1
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Qi LJ, Zhou B, Ye LW. Catalytic Epoxidation of Carbonyl Compounds via Carbonyl Ylides: from Racemic to Enantioselective. Chemistry 2024; 30:e202401389. [PMID: 38779789 DOI: 10.1002/chem.202401389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Transition metal-catalyzed epoxidation of carbonyl compounds through carbonyl ylides represents a highly effective method for synthesizing a diverse range of valuable epoxides. This review offers an in-depth overview of the latest developments in inter- and intramolecular epoxidation reactions involving metal carbenes and carbonyl compounds, encompassing both racemic to enantioselective transformations. These catalytic epoxidations are reviewed by highlighting their product selectivity, diversity and applicability, and the related mechanistic rationale is showcased where possible.
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Affiliation(s)
- Lin-Jun Qi
- School of Pharmaceutical and Chemical Engineering &, Institute for Advanced Studies, Taizhou University, Taizhou, Zhejiang, 318000, P. R. China
| | - Bo Zhou
- Key Laboratory for Chemical Biology of Fujian Province and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen, 361005, P. R. China
| | - Long-Wu Ye
- Key Laboratory for Chemical Biology of Fujian Province and State Key Laboratory for Physical Chemistry of Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen, 361005, P. R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, P. R. China
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2
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De Grazia G, Cucinotta L, Sciarrone D, Donato P, Trovato E, Riad N, Hattab ME, Mondello L, Rotondo A. Preparative three-dimensional GC and nuclear magnetic resonance for the isolation and identification of two sesquiterpene ethers from Dictyota Dichotoma. J Sep Sci 2023; 46:e2300261. [PMID: 37386802 DOI: 10.1002/jssc.202300261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Separation science plays a crucial role in the isolation of novel compounds contained in complex matrices. Yet their rationale employment needs preliminary structure elucidation, which usually requires sufficient aliquots of grade substances to characterize the molecule by nuclear magnetic resonance experiments. In this study, two peculiar oxa-tricycloundecane ethers were isolated by means of preparative multidimensional gas chromatography from the brown alga species Dictyota dichotoma (Huds.) Lam., aiming to assign their 3D structures. Density functional theory simulations were carried out to select the correct configurational species matching the experimental NMR data (in terms of enantiomeric couples). In this case, the theoretical approach was crucial as the protonic signal overlap and spectral overcrowding were preventing any other unambiguous structural information. Just after the identification through the density functional theory data matching of the correct relative configuration it was possible to verify an enhanced self-consistency with the experimental data, confirming the stereochemistry. The results obtained further pave the way toward structure elucidation of highly asymmetric molecules, whose configuration cannot be inferred by other means or strategies.
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Affiliation(s)
- Gemma De Grazia
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Lorenzo Cucinotta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Traceability Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Danilo Sciarrone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Paola Donato
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
| | - Emanuela Trovato
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Nacera Riad
- Laboratory of Natural Products Chemistry and Biomolecules, Faculty of Sciences, University Blida 1, Blida, Algeria
| | - Mohamed El Hattab
- Laboratory of Natural Products Chemistry and Biomolecules, Faculty of Sciences, University Blida 1, Blida, Algeria
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Chromaleont S.R.L., University of Messina, Messina, Italy
| | - Archimede Rotondo
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Messina, Italy
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3
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Guerrero De León E, Sánchez-Martínez H, Morán-Pinzón JA, Del Olmo Fernández E, López-Pérez JL. Computational Structural Revision of Elaeophorbate and Other Triterpenoids with the Help of NAPROC-13. A New Strategy for Structural Revision of Natural Products. JOURNAL OF NATURAL PRODUCTS 2023; 86:897-908. [PMID: 36881492 DOI: 10.1021/acs.jnatprod.2c01135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A considerable number of natural products have been published in recent years with misassigned structure, even though they had been correctly elucidated in the past. The availability of databases containing revised structures can prevent the amplification of errors in structural elucidation. NAPROC-13, a dereplication tool based on the 13C chemical shift, has been used to search for substances that, possessing the same chemical shifts, have been described with different structures. The correct structure of these different structural proposals is verified by computational chemistry. This paper reports the structural revision of nine triterpenoids following this methodology.
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Affiliation(s)
- Estela Guerrero De León
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Hugo Sánchez-Martínez
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Juan A Morán-Pinzón
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
| | - Esther Del Olmo Fernández
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS, IBSAL, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| | - José L López-Pérez
- CIPFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Avenue Octavio Mendez Pereira, Panama City 0824, Panama
- Departamento de Ciencias Farmacéuticas, Área de Química Farmacéutica, Facultad de Farmacia, CIETUS, IBSAL, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
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4
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Cohen RD, Wood JS, Lam YH, Buevich AV, Sherer EC, Reibarkh M, Williamson RT, Martin GE. DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking. Molecules 2023; 28:molecules28062449. [PMID: 36985422 PMCID: PMC10051451 DOI: 10.3390/molecules28062449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Density functional theory (DFT) benchmark studies of 1H and 13C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured 1H and 13C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for 1H and 13C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Maximum deviations were less than 0.5 and 6.5 ppm for 1H and 13C, respectively.
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Affiliation(s)
- Ryan D Cohen
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
| | - Jared S Wood
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Yu-Hong Lam
- Department of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Alexei V Buevich
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079, USA
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5
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Qi L, Li C, Huang Z, Jiang J, Zhu X, Lu X, Ye L. Enantioselective Copper‐Catalyzed Formal [2+1] and [4+1] Annulations of Diynes with Ketones via Carbonyl Ylides. Angew Chem Int Ed Engl 2022; 61:e202210637. [DOI: 10.1002/anie.202210637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Lin‐Jun Qi
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies Taizhou University Jiaojiang 318000 Zhejiang China
| | - Cui‐Ting Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zheng‐Qi Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Jia‐Tian Jiang
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xin‐Qi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Xin Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Long‐Wu Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces Key Laboratory of Chemical Biology of Fujian Province College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China
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6
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Novitskiy IM, Kutateladze AG. Brief overview of recently reported misassigned natural products and their in silico revisions enabled by DU8ML, a machine learning-augmented DFT computational NMR method. Nat Prod Rep 2022; 39:2003-2007. [PMID: 36004664 DOI: 10.1039/d2np00051b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mostly covering 2018 to 2022This Highlight article describes a personal selection of recent misassigned structures of natural products and their revision with the aid of DU8ML, a machine learning-augmented DFT computational method for fast and accurate calculations of solution NMR chemical shifts and spin-spin coupling constants.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA 80210.
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA 80210.
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7
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Qi LJ, Li CT, Huang ZQ, Jiang JT, Zhu XQ, Lu X, Ye LW. Enantioselective Copper‐Catalyzed Formal [2+1] and [4+1] Annulations of Diynes with Ketones via Carbonyl Ylides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lin-Jun Qi
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Cui-Ting Li
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Zheng-Qi Huang
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Jia-Tian Jiang
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Xin-Qi Zhu
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Xin Lu
- Xiamen University College of Chemistry and Chemical Engineering 361005 Xiamen CHINA
| | - Long-Wu Ye
- Xiamen University College of Chemistry and Chemical Engineering Jiaxi Building-624 361005 Xiamen CHINA
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8
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Elyashberg M, Novitskiy IM, Bates RW, Kutateladze AG, Williams CM. Reassignment of Improbable Natural Products Identified through Chemical Principle Screening. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mikhail Elyashberg
- Advanced Chemistry Development Inc. (ACD/Labs) Toronto ON, M5C 1B5 Canada
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Roderick W. Bates
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link Singapore 637371
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver Denver CO 80208 United States
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Queensland Australia
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9
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Novitskiy IM, Kutateladze AG. Peculiar Reaction Products and Mechanisms Revisited with Machine Learning-Augmented Computational NMR. J Org Chem 2022; 87:8589-8598. [PMID: 35723522 DOI: 10.1021/acs.joc.2c00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DU8ML, a fast and accurate machine learning-augmented density functional theory (DFT) method for computing nuclear magnetic resonance (NMR) spectra, proved effective for high-throughput revision of misassigned natural products. In this paper, we disclose another important aspect of its application: correction of unusual reaction mechanisms originally proposed because of incorrect product structures.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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10
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Shen SM, Appendino G, Guo YW. Pitfalls in the structural elucidation of small molecules. A critical analysis of a decade of structural misassignments of marine natural products. Nat Prod Rep 2022; 39:1803-1832. [PMID: 35770685 DOI: 10.1039/d2np00023g] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: July 2010 to August 2021This article summarizes more than 200 cases of misassigned marine natural products reported between July 2010 and August 2021, sorting out errors according to the structural elements. Based on a comparative analysis of the original and the revised structures, major pitfalls still plaguing the structural elucidation of small molecules were identified, emphasizing the role of total synthesis, crystallography, as well as chemical- and biosynthetic logic to complement spectroscopic data. Distinct "trends" in natural product misassignment are evident between compounds of marine and plant origin, with an overall much lower incidence of "impossible" structures within misassigned marine natural products.
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Affiliation(s)
- Shou-Mao Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Giovanni Appendino
- Dipartimento di Scienze del Farmaco, Universitá degli Studi del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Yue-Wei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. .,Drug Discovery Shandong Laboratory, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
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11
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Novitskiy IM, Kutateladze AG. DU8ML: Machine Learning-Augmented Density Functional Theory Nuclear Magnetic Resonance Computations for High-Throughput In Silico Solution Structure Validation and Revision of Complex Alkaloids. J Org Chem 2022; 87:4818-4828. [PMID: 35302771 DOI: 10.1021/acs.joc.2c00169] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Machine learning (ML) profoundly improves the accuracy of the fast DU8+ hybrid density functional theory/parametric computations of nuclear magnetic resonance spectra, allowing for high throughput in silico validation and revision of complex alkaloids and other natural products. Of nearly 170 alkaloids surveyed, 35 structures are revised with the next-generation ML-augmented DU8 method, termed DU8ML.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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12
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Reddy DS, Novitskiy IM, Kutateladze AG. Maximizing Step‐Normalized Increases in Molecular Complexity: Formal [4+2+2+2] Photoinduced Cyclization Cascade to Access Polyheterocycles Possessing Privileged Substructures. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- D. Sai Reddy
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Ivan M. Novitskiy
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Andrei G. Kutateladze
- Department of Chemistry and Biochemistry University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
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13
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Matsuda Y, Koyama T, Kawano S, Miura K, Simizu S, Saikawa Y, Nakata M. Scalable Syntheses and Biological Evaluation of Africane-type Sesquiterpenoids. Chem Biodivers 2022; 19:e202100890. [PMID: 35018704 DOI: 10.1002/cbdv.202100890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/11/2022] [Indexed: 11/05/2022]
Abstract
Practical total syntheses of africane-type sesquiterpenoids were realized by reexamination of a divergent strategy employing optimized three-component coupling followed by ring-closing metathesis and substrate-controlled cyclopropanation. This sequential eight-step conversion provided Δ9(15)-africanene, a common bicyclo[5.3.0]decane intermediate for the syntheses of africane derivatives, in more than twice the yield as in the previous approach. The scalability and robustness of this improved synthetic route were confirmed by gram-scale preparation of Δ9(15)-africanene. In vitro cell-based assays of the synthesized africane-type sesquiterpenoids disclosed that ester-incorporating derivatives showed cytotoxic activity against HeLa cells. The effect of relative and absolute stereochemistry of africane-9,15-diol monoacetates on the cytotoxicity against HeLa cells was also investigated.
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Affiliation(s)
- Yutaka Matsuda
- Keio University Faculty of Science and Technology Graduate School of Science and Technology: Keio Gijuku Daigaku Rikogakubu Daigakuin Rikogaku Kenkyuka, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
| | - Takayuki Koyama
- Keio University, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
| | - Sayaka Kawano
- Keio University: Keio Gijuku Daigaku, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
| | - Kazuki Miura
- Faculty of Science and Technology, Keio University, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
| | - Siro Simizu
- Faculty of Science of Technology, Keio University, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
| | - Yoko Saikawa
- Faculty of Science and Technology, Keio University, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, JAPAN
| | - Masaya Nakata
- Faculty of Science and Technology, Keio University, Department of Applied Chemistry, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, JAPAN
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14
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Novitskiy IM, Kutateladze AG. DU8+ Computations Reveal a Common Challenge in the Structure Assignment of Natural Products Containing a Carboxylic Anhydride Moiety. J Org Chem 2021; 86:17511-17515. [PMID: 34743508 DOI: 10.1021/acs.joc.1c02291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DU8+ computations of NMR spectra revealed a relatively common error in the structure assignment of carboxylic anhydride-containing natural products. Computationally driven revisions of ten of these structures are reported in this Note. The majority of the misassigned structures featured a hydroxy group that is proximal to the proposed anhydride moiety and capable of lactone formation.
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Affiliation(s)
- Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80210, United States
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15
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Reddy DS, Novitskiy IM, Kutateladze AG. Maximizing Step-Normalized Increases in Molecular Complexity: Formal [4+2+2+2] Photoinduced Cyclization Cascade to Access Polyheterocycles Possessing Privileged Substructures. Angew Chem Int Ed Engl 2021; 61:e202112573. [PMID: 34850525 DOI: 10.1002/anie.202112573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 11/10/2022]
Abstract
A new complexity building photoinduced cascade which amounts to an unprecedented formal [4+2+2+2] cycloaddition topology is developed to access complex nitrogen polyheterocycles. This photocascade is initiated by the excited state intramolecular proton transfer (ESIPT) in aromatic amino ketones with tethered dual unsaturated pendants, i.e. pyrrole and alkenic moieties, resulting in the formation of four σ-bonds and setting six new stereogenic centers in a single experimentally simple photochemical step with up to 220 mcbit complexity increases.
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Affiliation(s)
- D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
| | - Ivan M Novitskiy
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Denver, CO 80208, USA
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16
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Ren FC, Wang LX, Lv YF, Hu JM, Zhou J. Structure Revision of Four Classes of Prenylated Aromatic Natural Products Based on a Rule for Diagnostic 13C NMR Chemical Shifts. J Org Chem 2021; 86:10982-10990. [PMID: 33274942 DOI: 10.1021/acs.joc.0c02409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Errors in elucidating the structures of four natural classes of prenylated aromatic compounds with 2,3-epoxy, 2,3-dihydroxy, and cyclization with an ortho-phenolic hydroxyl to give a pyran or furan ring moiety are frequent and inevitable. Based on rigorous literature research and a series of chemical transformation experiments, a rule for the rapid determination of these four classes of prenylated derivates based on 13C NMR data was formulated, and 57 corrections featuring these fragments were accordingly reported.
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Affiliation(s)
- Fu-Cai Ren
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Xia Wang
- Key Laboratory of Pu-er Tea Science, Ministry of Education, and College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong-Feng Lv
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang-Miao Hu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Chini MG, Lauro G, Bifulco G. Addressing the Target Identification and Accelerating the Repositioning of Anti‐Inflammatory/Anti‐Cancer Organic Compounds by Computational Approaches. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone 86090 Pesche (IS) Italy
| | - Gianluigi Lauro
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giuseppe Bifulco
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
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18
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Novitskiy IM, Holt TA, Kutateladze AG. Structure revision of ent-kaurane diterpenoids, isoserrins A, B, and D, enabled by DU8+ computation of their NMR spectral data. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Novitskiy IM, Holt TA, Kutateladze AG. Structure revision of ent-kaurane diterpenoids, isoserrins A, B, and D, enabled by DU8+ computation of their NMR spectral data. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Drummond GJ, Grant PS, Brimble MA. ent-Atisane diterpenoids: isolation, structure and bioactivity. Nat Prod Rep 2021; 38:330-345. [PMID: 32716458 DOI: 10.1039/d0np00039f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to 2020 ent-Atisane diterpenoids are a class of over 150 members with diverse structures and valuable bioactivities. These compounds share a curious history in which the synthesis of the archetypal member preceded its isolation from natural sources. In this review, we provide a comprehensive summary of the isolation, structure, and bioactivity of ent-atisane diterpenoids from their discovery in 1965 to the present day.
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Affiliation(s)
- Grace J Drummond
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Phillip S Grant
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, Symonds Street, Auckland 1010, New Zealand and Maurice Wilkins Centre of Molecular Biodiscovery, The University of Auckland, Symonds Street, Auckland 1010, New Zealand.
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21
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Williams CM, Dallaston MA. The Future of Retrosynthesis and Synthetic Planning: Algorithmic, Humanistic or the Interplay? Aust J Chem 2021. [DOI: 10.1071/ch20371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The practice of deploying and teaching retrosynthesis is on the cusp of considerable change, which in turn forces practitioners and educators to contemplate whether this impending change will advance or erode the efficiency and elegance of organic synthesis in the future. A short treatise is presented herein that covers the concept of retrosynthesis, along with exemplified methods and theories, and an attempt to comprehend the impact of artificial intelligence in an era when freely and commercially available retrosynthetic and forward synthesis planning programs are increasingly prevalent. Will the computer ever compete with human retrosynthetic design and the art of organic synthesis?
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22
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Marcarino MO, Zanardi MM, Cicetti S, Sarotti AM. NMR Calculations with Quantum Methods: Development of New Tools for Structural Elucidation and Beyond. Acc Chem Res 2020; 53:1922-1932. [PMID: 32794691 DOI: 10.1021/acs.accounts.0c00365] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structural elucidation is an important and challenging stage in the discovery of new organic molecules. Single-crystal X-ray analysis provides the most unquestionable results, though in practice the availability of suitable crystals limits its broad use. On the other hand, NMR spectroscopy has become the leading and universal technique to accomplish the task. Despite continuous advances in the field, the misinterpretation of NMR data is commonplace, evidenced by the large number of erroneous structures being published in top journals. Quantum calculations of NMR chemical shifts and scalar coupling constants emerged as ideal complements to facilitate the elucidation process when experimental NMR data is inconclusive. Since seminal reports demonstrated that affordable DFT methods provide NMR predictions accurate enough to differentiate among closely related isomers, the discipline has experienced substantial growth. The impact has been felt in different areas, and nowadays the results of such calculations are routinely seen in high impact literature.This Account describes our investigations in the field of quantum NMR calculations, focusing on the development of tools for structural elucidation and practical applications. We pioneered the use of artificial intelligence methods in the development of novel strategies of structural validation. Our first generation of trained artificial neural networks (ANNs) showed excellent ability to identify mistakes at the atom connectivity level, whereas the use of multidimensional pattern recognition pushed the performance to the stereochemical limit. In a conceptually different approach, we developed DP4+, an updated version of the DP4 probability used to determine the most likely structure among two or more candidates when one set of experimental data is available. Increasing the level of theory in NMR calculations and including unscaled data in the formalism improved the performance of the method, further validated to settle the configuration of challenging motifs such as spiroepoxides or Mosher's derivatives. One of the limitations of DP4+ is related to the relatively large computational cost involved in obtaining DFT-optimized geometries, which led to the development of a fast variant including the valuable information provided by coupling constants (J-DP4 method).These tools were explored to suggest the most probable structure of controversial natural or unnatural products originally misassigned, with some predictions further validated by synthesis (as in the case of pseudorubriflordilactone B). The possibility of predicting the structure of a natural product without requiring authentic sample was investigated in collaboration with Prof. Pilli (UNICAMP, Brazil) in the computer-guided total synthesis and stereochemical revisions of several natural products. Despite these advances, there remain considerable challenges, such as the case of configurational assessment of polar systems featuring multiple intramolecular hydrogen bonding interactions because of the poor energy predictions provided by most DFT methods. In our latest work, we tackle this problem by averaging the results provided by randomly generated ensembles, paving the way for a new paradigm in quantum NMR-assisted structural elucidation.
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Affiliation(s)
- Maribel O. Marcarino
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Marı́a M. Zanardi
- Instituto de Ingenierı́a Ambiental, Quı́mica y Biotecnologı́a Aplicada (INGEBIO), Facultad de Quı́mica e Ingenierı́a del Rosario, Pontificia Universidad Católica Argentina, Av. Pellegrini 3314, S2002QEO Rosario, Argentina
| | - Soledad Cicetti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Ariel M. Sarotti
- Instituto de Quı́mica Rosario (CONICET), Facultad de Ciencias Bioquı́micas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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23
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Maslovskaya LA, Savchenko AI, Krenske EH, Chow S, Holt T, Gordon VA, Reddell PW, Pierce CJ, Parsons PG, Boyle GM, Kutateladze AG, Williams CM. EBC-232 and 323: A Structural Conundrum Necessitating Unification of Five In Silico Prediction and Elucidation Methods. Chemistry 2020; 26:11862-11867. [PMID: 32864777 DOI: 10.1002/chem.202001884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Indexed: 12/12/2022]
Abstract
Structurally unique halimanes EBC-232 and EBC-323, isolated from the Australian rainforest plant Croton insularis, proved considerably difficult to elucidate. The two diastereomers, which consist an unusual oxo-6,7-spiro ring system fused to a dihydrofuran, were solved by unification and consultation of five in silico NMR elucidation and prediction methods [i.e., ACDLabs, olefin strain energy (OSE), DP4, DU8+ and TD DFT CD]. Structure elucidation challenges of this nature are prime test case examples for empowering future AI learning in structure elucidation.
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Affiliation(s)
- Lidia A Maslovskaya
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia.,QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei I Savchenko
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Sharon Chow
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Victoria A Gordon
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Paul W Reddell
- EcoBiotics Limited, PO Box 1, Yungaburra, 4884, Queensland, Australia
| | - Carly J Pierce
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Peter G Parsons
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Glen M Boyle
- QIMR Berghofer Medical Research Institute, PO Royal Brisbane Hospital, Brisbane, 4029, Australia
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208, USA
| | - Craig M Williams
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, 4072, Australia
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24
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De Vita S, Terracciano S, Bruno I, Chini MG. From Natural Compounds to Bioactive Molecules through NMR and
In Silico
Methodologies. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simona De Vita
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Stefania Terracciano
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Ines Bruno
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone‐ 86090 Pesche (IS) Italy
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25
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Holt TA, Reddy DS, Huple DB, West LM, Rodríguez AD, Crimmins MT, Kutateladze AG. The Discreet Structural Diversity of Briarellins: DU8+ Guided Multiple Structure Revisions Yielded Two Unknown Structural Types. J Org Chem 2020; 85:6201-6205. [PMID: 32323536 DOI: 10.1021/acs.joc.0c00555] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Briarellins, a subset of C2-C11 cyclized cembranoids, were proposed to contain a C3-C14 ether or lactone bridge, similar to asbestinins. However, the total synthesis of the proposed structure of briarellin J revealed a misassignment. We revisited briarellins, computationally, with the help of a recently developed hybrid DFT/parametric method, DU8+, and revised the structures of briarellin C14-C3 ε-lactones to new structural types containing either a C14-C11 or C14-C12 lactone bridge. The original structures of briarellin and asbestinin ethers were confirmed.
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Affiliation(s)
- Tina A Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - D Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Deepak B Huple
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Lyndon M West
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Abimael D Rodríguez
- Molecular Science Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, 00926, Puerto Rico
| | - Michael T Crimmins
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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26
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Yaoita Y, Machida K. Misassigned Polyoxygenated Sterols and Reassignments of Their Structures. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20907724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This review will summarize the authors’ studies on the reassignments of structures of 9 natural polyoxygenated sterols (24 S)-24-ethylcholest-8-ene-3β,5α,6β,7α-tetrol (1), (24 S)-24-ethylcholest-8(14)-ene-3β,5α,6β,7α-tetrol (2), (22 E)-24-methylcholesta-8(14),22-diene-3β,5α,6β,7α-tetrol (3), 5β,6β-epoxy-(22 E)-ergosta-8,22-diene-3β,7β-diol (4), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14α-pentol (5), 3β,5α,6β,8β,14α-pentahydroxy-(22 E)-ergost-22-en-7-one (6), 5β,6β-epoxy-24-methylenecholesta-8,24(28)-diene-3β,7α,11α-triol (7), 6β-acetoxy-(22 E)-10α-ergosta-7,22-diene-3β,5α-diol (8), and 8α,9α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,14α-triol (9). The structures of 1 to 9 have been reassigned as (24 S)-5α,6α-epoxy-24-ethylcholest-8-ene-3β,7α-diol (16), (24 S)-5α,6α-epoxy-24-ethylcholest-8(14)-ene-3β,7α-diol (17), 5α,6α-epoxy-(22 E)-ergosta-8(14),22-diene-3β,7α-diol (13), 5α,6α-epoxy-(22 E)-ergosta-8,22-diene-3β,7α-diol (12), (22 E)-ergosta-7,22-diene-3β,5α,6β,9α,14β-pentol (25), 5α,6α;8α,14α-diepoxy-3β-hydroxy-(22 E)-ergost-22-en-7-one (18), 5α,6α-epoxyergosta-8,24(28)-diene-3β,7α,11α-triol (21), 6β-acetoxy-(22 E)-ergosta-7,22-diene-3β,5α-diol (26), and 8α,14α-epoxy-(22 E)-ergosta-6,22-diene-3β,5α,9α-triol (28), respectively, from the results of careful reexamination of the published1H and13C NMR spectral data.
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Affiliation(s)
- Yasunori Yaoita
- Pharmaceutical Education Center, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Koichi Machida
- Pharmaceutical Education Center, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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27
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Lin S, Yu H, Yang B, Li F, Chen X, Li H, Zhang S, Wang J, Hu Y, Hu Z, Zhang Y. Reisolation and Configurational Reinvestigation of Cottoquinazolines E-G from an Arthropod-Derived Strain of the Fungus Neosartorya fischeri. JOURNAL OF NATURAL PRODUCTS 2020; 83:169-173. [PMID: 31920082 DOI: 10.1021/acs.jnatprod.9b01000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The reported fumiquinazoline-related alkaloids cottoquinazolines E-G (1-3) were reisolated from solid cultures of the fungus Neosartorya fischeri, which was isolated from the medicinal arthropod Cryptotympana atrata. The unresolved issues regarding the absolute configurations (for cottoquinazolines E and F) prompted a reinvestigation of the configurations for all three compounds, as enabled by extensive spectroscopic methods, comparisons of experimental electronic circular dichroism data, and X-ray crystallography. In addition, cottoquinazoline F (2) showed significant antibacterial activity against ESBL-producing Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus faecalis with MIC values of 8, 32, 32, and 16 μg/mL, respectively.
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Affiliation(s)
- Shuang Lin
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Huimin Yu
- Department of Periodontics , Stomatological Hospital of Southern Medical University, Guangdong Provincial Stomatological Hospital , Guangzhou 510280 , People's Republic of China
| | - Beiye Yang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Fengli Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Xia Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Huaqiang Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Sitian Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - Zhengxi Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College , Huazhong University of Science and Technology , Wuhan 430030 , People's Republic of China
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28
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Gerrard W, Bratholm LA, Packer MJ, Mulholland AJ, Glowacki DR, Butts CP. IMPRESSION - prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy. Chem Sci 2020; 11:508-515. [PMID: 32190270 PMCID: PMC7067266 DOI: 10.1039/c9sc03854j] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
The IMPRESSION (Intelligent Machine PREdiction of Shift and Scalar information Of Nuclei) machine learning system provides an efficient and accurate method for the prediction of NMR parameters from 3-dimensional molecular structures. Here we demonstrate that machine learning predictions of NMR parameters, trained on quantum chemical computed values, can be as accurate as, but computationally much more efficient (tens of milliseconds per molecular structure) than, quantum chemical calculations (hours/days per molecular structure) starting from the same 3-dimensional structure. Training the machine learning system on quantum chemical predictions, rather than experimental data, circumvents the need for the existence of large, structurally diverse, error-free experimental databases and makes IMPRESSION applicable to solving 3-dimensional problems such as molecular conformation and stereoisomerism.
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Affiliation(s)
| | | | - Martin J Packer
- Chemistry , R&D Oncology , AstraZeneca , Cambridge CB4 0QA , UK
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29
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Bondarenko OB, Komarov AI, Karetnikov GL, Nikolaeva SN, Zyk NV, Holt T, Kutateladze AG. Diastereoselective heterocyclization of geminal bromo-fluoro arylcyclopropanes by nitrosonium tetrafluoroborate: Access to 4-fluorinated isoxazolines and isoxazoles. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.130666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Varmazyar A, Sedaghat S, Goli-Kand AN, Khalaj M, Arab-Salmanabadi S. Domino ring opening/cyclization of oxiranes for synthesis of functionalized 2H-pyran-5-carboxylate. Mol Divers 2019; 24:707-716. [PMID: 31363886 DOI: 10.1007/s11030-019-09978-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 07/13/2019] [Indexed: 11/30/2022]
Abstract
A simple method for the synthesis of functionalized 2H-pyrans via a catalytic reaction of an oxirane, an alkyne, and a malonate has been developed in which a 6-exo-dig cyclization pathway is observed. In this transformation, the attack of in situ generated copper acetylides on oxiranes formed homopropargylic alcohol intermediates which further transferred to 2H-pyrans with the help of malonates.
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Affiliation(s)
- Alireza Varmazyar
- Department of Chemistry, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Sajjad Sedaghat
- Department of Chemistry, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran.
| | - Ahmad Nozad Goli-Kand
- Department of Chemistry, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran.,Material and Nuclear Fuel Cyclic Research School, NSTRI, Tehran, Iran
| | - Mehdi Khalaj
- Department of Chemistry, Buinzahra Branch, Islamic Azad University, Buinzahra, Iran.
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31
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Kutateladze AG, Holt T. Structure Validation of Complex Natural Products: Time to Change the Paradigm. What did Synthesis of Alstofolinine A Prove? J Org Chem 2019; 84:8297-8299. [DOI: 10.1021/acs.joc.9b00969] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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32
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Kutateladze AG, Holt T, Reddy DS. Natural Products Containing the Oxetane and Related Moieties Present Additional Challenges for Structure Elucidation: A DU8+ Computational Case Study. J Org Chem 2019; 84:7575-7586. [DOI: 10.1021/acs.joc.9b01005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Andrei G. Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Tina Holt
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - D. Sai Reddy
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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33
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Lardon N, Liffert R, Linden A, Gademann K. The Furan Shuffling Hypothesis: A Biogenetic Proposal for Eremophilane Sesquiterpenoids. Angew Chem Int Ed Engl 2019; 58:7004-7007. [PMID: 30901154 DOI: 10.1002/anie.201901898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Indexed: 12/12/2022]
Abstract
Based on the structural similarities of the recently isolated eremophilane-type sesquiterpenoids microsphaeropsisin B and C and the iso-eremophilane periconianone C, a revised biogenetic hypothesis for C8-C11-connected iso-eremophilanes is presented and corroborated by strong experimental evidence. The first enantioselective total syntheses of microsphaeropsisin B and C were achieved starting from a known intermediate, whose synthesis was elaborated previously in the total synthesis of periconianone A, and in a total of 15 steps starting from γ-hydroxy carvone. Mild reaction conditions for the subsequent α-ketol rearrangement not only resulted in the herein proposed conversion of microsphaeropsisin B into periconianone C, but also in the conversion of microsphaeropsisin C into 4-epi-periconianone C.
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Affiliation(s)
- Nicolas Lardon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Raphael Liffert
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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34
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Lardon N, Liffert R, Linden A, Gademann K. The Furan Shuffling Hypothesis: A Biogenetic Proposal for Eremophilane Sesquiterpenoids. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nicolas Lardon
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Raphael Liffert
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Anthony Linden
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Karl Gademann
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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35
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Kutateladze AG, Krenske EH, Williams CM. Reassignments and Corroborations of Oxo‐Bridged Natural Products Directed by OSE and DU8+ NMR Computation. Angew Chem Int Ed Engl 2019; 58:7107-7112. [DOI: 10.1002/anie.201902777] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Indexed: 11/09/2022]
Affiliation(s)
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular BiosciencesUniversity of Queensland Brisbane 4072 Queensland Australia
| | - Craig M. Williams
- School of Chemistry and Molecular BiosciencesUniversity of Queensland Brisbane 4072 Queensland Australia
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Bondarenko OB, Vinogradov AA, Komarov AI, Karetnikov GL, Zyk NV, Holt T, Kutateladze AG. Access to 5-fluoroisoxazoles via the nitrosation of geminal bromo-fluoro arylcyclopropanes. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.03.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kutateladze AG, Krenske EH, Williams CM. Reassignments and Corroborations of Oxo‐Bridged Natural Products Directed by OSE and DU8+ NMR Computation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular BiosciencesUniversity of Queensland Brisbane 4072 Queensland Australia
| | - Craig M. Williams
- School of Chemistry and Molecular BiosciencesUniversity of Queensland Brisbane 4072 Queensland Australia
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Reddy DS, Kutateladze AG. Photoinitiated Cascade for Rapid Access to Pyrroloquinazolinone Core of Vasicinone, Luotonins, and Related Alkaloids. Org Lett 2019; 21:2855-2858. [PMID: 30933523 DOI: 10.1021/acs.orglett.9b00858] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Furylimines of aromatic o-nitro aldehydes undergo a photoinduced cascade transformation offering rapid atom- and step-economical access to complex polyheterocyclic scaffolds possessing a privileged pyrroloquinazolinone core.
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Affiliation(s)
- D Sai Reddy
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
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