basis of empirical NMR chemical shift prediction. However, in some cases, empirical chemical shift prediction is incapable of distinguishing the correct structure. Herein, we demonstrate for the first time that the combination of CASE and density functional theory (DFT) methods for NMR chemical shift prediction allows the determination of the correct structure even in difficult situations. An expert system, ACD/Structure Elucidator, was used for the CASE analysis. This approach has been tested on three challenging natural products: aquatolide, coniothyrione, and chiral epoxyroussoenone. This work has demonstrated that the proposed synergistic approach is an unbiased, reliable, and very efficient structure verification and de novo structure elucidation method that can be applied to difficult structural problems when other experimental methods would be difficult or impossible to use.
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Affiliation(s)
- Alexei V Buevich
- Department of Discovery and Preclinical Sciences, Process Research and Development, NMR Structure Elucidation, Merck & Co., Inc. , Kenilworth, New Jersey 07033, United States
| | - Mikhail E Elyashberg
- Advanced Chemistry Development (ACD/Laboratories) , Akademik Bakulev Street 6, 117513 Moscow, Russian Federation
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30
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Zhang C, Tutkowski B, DeLuca RJ, Joyce LA, Wiest O, Sigman MS. Palladium-Catalyzed Enantioselective Heck Alkenylation of Trisubstituted Allylic Alkenols: A Redox-Relay Strategy to Construct Vicinal Stereocenters. Chem Sci 2016; 8:2277-2282. [PMID: 28435657 PMCID: PMC5395252 DOI: 10.1039/c6sc04585e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An enantioselective, redox-relay Heck alkenylation of trisubstituted allylic alkenol substrates has been developed. This process enables the construction of vicinal stereocenters in high diastereo- and enantioselectivity and allows the formation of enolizable α-carbonyl methyl-substituted stereocenters with no observed epimerization under the reported reaction conditions.
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Affiliation(s)
- Chun Zhang
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Brandon Tutkowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
| | - Ryan J DeLuca
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
| | - Leo A Joyce
- Process Research & Development, Merck Research Laboratories, Rahway, New Jersey, 07065, USA
| | - Olaf Wiest
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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31
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Brown FK, Sherer EC, Johnson SA, Holloway MK, Sherborne BS. The evolution of drug design at Merck Research Laboratories. J Comput Aided Mol Des 2016; 31:255-266. [PMID: 27878643 DOI: 10.1007/s10822-016-9993-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022]
Abstract
On October 5, 1981, Fortune magazine published a cover article entitled the "Next Industrial Revolution: Designing Drugs by Computer at Merck". With a 40+ year investment, we have been in the drug design business longer than most. During its history, the Merck drug design group has had several names, but it has always been in the "design" business, with the ultimate goal to provide an actionable hypothesis that could be tested experimentally. Often the result was a small molecule but it could just as easily be a peptide, biologic, predictive model, reaction, process, etc. To this end, the concept of design is now front and center in all aspects of discovery, safety assessment and early clinical development. At present, the Merck design group includes computational chemistry, protein structure determination, and cheminformatics. By bringing these groups together under one umbrella, we were able to align activities and capabilities across multiple research sites and departments. This alignment from 2010 to 2016 resulted in an 80% expansion in the size of the department, reflecting the increase in impact due to a significant emphasis across the organization to "design first" along the entire drug discovery path from lead identification (LID) to first in human (FIH) dosing. One of the major advantages of this alignment has been the ability to access all of the data and create an adaptive approach to the overall LID to FIH pathway for any modality, significantly increasing the quality of candidates and their probability of success. In this perspective, we will discuss how we crafted a new strategy, defined the appropriate phenotype for group members, developed the right skillsets, and identified metrics for success in order to drive continuous improvement. We will not focus on the tactical implementation, only giving specific examples as appropriate.
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Affiliation(s)
- Frank K Brown
- Structural Chemistry Department, MRL Research Laboratories, West Point, PA, USA.
| | - Edward C Sherer
- Structural Chemistry Department, MRL Research Laboratories, Rahway, NJ, USA
| | - Scott A Johnson
- Structural Chemistry Department, MRL Research Laboratories, Boston, MA, USA
| | | | - Bradley S Sherborne
- Structural Chemistry Department, MRL Research Laboratories, Kenilworth, NJ, USA
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32
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Pušavec Kirar E, Grošelj U, Golobič A, Požgan F, Pusch S, Weber C, Andernach L, Štefane B, Opatz T, Svete J. Absolute Configuration Determination of 2,3-Dihydro-1H,5H-pyrazolo[1,2-a]pyrazoles Using Chiroptical Methods at Different Wavelengths. J Org Chem 2016; 81:11802-11812. [PMID: 27801585 DOI: 10.1021/acs.joc.6b02270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A correlation between the absolute configuration and chiroptical properties of nonracemic 1,6,7-trisubstituted 2,3-dihydro-1H,5H-pyrazolo[1,2-a]pyrazoles was studied. A series of 16 novel representatives were prepared by Cu-catalyzed [3 + 2] cycloadditions of racemic (Z)-2-benzylidene-5-oxopyrazolidin-2-ium-1-ides to tert-butyl (S)-(3-oxopent-4-yn-2-yl)carbamate, and their structures were determined by NMR, VCD, ECD, and X-ray diffraction. A clear correlation between the sign of specific rotation and configuration at position C(1) allows for easy determination of the absolute configuration of 1,6,7-trisubstituted 2,3-dihydro-1H,5H-pyrazolo[1,2-a]pyrazoles by ECD and NMR. While VCD, requiring milligram quantities, allowed the determination of the correct relative and absolute configuration without additional information from other methods, the stereochemical analysis by ECD required knowledge of the relative configuration derived from NMR at a comparable computational level.
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Affiliation(s)
- Eva Pušavec Kirar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Uroš Grošelj
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Amalija Golobič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Franc Požgan
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Stefan Pusch
- Institut für Organische Chemie, Johannes Gutenberg-Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Carina Weber
- Institut für Organische Chemie, Johannes Gutenberg-Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Lars Andernach
- Institut für Organische Chemie, Johannes Gutenberg-Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Bogdan Štefane
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Till Opatz
- Institut für Organische Chemie, Johannes Gutenberg-Universität Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Jurij Svete
- Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
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33
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Polavarapu PL. Determination of the Absolute Configurations of Chiral Drugs Using Chiroptical Spectroscopy. Molecules 2016; 21:molecules21081056. [PMID: 27529201 PMCID: PMC6273303 DOI: 10.3390/molecules21081056] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 02/07/2023] Open
Abstract
Chiroptical spectroscopy has emerged as a promising tool for the determination of absolute configurations and predominant conformations of chiral molecules in academic laboratories. This promise has led to the adaption of chiroptical spectroscopic methods as valuable tools in chiral drug discovery research programs of the pharmaceutical industry. Most major pharmaceutical companies have invested in in-house chiroptical spectroscopy applications and reported successful outcomes. In the context of continuously increasing applications of chiroptical spectroscopy for chiral molecular structure determination, a review of recent developments and applications for chiral drugs is presented in this manuscript.
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34
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Reinscheid F, Reinscheid U. Stereochemical analysis of (+)-limonene using theoretical and experimental NMR and chiroptical data. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.061] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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35
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Buevich AV. Atropisomerization of 8-Membered Dibenzolactam: Experimental NMR and Theoretical DFT Study. J Org Chem 2015; 81:485-501. [DOI: 10.1021/acs.joc.5b02321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexei V. Buevich
- Merck Research Laboratories,
Discovery and Preclinical Sciences, Process and Analytical Chemistry, NMR Structure Elucidation, Kenilworth, New Jersey 07033, United States
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36
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Burgueño-Tapia E, Joseph-Nathan P. Vibrational Circular Dichroism: Recent Advances for the Assignment of the Absolute Configuration of Natural Products. Nat Prod Commun 2015. [DOI: 10.1177/1934578x1501001036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Vibrational circular dichroism (VCD) emerged during the last decade as a reliable tool for the absolute configuration (AC) determination of organic compounds. The principles, instrumentation, and methodology applied prior to early 2013 were recently reviewed by us. Since VCD is a very dynamic field, the aim of this review is to update VCD advances for the AC assignment of terpenoids, aromatic compounds, alkaloids, and other natural products for the 2013-2014 period, when VCD was applied to the AC assignment of some 70 natural products. In addition, although discovered in 2012, a brief introduction to the VCD exciton coupling approach and its applications in natural products AC assignment is presented.
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Affiliation(s)
- Eleuterio Burgueño-Tapia
- Departamento de Quimica Orgdnica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico National, Prolongatión de Carpio y Plan de Ayala, Col. Santo Tomás, México D.F., 11340 Mexico
| | - Pedro Joseph-Nathan
- Departamento de Química, Centro de Investigatión y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, México D.F., 07000 Mexico
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37
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Lai Z, He S, Sherer EC, Wu Z, Yu Y, Ball R, Hong Q, Yang DX, Guo L, Li D, Tuang Q, Chicchi GG, Trusca D, Tsao KL, Zhou YP, Howard AD, Nargund RP, Hagmann WK. Discovery of substituted (4-phenyl-1H-imidazol-2-yl)methanamine as potent somatostatin receptor 3 agonists. Bioorg Med Chem Lett 2015. [DOI: 10.1016/j.bmcl.2015.06.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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38
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Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Black T, Nargund R, Meinke PT, Olsen DB, Lagrutta A, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Sherer E, Joyce LA, Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Takano H, Shibasaki M, Yajima M, Nishimura A, Shibata T, Fukuda Y. Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2). Bioorg Med Chem Lett 2015; 25:1831-5. [PMID: 25851938 DOI: 10.1016/j.bmcl.2015.03.044] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 12/25/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of broad-spectrum antibacterial agents targeting bacterial Gyrase A and ParC and have potential utility in combating antibiotic resistance. A series of novel oxabicyclooctane-linked NBTIs with new tricyclic-1,5-naphthyridinone left hand side moieties have been described. Compounds with a (R)-hydroxy-1,5-naphthyridinone moiety (7) showed potent antibacterial activity (e.g., Staphylococcus aureus MIC 0.25 μg/mL), acceptable Gram-positive and Gram-negative spectrum with rapidly bactericidal activity. The compound 7 showed intravenous and oral efficacy (ED50) at 3.2 and 27 mg/kg doses, respectively, in a murine model of bacteremia. Most importantly they showed significant attenuation of functional hERG activity (IC50 >170 μM). In general, lower logD attenuated hERG activity but also reduced Gram-negative activity. The co-crystal structure of a hydroxy-tricyclic NBTI bound to a DNA-gyrase complex exhibited a binding mode that show enantiomeric preference for R isomer and explains the activity and SAR. The discovery, synthesis, SAR and X-ray crystal structure of the left-hand-side tricyclic 1,5-naphthyridinone based oxabicyclooctane linked NBTIs are described.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - Todd Black
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Ravi Nargund
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Peter T Meinke
- Merck Research Laboratories, Rahway 07065, United States
| | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Jun Lu
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Sangita Patel
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Keith W Rickert
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Robert F Smith
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Stephen Soisson
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Edward Sherer
- Merck Research Laboratories, Rahway 07065, United States
| | - Leo A Joyce
- Merck Research Laboratories, Rahway 07065, United States
| | | | - Xuanjia Peng
- WuXi AppTec, Shanghai, People's Republic of China
| | - Xiu Wang
- WuXi AppTec, Shanghai, People's Republic of China
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Mitsuhito Shibasaki
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masanobu Yajima
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 2399-1, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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39
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Sherer EC, Cheeseman JR, Williamson RT. Absolute configuration of remisporines A & B. Org Biomol Chem 2015; 13:4169-73. [DOI: 10.1039/c5ob00082c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The absolute configuration of remisporine B was determined based on a comparison of experimental and calculated electronic circular dichorism (ECD) spectra.
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Affiliation(s)
| | | | - R. Thomas Williamson
- NMR Structure Elucidation Group
- Process & Analytical Chemistry
- Merck Research Labs
- Rahway
- USA
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Joyce LA, Sherer EC, Welch CJ. Imine-based chiroptical sensing for analysis of chiral amines: from method design to synthetic application. Chem Sci 2014. [DOI: 10.1039/c4sc01006j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A robust chiroptical method for fast enantiopurity determination of chiral amines utilizing HPLC-CD, applied to monitoring crude transamination reactions.
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Affiliation(s)
- Leo A. Joyce
- Process and Analytical Chemistry
- Merck Research Laboratories
- Rahway, USA
| | - Edward C. Sherer
- Process and Analytical Chemistry
- Merck Research Laboratories
- Rahway, USA
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