1
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Bag S, Liu J, Patil S, Bonowski J, Koska S, Schölermann B, Zhang R, Wang L, Pahl A, Sievers S, Brieger L, Strohmann C, Ziegler S, Grigalunas M, Waldmann H. A divergent intermediate strategy yields biologically diverse pseudo-natural products. Nat Chem 2024; 16:945-958. [PMID: 38365941 PMCID: PMC11164679 DOI: 10.1038/s41557-024-01458-4] [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] [Received: 11/22/2022] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The efficient exploration of biologically relevant chemical space is essential for the discovery of bioactive compounds. A molecular design principle that possesses both biological relevance and structural diversity may more efficiently lead to compound collections that are enriched in diverse bioactivities. Here the diverse pseudo-natural product (PNP) strategy, which combines the biological relevance of the PNP concept with synthetic diversification strategies from diversity-oriented synthesis, is reported. A diverse PNP collection was synthesized from a common divergent intermediate through developed indole dearomatization methodologies to afford three-dimensional molecular frameworks that could be further diversified via intramolecular coupling and/or carbon monoxide insertion. In total, 154 PNPs were synthesized representing eight different classes. Cheminformatic analyses showed that the PNPs are structurally diverse between classes. Biological investigations revealed the extent of diverse bioactivity enrichment of the collection in which four inhibitors of Hedgehog signalling, DNA synthesis, de novo pyrimidine biosynthesis and tubulin polymerization were identified from four different PNP classes.
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Affiliation(s)
- Sukdev Bag
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Jie Liu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sohan Patil
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jana Bonowski
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sandra Koska
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Beate Schölermann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ruirui Zhang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lin Wang
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Lukas Brieger
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, Inorganic Chemistry, TU Dortmund University, Dortmund, Germany
| | - Slava Ziegler
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
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2
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Huang Y, Li X, Mai BK, Tonogai EJ, Smith AJ, Hergenrother PJ, Liu P, Hoveyda AH. A catalytic process enables efficient and programmable access to precisely altered indole alkaloid scaffolds. Nat Chem 2024; 16:1003-1014. [PMID: 38374457 DOI: 10.1038/s41557-024-01455-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
A compound's overall contour impacts its ability to elicit biological response, rendering access to distinctly shaped molecules desirable. A natural product's framework can be modified, but only if it is abundant and contains suitably modifiable functional groups. Here we introduce a programmable strategy for concise synthesis of precisely altered scaffolds of scarce bridged polycyclic alkaloids. Central to our approach is a scalable catalytic multi-component process that delivers diastereo- and enantiomerically enriched tertiary homoallylic alcohols bearing differentiable alkenyl moieties. We used one product to launch progressively divergent syntheses of a naturally occurring alkaloid and its precisely expanded, contracted and/or distorted framework analogues (average number of steps/scaffold of seven). In vitro testing showed that a skeleton expanded by one methylene in two regions is cytotoxic against four types of cancer cell line. Mechanistic and computational studies offer an account for several unanticipated selectivity trends.
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Affiliation(s)
- Youming Huang
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Xinghan Li
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily J Tonogai
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Amanda J Smith
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Amir H Hoveyda
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France.
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA.
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3
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Luz Tibaldi-Bollati M, Nicotra V, Oksdath-Mansilla G, García ME. Expanding Diterpene Complexity and Diversity via Photoinduced Ring Distortions. Chempluschem 2024; 89:e202300537. [PMID: 38029375 DOI: 10.1002/cplu.202300537] [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] [Received: 09/23/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/01/2023]
Abstract
Natural products and their semi-synthetic derivatives undoubtedly constitute an important source of therapeutic agents. Their importance lies in their own origin and evolution, since they have great chemical diversity, biochemical specificity, and pharmacological properties. Currently, there is a renewed interest in the development of methodologies capable of efficiently modifying the chemical structure of these bioactive platforms. In this work, the photoderivatization of the diterpene solidagenone was performed using a complexity-to-diversity-oriented approach. By exploring [2+2]-photocycloaddition, photoinduced-hydrogen abstraction, and photoxygenation reactions, a set of solidagenone derivatives was obtained, showing different ring fusions, side chain rearrangements, and modifications of the original furan ring's substitution pattern. The derivatives obtained were characterised by NMR methodologies. To evaluate the structural diversity of the labdane-derived compounds, their physicochemical properties, structural similarity, and chemical space were analysed. These results suggest that photochemical reactions are a useful tool for performing ring distortion transformations, generating derivatives of natural compounds with wide diversity, structural complexity, and with potential biological properties.
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Affiliation(s)
- María Luz Tibaldi-Bollati
- Dpto. de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Viviana Nicotra
- Dpto. de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Gabriela Oksdath-Mansilla
- Dpto. de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Manuela E García
- Dpto. de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
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4
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Cheng S, Dong C, Ma Y, Xu X, Zhao Y. Skeletal Transformations of Terpenoid Forskolin Employing an Oxidative Rearrangement Strategy. J Org Chem 2024; 89:5741-5745. [PMID: 38568052 DOI: 10.1021/acs.joc.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The skeletal transformations of diterpenoid forskolin were achieved by employing an oxidative rearrangement strategy. A library of 36 forskolin analogues with structural diversity was effectively generated. Computational analysis shows that 12 CTD compounds with unique scaffolds and ring systems were produced during the course of this work.
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Affiliation(s)
- Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Chenhu Dong
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yujie Ma
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Xiaoyu Xu
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China
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5
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Lee H, Kim J, Koh M. Medium-Sized Ring Expansion Strategies: Enhancing Small-Molecule Library Development. Molecules 2024; 29:1562. [PMID: 38611841 PMCID: PMC11013129 DOI: 10.3390/molecules29071562] [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] [Received: 03/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The construction of a small molecule library that includes compounds with medium-sized rings is increasingly essential in drug discovery. These compounds are essential for identifying novel therapeutic agents capable of targeting "undruggable" targets through high-throughput and high-content screening, given their structural complexity and diversity. However, synthesizing medium-sized rings presents notable challenges, particularly with direct cyclization methods, due to issues such as transannular strain and reduced degrees of freedom. This review presents an overview of current strategies in synthesizing medium-sized rings, emphasizing innovative approaches like ring-expansion reactions. It highlights the challenges of synthesis and the potential of these compounds to diversify the chemical space for drug discovery, underscoring the importance of medium-sized rings in developing new bioactive compounds.
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Affiliation(s)
- Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Republic of Korea;
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
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6
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Tse MW, Zhu M, Peters B, Hamami E, Chen J, Davis KP, Nitz S, Weller J, Warrier T, Hunt DK, Morales Y, Kawate T, Gaulin JL, Come JH, Hernandez-Bird J, Huo W, Neisewander I, Kiessling LL, Hung DT, Mecsas J, Aldridge BB, Isberg RR, Blainey PC. Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586803. [PMID: 38585790 PMCID: PMC10996685 DOI: 10.1101/2024.03.26.586803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide problem. Combination antimicrobial therapies may be an important strategy to overcome resistance and broaden the spectrum of existing antibiotics. However, this strategy is limited by the ability to efficiently screen large combinatorial chemical spaces. Here, we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique strain-antibiotic-compound combinations. In this dataset, compounds more frequently exhibited synergy with known antibiotics than single-agent activity. We identified a compound, P2-56, and developed a more potent analog, P2-56-3, which potentiated rifampin (RIF) activity against Acinetobacter baumannii and Klebsiella pneumoniae. Using phenotypic assays, we showed P2-56-3 disrupts the outer membrane of A. baumannii. To identify pathways involved in the mechanism of synergy between P2-56-3 and RIF, we performed genetic screens in A. baumannii. CRISPRi-induced partial depletion of lipooligosaccharide transport genes (lptA-D, lptFG) resulted in hypersensitivity to P2-56-3/RIF treatment, demonstrating the genetic dependency of P2-56-3 activity and RIF sensitization on lpt genes in A. baumannii. Consistent with outer membrane homeostasis being an important determinant of P2-56-3/RIF tolerance, knockout of maintenance of lipid asymmetry complex genes and overexpression of certain resistance-nodulation-division efflux pumps - a phenotype associated with multidrug-resistance - resulted in hypersensitivity to P2-56-3. These findings demonstrate the immense scale of phenotypic antibiotic combination screens using DropArray and the potential for such approaches to discover new small molecule synergies against multidrug-resistant ESKAPE strains.
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Affiliation(s)
- Megan W. Tse
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- These authors contributed equally
| | - Meilin Zhu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- These authors contributed equally
| | - Benjamin Peters
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- These authors contributed equally
| | - Efrat Hamami
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
- These authors contributed equally
| | - Julie Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kathleen P. Davis
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Samuel Nitz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Tri-Institutional Program in Computational Biology and Medicine, New York, New York, 10065
| | - Juliane Weller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Wellcome Sanger Institute, Hinxton, Saffron Walden CB10 1RQ, United Kingdom
| | - Thulasi Warrier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114
| | - Diana K. Hunt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Yoelkys Morales
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Tomohiko Kawate
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114
| | | | - Jon H. Come
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Tango Therapeutics, Boston, MA, USA 02215
| | - Juan Hernandez-Bird
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Isabelle Neisewander
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Joan Mecsas
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155
| | - Ralph R. Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, 02111
- These authors are co-corresponding and contributed equally
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- These authors are co-corresponding and contributed equally
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7
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Khdar ZA, Le TM, Schelz Z, Zupkó I, Szakonyi Z. Stereoselective synthesis and antiproliferative activity of allo-gibberic acid-based 1,3-aminoalcohol regioisomers. RSC Med Chem 2024; 15:874-887. [PMID: 38516597 PMCID: PMC10953481 DOI: 10.1039/d3md00665d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024] Open
Abstract
A new library of allo-gibberic acid-based aminoalcohol regioisomers was synthesised stereoselectively starting from commercially available gibberellic acid, which yields allo-gibberic acid under mild acidic conditions. The successful formation of hydroxymethyl ketone derivative 5, by acid-mediated rearrangement of previously prepared epoxide, paved the way to obtain the desired 1,3-aminoalcohols through Schiff base formation. To obtain the desired regioisomers, the primary alcohol functionality of 5 was subjected to mesylation, then replaced with either primary amine or sodium azide. The formed azide derivative was subjected to either CuAAC reaction to obtain 1,2,3-triazoles or underwent Pd-catalysed hydrogenolysis to obtain primary aminoalcohol, which was further transformed into 1,3-aminoalcohols by reductive alkylation. All prepared aminoalcohols were identified in a satisfactory manner using modern spectroscopic techniques and assessed for their antiproliferative activity against a panel of human cancer cell lines. The antiproliferative effects of the prepared compounds were assayed by in vitro MTT method against a panel of human cancer cell lines (HeLa, SiHa, A2780, MCF-7 and MDA-MB-231). A significant difference was observed in the antiproliferative activity between the regioisomers. Some compounds exerted outstanding activities against the malignant cells with limited action on fibroblasts, indicating considerable cancer selectivity.
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Affiliation(s)
- Zein Alabdeen Khdar
- Institute of Pharmaceutical Chemistry, University of Szeged Eötvös utca 6 H-6720 Szeged Hungary +36 62 545705 +36 62 546809
| | - Tam Minh Le
- Institute of Pharmaceutical Chemistry, University of Szeged Eötvös utca 6 H-6720 Szeged Hungary +36 62 545705 +36 62 546809
- HUN-REN-SZTE Stereochemistry Research Group, University of Szeged Eötvös u. 6 H-6720 Szeged Hungary
| | - Zsuzsanna Schelz
- Institute of Pharmacodynamics and Biopharmacy, University of Szeged H-6720 Szeged Hungary
| | - István Zupkó
- Institute of Pharmacodynamics and Biopharmacy, University of Szeged H-6720 Szeged Hungary
| | - Zsolt Szakonyi
- Institute of Pharmaceutical Chemistry, University of Szeged Eötvös utca 6 H-6720 Szeged Hungary +36 62 545705 +36 62 546809
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8
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Mañas C, Merino E. Visible Light-Mediated Heterodifunctionalization of Alkynylazobenzenes for 2 H-Indazole Synthesis. Org Lett 2024; 26:1868-1873. [PMID: 38386928 DOI: 10.1021/acs.orglett.4c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
We disclose the heterodifunctionalization of alkynylazobenzenes promoted exclusively by visible light in the absence of any transition metal and/or photocatalyst. This reaction features excellent regioselectivity on a broad variety of substrates with perfect atom economy. Alcohols, carboxylic acids, thiols, amides, heterocycles, and even water are suitable substrates for the promotion of the oxyamination, sulfenoamination, and diamination reactions. In this manner, biologically active indazole scaffolds can be rapidly assembled from alkyne feedstocks.
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Affiliation(s)
- Clara Mañas
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Andrés del Río (IQAR), Facultad de Farmacia, 28805 Alcalá de Henares, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. de Colmenar Viejo, Km. 9.100, 28034 Madrid, Spain
| | - Estíbaliz Merino
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Andrés del Río (IQAR), Facultad de Farmacia, 28805 Alcalá de Henares, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Ctra. de Colmenar Viejo, Km. 9.100, 28034 Madrid, Spain
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9
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Cain BN, Hergenrother PJ. Using permeation guidelines to design new antibiotics-A PASsagE into Pseudomonas aeruginosa. Clin Transl Med 2024; 14:e1600. [PMID: 38426413 PMCID: PMC10905542 DOI: 10.1002/ctm2.1600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Brett N. Cain
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
| | - Paul J. Hergenrother
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
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10
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Aoyama H, Davies C, Liu J, Pahl A, Kirchhoff JL, Scheel R, Sievers S, Strohmann C, Grigalunas M, Waldmann H. Collective Synthesis of Sarpagine and Macroline Alkaloid-Inspired Compounds. Chemistry 2024; 30:e202303027. [PMID: 37755456 DOI: 10.1002/chem.202303027] [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] [Received: 09/17/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 09/28/2023]
Abstract
Design strategies that can access natural-product-like chemical space in an efficient manner may facilitate the discovery of biologically relevant compounds. We have employed a divergent intermediate strategy to construct an indole alkaloid-inspired compound collection derived from two different molecular design principles, i.e. biology-oriented synthesis and pseudo-natural products. The divergent intermediate was subjected to acid-catalyzed or newly discovered Sn-mediated conditions to selectively promote intramolecular C- or N-acylation, respectively. After further derivatization, a collection totalling 84 compounds representing four classes was obtained. Morphological profiling via the cell painting assay coupled with a subprofile analysis showed that compounds derived from different design principles have different bioactivity profiles. The subprofile analysis suggested that a pseudo-natural product class is enriched in modulators of tubulin, and subsequent assays led to the identification of compounds that suppress in vitro tubulin polymerization and mitotic progression.
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Affiliation(s)
- Hikaru Aoyama
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Caitlin Davies
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Jan-Lukas Kirchhoff
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Compound Management and Screening Center, 44227, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, 44227, Dortmund, Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, 44227, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry, Chemical Biology, 44227, Dortmund, Germany
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11
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Kazi A, Ranjan A, Kumar M.V. V, Agianian B, Garcia Chavez M, Vudatha V, Wang R, Vangipurapu R, Chen L, Kennedy P, Subramanian K, Quirke JC, Beato F, Underwood PW, Fleming JB, Trevino J, Hergenrother PJ, Gavathiotis E, Sebti SM. Discovery of KRB-456, a KRAS G12D Switch-I/II Allosteric Pocket Binder That Inhibits the Growth of Pancreatic Cancer Patient-derived Tumors. CANCER RESEARCH COMMUNICATIONS 2023; 3:2623-2639. [PMID: 38051103 PMCID: PMC10754035 DOI: 10.1158/2767-9764.crc-23-0222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/26/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
Currently, there are no clinically approved drugs that directly thwart mutant KRAS G12D, a major driver of human cancer. Here, we report on the discovery of a small molecule, KRB-456, that binds KRAS G12D and inhibits the growth of pancreatic cancer patient-derived tumors. Protein nuclear magnetic resonance studies revealed that KRB-456 binds the GDP-bound and GCP-bound conformation of KRAS G12D by forming interactions with a dynamic allosteric binding pocket within the switch-I/II region. Isothermal titration calorimetry demonstrated that KRB-456 binds potently to KRAS G12D with 1.5-, 2-, and 6-fold higher affinity than to KRAS G12V, KRAS wild-type, and KRAS G12C, respectively. KRB-456 potently inhibits the binding of KRAS G12D to the RAS-binding domain (RBD) of RAF1 as demonstrated by GST-RBD pulldown and AlphaScreen assays. Treatment of KRAS G12D-harboring human pancreatic cancer cells with KRB-456 suppresses the cellular levels of KRAS bound to GTP and inhibits the binding of KRAS to RAF1. Importantly, KRB-456 inhibits P-MEK, P-AKT, and P-S6 levels in vivo and inhibits the growth of subcutaneous and orthotopic xenografts derived from patients with pancreatic cancer whose tumors harbor KRAS G12D and KRAS G12V and who relapsed after chemotherapy and radiotherapy. These results warrant further development of KRB-456 for pancreatic cancer. SIGNIFICANCE There are no clinically approved drugs directly abrogating mutant KRAS G12D. Here, we discovered a small molecule, KRB-456, that binds a dynamic allosteric binding pocket within the switch-I/II region of KRAS G12D. KRB-456 inhibits P-MEK, P-AKT, and P-S6 levels in vivo and inhibits the growth of subcutaneous and orthotopic xenografts derived from patients with pancreatic cancer. This discovery warrants further advanced preclinical and clinical studies in pancreatic cancer.
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Affiliation(s)
- Aslamuzzaman Kazi
- Department of Pharmacology and Toxicology and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Alok Ranjan
- Department of Pharmacology and Toxicology and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Vasantha Kumar M.V.
- Department of Biochemistry, Department of Medicine, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, New York
| | - Bogos Agianian
- Department of Biochemistry, Department of Medicine, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, New York
| | - Martin Garcia Chavez
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University, Richmond, Virginia
| | - Rui Wang
- Department of Pharmacology and Toxicology and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | | | - Liwei Chen
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Perry Kennedy
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
| | - Karthikeyan Subramanian
- Department of Pharmacology and Toxicology and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Jonathan C.K. Quirke
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Francisca Beato
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida
| | | | - Jason B. Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Jose Trevino
- Department of Surgery, Virginia Commonwealth University, Richmond, Virginia
- Department of Surgery, University of Florida, Gainesville, Florida
| | - Paul J. Hergenrother
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Evripidis Gavathiotis
- Department of Biochemistry, Department of Medicine, Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, New York
| | - Said M. Sebti
- Department of Pharmacology and Toxicology and Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, Virginia
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida
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12
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Faleye OS, Boya BR, Lee JH, Choi I, Lee J. Halogenated Antimicrobial Agents to Combat Drug-Resistant Pathogens. Pharmacol Rev 2023; 76:90-141. [PMID: 37845080 DOI: 10.1124/pharmrev.123.000863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/07/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Antimicrobial resistance presents us with a potential global crisis as it undermines the abilities of conventional antibiotics to combat pathogenic microbes. The history of antimicrobial agents is replete with examples of scaffolds containing halogens. In this review, we discuss the impacts of halogen atoms in various antibiotic types and antimicrobial scaffolds and their modes of action, structure-activity relationships, and the contributions of halogen atoms in antimicrobial activity and drug resistance. Other halogenated molecules, including carbohydrates, peptides, lipids, and polymeric complexes, are also reviewed, and the effects of halogenated scaffolds on pharmacokinetics, pharmacodynamics, and factors affecting antimicrobial and antivirulence activities are presented. Furthermore, the potential of halogenation to circumvent antimicrobial resistance and rejuvenate impotent antibiotics is addressed. This review provides an overview of the significance of halogenation, the abilities of halogens to interact in biomolecular settings and enhance pharmacological properties, and their potential therapeutic usages in preventing a postantibiotic era. SIGNIFICANCE STATEMENT: Antimicrobial resistance and the increasing impotence of antibiotics are critical threats to global health. The roles and importance of halogen atoms in antimicrobial drug scaffolds have been established, but comparatively little is known of their pharmacological impacts on drug resistance and antivirulence activities. This review is the first to extensively evaluate the roles of halogen atoms in various antibiotic classes and pharmacological scaffolds and to provide an overview of their ability to overcome antimicrobial resistance.
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Affiliation(s)
- Olajide Sunday Faleye
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Bharath Reddy Boya
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jin-Hyung Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Inho Choi
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
| | - Jintae Lee
- School of Chemical Engineering (O.S.F., B.R.B., J.-H.L., J.L.) and Department of Medical Biotechnology (I.C.), Yeungnam University, Gyeongsan, Republic of Korea
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13
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Geddes EJ, Gugger MK, Garcia A, Chavez MG, Lee MR, Perlmutter SJ, Bieniossek C, Guasch L, Hergenrother PJ. Porin-independent accumulation in Pseudomonas enables antibiotic discovery. Nature 2023; 624:145-153. [PMID: 37993720 DOI: 10.1038/s41586-023-06760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
Gram-negative antibiotic development has been hindered by a poor understanding of the types of compounds that can accumulate within these bacteria1,2. The presence of efflux pumps and substrate-specific outer-membrane porins in Pseudomonas aeruginosa renders this pathogen particularly challenging3. As a result, there are few antibiotic options for P. aeruginosa infections4 and its many porins have made the prospect of discovering general accumulation guidelines seem unlikely5. Here we assess the whole-cell accumulation of 345 diverse compounds in P. aeruginosa and Escherichia coli. Although certain positively charged compounds permeate both bacterial species, P. aeruginosa is more restrictive compared to E. coli. Computational analysis identified distinct physicochemical properties of small molecules that specifically correlate with P. aeruginosa accumulation, such as formal charge, positive polar surface area and hydrogen bond donor surface area. Mode of uptake studies revealed that most small molecules permeate P. aeruginosa using a porin-independent pathway, thus enabling discovery of general P. aeruginosa accumulation trends with important implications for future antibiotic development. Retrospective antibiotic examples confirmed these trends and these discoveries were then applied to expand the spectrum of activity of a gram-positive-only antibiotic, fusidic acid, into a version that demonstrates a dramatic improvement in antibacterial activity against P. aeruginosa. We anticipate that these discoveries will facilitate the design and development of high-permeating antipseudomonals.
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Affiliation(s)
- Emily J Geddes
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Morgan K Gugger
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Alfredo Garcia
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Martin Garcia Chavez
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Myung Ryul Lee
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Sarah J Perlmutter
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Laura Guasch
- Roche Pharma Research and Early Development, Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Paul J Hergenrother
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
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14
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Mucke HA. Patent Highlights April-May 2023. Pharm Pat Anal 2023; 12:253-259. [PMID: 38197382 DOI: 10.4155/ppa-2023-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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15
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Yao R, Jensen AA, Bryce-Rogers HP, Schultz-Knudsen K, Zhou L, Hovendal NP, Pedersen H, Kubus M, Ulven T, Laraia L. Identification of 5-HT2 Serotonin Receptor Modulators through the Synthesis of a Diverse, Tropane- and Quinuclidine-alkaloid-Inspired Compound Library. J Med Chem 2023; 66:11536-11554. [PMID: 37566000 DOI: 10.1021/acs.jmedchem.3c01059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The recombination of natural product (NP) fragments in unprecedented ways has emerged as an important strategy for bioactive compound discovery. In this context, we propose that privileged primary fragments predicted to be enriched in activity against a specific target class can be coupled to diverse secondary fragments to engineer selectivity among closely related targets. Here, we report the synthesis of an alkaloid-inspired compound library enriched in spirocyclic ring fusions, comprising 58 compounds from 12 tropane- or quinuclidine-containing scaffolds, all of which can be considered pseudo-NPs. The library displays excellent predicted drug-like properties including high Fsp3 content and Lipinski's rule-of-five compliance. Targeted screening against selected members of the serotonin and dopamine G protein-coupled receptor family led to the identification of several hits that displayed significant agonist or antagonist activity against 5-HT2A and/or 5-HT2C, and subsequent optimization of one of these delivered a lead dual 5-HT2B/C antagonist with a highly promising selectivity profile.
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Affiliation(s)
- Ruwei Yao
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Hogan P Bryce-Rogers
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Katrine Schultz-Knudsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Libin Zhou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nicklas P Hovendal
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Henrik Pedersen
- Medicinal Chemistry, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Mariusz Kubus
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Trond Ulven
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
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16
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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17
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Li L, Wang Y, Chen N, Li X, Li H, Jin L, Ou Y, Kong XJ, Cao S, Xu Q, Wu X, Han J, Deng X. Exploring Diversity through Dimerization in Natural Products by a Rational Tandem Mass-Based Molecular Network Strategy. Org Lett 2023; 25:4016-4021. [PMID: 37249258 DOI: 10.1021/acs.orglett.3c01038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The step- and atom-efficient dimerization strategy is frequently used in nature to build structural complexity and diversity. We propose the rationale and structural features of the versatile monomers that are responsible for "diversity through dimerization". Using 5-FAM-maleimide combined with a UHPLC-MS/MS-FBMN workflow, we successfully identified a diverse set of dimeric natural products from fungus Panus rudis F01315, in which all four complex 4'5-ring scaffolds are derived from one monomeric epoxyquinol and endowed with functional diversity.
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Affiliation(s)
- Li Li
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuezhou Wang
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Naixin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyang Li
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hanpeng Li
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ling Jin
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yixin Ou
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiang-Jian Kong
- Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, 200 W. Kawili St., Hilo, Hawaii 96720, USA
| | - Qingyan Xu
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaobing Wu
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianyong Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
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18
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Li X, Zhang J, Chen Q, Tang P, Zhang T, Feng Q, Chen J, Liu Y, Wang FP, Peng C, Qin Y, Ouyang L, Xiao K, Liu XY. Diversity-oriented synthesis of diterpenoid alkaloids yields a potent anti-inflammatory agent. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 117:154907. [PMID: 37295024 DOI: 10.1016/j.phymed.2023.154907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/22/2023] [Accepted: 05/28/2023] [Indexed: 06/11/2023]
Abstract
BACKGROUND The diterpenoid alkaloids belong to a highly esteemed group of natural compounds, which display significant biological activities. It is a productive strategy to expand the chemical space of these intriguing natural compounds for drug discovery. METHODS We prepared a series of new derivatives bearing diverse skeletons and functionalities from the diterpenoid alkaloids deltaline and talatisamine based on a diversity-oriented synthesis strategy. The anti-inflammatory activity of these derivatives was initially screened and evaluated by the release of nitric oxide (NO), tumor necrosis factor (TNF-α), and interleukin-6 (IL-6) in lipopolysaccharide (LPS)-activated RAW264.7 cells. Futhermore, the anti-inflammatory activity of the representative derivative 31a was validated in various inflammatory animal models, including phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced mice ear edema, LPS-stimulated acute kidney injury, and collagen-induced arthritis (CIA). RESULTS It was found that several derivatives were able to suppress the secretion of NO, TNF-α, and IL-6 in LPS-activated RAW264.7 cells. Compound 31a, one of the representative derivatives named as deltanaline, demonstrated the strongest anti-inflammatory effects in LPS-activated macrophages and three different animal models of inflammatory diseases by inhibiting nuclear factor kappa-B (NF-κB)/mitogen-activated protein kinase (MAPK) signaling and inducing autophagy. CONCLUSION Deltanaline is a new structural compound derived from natural diterpenoid alkaloids, which may serve as a new lead compound for the treatment of inflammatory diseases.
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Affiliation(s)
- Xiaojie Li
- Precision Medicine Research Center, Sichuan Provincial Key Laboratory of Precision Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qifeng Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Zhang
- Precision Medicine Research Center, Sichuan Provincial Key Laboratory of Precision Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qiyi Feng
- Precision Medicine Research Center, Sichuan Provincial Key Laboratory of Precision Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiajun Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yun Liu
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng-Peng Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Cheng Peng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yong Qin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Kai Xiao
- Precision Medicine Research Center, Sichuan Provincial Key Laboratory of Precision Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Xiao-Yu Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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19
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Soro DM, Roque JB, Rackl JW, Park B, Payer S, Shi Y, Ruble JC, Kaledin AL, Baik MH, Musaev DG, Sarpong R. Photo- and Metal-Mediated Deconstructive Approaches to Cyclic Aliphatic Amine Diversification. J Am Chem Soc 2023; 145:11245-11257. [PMID: 37171220 DOI: 10.1021/jacs.3c01318] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Described herein are studies toward the core modification of cyclic aliphatic amines using either a riboflavin/photo-irradiation approach or Cu(I) and Ag(I) to mediate the process. Structural remodeling of cyclic amines is explored through oxidative C-N and C-C bond cleavage using peroxydisulfate (persulfate) as an oxidant. Ring-opening reactions to access linear aldehydes or carboxylic acids with flavin-derived photocatalysis or Cu salts, respectively, are demonstrated. A complementary ring-opening process mediated by Ag(I) facilitates decarboxylative Csp3-Csp2 coupling in Minisci-type reactions through a key alkyl radical intermediate. Heterocycle interconversion is demonstrated through the transformation of N-acyl cyclic amines to oxazines using Cu(II) oxidation of the alkyl radical. These transformations are investigated by computation to inform the proposed mechanistic pathways. Computational studies indicate that persulfate mediates oxidation of cyclic amines with concomitant reduction of riboflavin. Persulfate is subsequently reduced by formal hydride transfer from the reduced riboflavin catalyst. Oxidation of the cyclic aliphatic amines with a Cu(I) salt is proposed to be initiated by homolysis of the peroxy bond of persulfate followed by α-HAT from the cyclic amine and radical recombination to form an α-sulfate adduct, which is hydrolyzed to the hemiaminal. Investigation of the pathway to form oxazines indicates a kinetic preference for cyclization over more typical elimination pathways to form olefins through Cu(II) oxidation of alkyl radicals.
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Affiliation(s)
- David M Soro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jose B Roque
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Jonas W Rackl
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Bohyun Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Stefan Payer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Yuan Shi
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - J Craig Ruble
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Mu-Hyun Baik
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Djamaladdin G Musaev
- Cherry L. Emerson Center for Scientific Computation, and Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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20
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Bakanas I, Tang JC, Sarpong R. Skeletal diversification by C-C cleavage to access bicyclic frameworks from a common tricyclooctane intermediate. Chem Commun (Camb) 2023; 59:3858-3861. [PMID: 36916206 PMCID: PMC10518267 DOI: 10.1039/d3cc00945a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Herein, the diversification of tricyclo[3.2.1.03,6]octane scaffolds to afford diverse bicyclic scaffolds is described. The strained tricyclooctanes are prepared in two steps featuring a blue light-mediated [2+2] cycloaddition. Strategies for the cleavage of this scaffold were then explored resulting in the selective syntheses of the bicyclo[3.1.1]heptane, bicyclo[3.2.1]octane, and bicyclo[3.2.0]heptane cores. These findings may guide future studies of C-C cleavage reactions in strained carbon frameworks and their application in complex molecule synthesis.
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Affiliation(s)
- Ian Bakanas
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA.
| | - Jess C Tang
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA.
| | - Richmond Sarpong
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA.
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21
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Alkubaisi BO, Ravi A, Srikanth G, Sebastian A, Khanfar MA, El-Gamal MI, Sieburth SM, Shahin AI, Al-Tel TH. Divergent Protocol for the Synthesis of Isoquinolino[1,2- b]quinazolinone and Isoquinolino[2,1- a]quinazolinone Derivatives. J Org Chem 2023; 88:4244-4253. [PMID: 36926917 DOI: 10.1021/acs.joc.2c02791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The development of robust and step-economic strategies to access structurally diverse drug-like compound collections remains a challenge. A distinct structural option that constitutes the core scaffold of many biologically significant molecules is the quinazolinone ring system. Several members of this family of privileged substructures have gained attention due to their diverse biological activities. In this context, the development of an efficient strategy for their access is needed. Herein, we report a divergent metal-free operation to access a diverse collection of C6-substituted pyrrolo[4',3',2':4,5]isoquinolino[1,2-b]quinazolin-8(6H)-one and pyrrolo[4',3',2':4,5]isoquinolino[2,1-a]quinazolin-12(6H)-one architectures. The described cascade unites Friedel-Crafts and aza-Michael addition reactions. This operationally simple protocol enables a rapid access to these scaffolds and is compatible with a wide scope of starting materials. In addition, the cascade features a promising approach for the design of unique compound libraries for drug design and discovery programs.
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Affiliation(s)
- Bilal O Alkubaisi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Anil Ravi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Gourishetty Srikanth
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, Sharjah 26666, United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Monther A Khanfar
- College of Science, Department of Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammed I El-Gamal
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Scott McN Sieburth
- Department of Chemistry, Temple University, 201 Beury Hall, Philadelphia, Pennsylvania 19122, United States
| | - Afnan I Shahin
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
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22
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Sanguinarine Exhibits Antiviral Activity against Porcine Reproductive and Respiratory Syndrome Virus via Multisite Inhibition Mechanisms. Viruses 2023; 15:v15030688. [PMID: 36992397 PMCID: PMC10052745 DOI: 10.3390/v15030688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of PRRS, is prevalent worldwide, causing substantial and immense economic losses to the global swine industry. While current commercial vaccines fail to efficiently control PRRS, the development of safe and effective antiviral drugs against PRRSV is urgently required. Alkaloids are natural products with wide pharmacological and biological activities. Herein, sanguinarine, a benzophenanthridine alkaloid that occurs in many plants such as Macleaya cordata, was demonstrated as a potent antagonist of PRRSV. Sanguinarine attenuated PRRSV proliferation by targeting the internalization, replication, and release stages of the viral life cycle. Furthermore, ALB, AR, MAPK8, MAPK14, IGF1, GSK3B, PTGS2, and NOS2 were found as potential key targets related to the anti-PRRSV effect of sanguinarine as revealed by network pharmacology and molecular docking. Significantly, we demonstrated that the combination of sanguinarine with chelerythrine, another key bioactive alkaloid derived from Macleaya cordata, improved the antiviral activity. In summary, our findings reveal the promising potential of sanguinarine as a novel candidate for the development of anti-PRRSV agents.
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23
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Song L, Tian X, Farshadfar K, Shiri F, Rominger F, Ariafard A, Hashmi ASK. An unexpected synthesis of azepinone derivatives through a metal-free photochemical cascade reaction. Nat Commun 2023; 14:831. [PMID: 36788212 PMCID: PMC9929248 DOI: 10.1038/s41467-023-36190-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/17/2023] [Indexed: 02/16/2023] Open
Abstract
Azepinone derivatives are privileged in organic synthesis and pharmaceuticals. Synthetic approaches to these frameworks are limited to complex substrates, strong bases, high power UV light or noble metal catalysis. We herein report a mild synthesis of azepinone derivatives by a photochemical generation of 2-aryloxyaryl nitrene, [2 + 1] annulation, ring expansion/water addition cascade reaction without using any metal catalyst. Among the different nitrene precursors tested, 2-aryloxyaryl azides performed best under blue light irradiation and Brønsted acid catalysis. The reaction scope is broad and the obtained products underwent divergent transformations to afford other related compounds. A computational study suggests a pathway involving a step-wise aziridine formation, followed by a ring-expansion to the seven-membered heterocycle. Finally, water is added in a regio-selective manner, this is accelerated by the added TsOH.
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Affiliation(s)
- Lina Song
- grid.7700.00000 0001 2190 4373Institut für Organische Chemie, Heidelberg University, Heidelberg, Germany
| | - Xianhai Tian
- Institut für Organische Chemie, Heidelberg University, Heidelberg, Germany.
| | - Kaveh Farshadfar
- grid.411463.50000 0001 0706 2472Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran, Iran ,grid.5373.20000000108389418Research Group of Computational Chemistry, Department of Chemistry and Materials Science, Aalto University, Aalto, Finland
| | - Farshad Shiri
- grid.411463.50000 0001 0706 2472Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran, Iran
| | - Frank Rominger
- grid.7700.00000 0001 2190 4373Institut für Organische Chemie, Heidelberg University, Heidelberg, Germany
| | - Alireza Ariafard
- Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran, Iran. .,School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia.
| | - A. Stephen K. Hashmi
- grid.7700.00000 0001 2190 4373Institut für Organische Chemie, Heidelberg University, Heidelberg, Germany ,grid.412125.10000 0001 0619 1117Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Wang J, Wang Y, Liang Y, Zhou L, Liu L, Zhang Z. Late-Stage Modification of Drugs via Alkene Formal Insertion into Benzylic C-F Bond. Angew Chem Int Ed Engl 2023; 62:e202215062. [PMID: 36418222 DOI: 10.1002/anie.202215062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
C-F insertion of carbon-atom units is underdeveloped although it poses significant potential applications in both drug discovery and development. Herein, we report a photocatalytic protocol for late-stage modification of trifluoromethyl aromatic drugs involving formal insertion of abundant alkene feedstocks into a benzylic C-F bond selectively. This redox-neutral transformation features mild conditions and extraordinary functional group tolerance. Preliminary studies are consistent with this transformation involving a radical-polar crossover pathway. Additionally, it offers an alternative strategy for difunctionalization of alkenes via quenching of the carbocation intermediate with nucleophiles other than external fluoride.
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Affiliation(s)
- Jing Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Yahui Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Yan Liang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Liejin Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Lijuan Liu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
| | - Zuxiao Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, 321004, Jinhua, China
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25
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Caboni P, Laus A, Eloh K, Ntalli NG, Casula M, Di Giorgi S, Tocco G. Structural Elucidation of Relevant Gibberellic Acid Impurities and In Silico Investigation of Their Interaction with Soluble Gibberellin Receptor GID1. ACS OMEGA 2023; 8:1957-1966. [PMID: 36687088 PMCID: PMC9850740 DOI: 10.1021/acsomega.2c04743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Gibberellin derivatives are a family of tetracyclic diterpenoid plant hormones used in agriculture as plant growth regulators included in the European Directive 91/414. In the pesticide peer review process and to assess their toxicological relevance and product chemical equivalence, the European Food Safety Authority (EFSA) highlighted data gaps such as the identification of hydrolysis products and unknown impurities. The aspect of impurity characterization and quantitation is challenging and requires the use of hyphenated analytical techniques. In this regard, we used an LC-QTOF/MS and NMR analysis for the characterization of gibberellic acid impurities found in technical products. Gibberellic acid impurities such as gibberellin A1 (GA 1 ), 3-isolactone gibberellic acid (iso-GA 3 ), gibberellenic acid, 1α,2α-epoxygibberellin A3 (2-epoxy- GA 3 ), and (1α,2β,3α,4bβ,10β)-2,3,7-trihydroxy-1-methyl-8-methylenegibb-4-ene-1,10-dicarboxylic acid were identified and successfully characterized. Moreover, an in silico investigation on selected gibberellic acid impurities and derivatives and their interactions with a gibberellin insensitive dwarf1 (GID1) receptor has been carried out by means of induced fit docking (IFD), generalized-Born surface area (MM-GBSA), and metadynamics (MTD) experiments. A direct HPLC method with DAD and MS for the detection of gibberellic acid and its impurities in a technical sample has been developed. Moreover, by means of the in silico characterization of the GID1 receptor-binding pocket, we investigated the receptor affinity of the selected gibberellins, identifying compounds (2) and (4) as the most promising hit to lead compounds.
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Affiliation(s)
- Pierluigi Caboni
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
| | - Antonio Laus
- Department
of Biomedical Sciences, Cittadella Universitaria
di Monserrato, Blocco
A, 09042, Monserrato, Italy
| | - Kodjo Eloh
- University
of Kara, Po Box 404 Kara, Togo
| | - Nikoletta G. Ntalli
- Department
of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece
| | - Mattia Casula
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
| | - Sabrina Di Giorgi
- Ministero
della Salute, Direzione Generale per l’Igiene
e la Sicurezza degli Alimenti e della Nutrizione, Viale Giorgio Ribotta, 5, 00144 Roma, Italy
| | - Graziella Tocco
- Department
of Life and Environmental Sciences, Cittadella
Universitaria di Monserrato, Blocco A, 09042, Monserrato, Italy
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26
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Duñabeitia E, Landa A, López R, Palomo C. Accessing Chiral Pyrrolodiketopiperazines under Organocatalytic Conditions. Org Lett 2023; 25:125-129. [PMID: 36579971 PMCID: PMC10018776 DOI: 10.1021/acs.orglett.2c03924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The production of chiral pyrrolodiketopiperazines under organocatalytic conditions demonstrates the capacity of bicyclic acylpyrrol lactims to perform as pronucleophiles in direct carbon-carbon bond forming reactions. The good performance of ureidoaminal-derived Brønsted bases in the Michael addition to nitroolefins affords these heterocyclic scaffolds with high skeleton diversity.
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Affiliation(s)
- Eider Duñabeitia
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country (UPV-EHU), Manuel de Lardizabal 3, 20018 San Sebastián, Spain
| | - Aitor Landa
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country (UPV-EHU), Manuel de Lardizabal 3, 20018 San Sebastián, Spain
| | - Rosa López
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country (UPV-EHU), Manuel de Lardizabal 3, 20018 San Sebastián, Spain
| | - Claudio Palomo
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country (UPV-EHU), Manuel de Lardizabal 3, 20018 San Sebastián, Spain
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27
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Meng FT, Wang YN, Qin XY, Li SJ, Li J, Hao WJ, Tu SJ, Lan Y, Jiang B. Azoarene activation for Schmidt-type reaction and mechanistic insights. Nat Commun 2022; 13:7393. [PMID: 36450750 PMCID: PMC9712421 DOI: 10.1038/s41467-022-35141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
The Schmidt rearrangement, a reaction that enables C-C or C-H σ bond cleavage and nitrogen insertion across an aldehyde or ketone substrate, is one of the most important and widely used synthetic tools for the installation of amides and nitriles. However, such a reaction frequently requires volatile, potentially explosive, and highly toxic azide reagents as the nitrogen donor, thus limiting its application to some extent. Here, we show a Schmidt-type reaction where aryldiazonium salts act as the nitrogen precursor and in-situ-generated cyclopenta-1,4-dien-1-yl acetates serve as pronucleophiles from gold-catalyzed Nazarov cyclization of 1,3-enyne acetates. Noteworthy is that cycloketone-derived 1,3-enyne acetates enabled ring-expansion relay to access a series of 2-pyridone-containing fused heterocycles, in which nonsymmetric cycloketone-derived counterparts demonstrated high regioselectivity. Aside from investigating the scope of this Schmidt-type reaction, mechanistic details of this transformation are provided by performing systematic theoretical calculations.
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Affiliation(s)
- Fan-Tao Meng
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China
| | - Ya-Nan Wang
- College of Chemistry and Institute of Green Catalysis, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Xiao-Yan Qin
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China
| | - Shi-Jun Li
- College of Chemistry and Institute of Green Catalysis, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Jing Li
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China
| | - Wen-Juan Hao
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China.
| | - Shu-Jiang Tu
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China
| | - Yu Lan
- College of Chemistry and Institute of Green Catalysis, Zhengzhou University, Zhengzhou, Henan, 450001, China.
| | - Bo Jiang
- School of Chemistry & Materials Science, Jiangsu Normal University, Xuzhou, 221116, P. R. China.
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28
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Grigalunas M, Patil S, Krzyzanowski A, Pahl A, Flegel J, Schölermann B, Xie J, Sievers S, Ziegler S, Waldmann H. Unprecedented Combination of Polyketide Natural Product Fragments Identifies the New Hedgehog Signaling Pathway Inhibitor Grismonone. Chemistry 2022; 28:e202202164. [PMID: 36083197 PMCID: PMC10091983 DOI: 10.1002/chem.202202164] [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] [Received: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Pseudo-natural products (pseudo-NPs) are de novo combinations of natural product (NP) fragments that define novel bioactive chemotypes. For their discovery, new design principles are being sought. Previously, pseudo-NPs were synthesized by the combination of fragments originating from biosynthetically unrelated NPs to guarantee structural novelty and novel bioactivity. We report the combination of fragments from biosynthetically related NPs in novel arrangements to yield a novel chemotype with activity not shared by the guiding fragments. We describe the synthesis of the polyketide pseudo-NP grismonone and identify it as a structurally novel and potent inhibitor of Hedgehog signaling. The insight that the de novo combination of fragments derived from biosynthetically related NPs may also yield new biologically relevant compound classes with unexpected bioactivity may be considered a chemical extension or diversion of existing biosynthetic pathways and greatly expands the opportunities for exploration of biologically relevant chemical space by means of the pseudo-NP principle.
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Affiliation(s)
- Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sohan Patil
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Adrian Krzyzanowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Jana Flegel
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Jianing Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
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29
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Stereoselective Synthesis and Application of Gibberellic Acid-Derived Aminodiols. Int J Mol Sci 2022; 23:ijms231810366. [PMID: 36142293 PMCID: PMC9499365 DOI: 10.3390/ijms231810366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022] Open
Abstract
A series of gibberellic acid-based aminodiols was designed and synthesized from commercially available gibberellic acid. Exposure of gibberellic acid to hydrochloric acid under reflux conditions resulted in aromatization followed by rearrangement to form allo-gibberic acid. The key intermediate, ethyl allo-gibberate, was prepared according to literature methods. Epoxidation of key intermediate and subsequent ring-opening of the corresponding epoxide with different nucleophiles resulted in N-substituted aminodiols. The regioselective ring closure of N-benzyl-substituted aminodiol with formaldehyde was also investigated. All aminodiol derivatives were well characterized using modern spectroscopic techniques and evaluated for their antiproliferative activity against a panel of human cancer cell lines. In addition, structure–activity relationships were examined by assessing substituent effects on the aminodiol systems. The results indicated that aminodiols containing aromatic rings on their nitrogen substituents displayed significant cytotoxic effects. Among these agents, N-naphthylmethyl-substituted aminodiols were found to be the most potent candidates in this series. One of these molecules exhibited a modest cancer selectivity determined by non-cancerous fibroblast cells. A docking study was also made to exploit the observed results.
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30
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Li Y, Cheng S, Tian Y, Zhang Y, Zhao Y. Recent ring distortion reactions for diversifying complex natural products. Nat Prod Rep 2022; 39:1970-1992. [PMID: 35972343 DOI: 10.1039/d2np00027j] [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
Covering: 2013-2022.Chemical diversification of natural products is an efficient way to generate natural product-like compounds for modern drug discovery programs. Utilizing ring-distortion reactions for diversifying natural products would directly alter the core ring systems of small molecules and lead to the production of structurally complex and diverse compounds for high-throughput screening. We review the ring distortion reactions recently used in complexity-to-diversity (CtD) and pseudo natural products (pseudo-NPs) strategies for diversifying complex natural products. The core ring structures of natural products are altered via ring expansion, ring cleavage, ring edge-fusion, ring spiro-fusion, ring rearrangement, and ring contraction. These reactions can rapidly provide natural product-like collections with properties suitable for a wide variety of biological and medicinal applications. The challenges and limitations of current ring distortion reactions are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We also provide a toolbox for chemists for the application of ring distortion reactions to access natural product-like molecules.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yun Tian
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yanan Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China.
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31
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Che C, Jiang D, Zhang J, Xing Q, Li T, Zhao Y, Guan L, Chen H, Xiang D, Di M, Zhu Z. Tricyclic Aza-Andrographolide Derivatives from Late-Stage Hydroamination and Their Anti-human Coronavirus (Anti-HCoV) Activity. ACS OMEGA 2022; 7:24824-24837. [PMID: 35874238 PMCID: PMC9301648 DOI: 10.1021/acsomega.2c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A late-stage functionalization (LSF) of the natural product andrographolide for the efficient assembly of a range of structurally interesting and diverse tricyclic-aza derivatives was developed. The key to the diversification is a photo-catalyzed intramolecular hydroamination reaction, and acridinium derivatives were demonstrated to be the optimal catalysts. Additionally, the synthesized tricyclic aza-andrographolide derivatives were found to inhibit human coronavirus with high potency.
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Affiliation(s)
- Chao Che
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, Peking
University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ding Jiang
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Jiayin Zhang
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Qi Xing
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Ting Li
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Yi Zhao
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Liangyu Guan
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Huangcan Chen
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Dehu Xiang
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Man Di
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
| | - Zhendong Zhu
- BayRay
Innovative Center, Shenzhen Bay Laboratory, Shenzhen 518032, China
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32
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Kelly AM, Berry MR, Tasker SZ, McKee SA, Fan TM, Hergenrother PJ. Target-Agnostic P-Glycoprotein Assessment Yields Strategies to Evade Efflux, Leading to a BRAF Inhibitor with Intracranial Efficacy. J Am Chem Soc 2022; 144:12367-12380. [PMID: 35759775 DOI: 10.1021/jacs.2c03944] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The blood-brain barrier (BBB) presents a major hurdle in the development of central nervous system (CNS) active therapeutics, and expression of the P-glycoprotein (P-gp) efflux transporter at the blood-brain interface further impedes BBB penetrance of most small molecules. Designing efflux liabilities out of compounds can be laborious, and there is currently no generalizable approach to directly transform periphery-limited agents to ones active in the CNS. Here, we describe a target-agnostic, prospective assessment of P-gp efflux using diverse compounds. Our results demonstrate that reducing the molecular size or appending a carboxylic acid in many cases enables evasion of P-gp efflux in cell-based experiments and in mice. These strategies were then applied to transform a periphery-limited V600EBRAF inhibitor, dabrafenib, into versions that possess potent and selective anti-cancer activity but now also evade P-gp-mediated efflux. When compared to dabrafenib, the compound developed herein (everafenib) has superior BBB penetrance and superior efficacy in an intracranial mouse model of metastatic melanoma, suggesting it as a lead candidate for the treatment of melanoma metastases to the brain and gliomas with BRAF mutation. More generally, the results described herein suggest the actionability of the trends observed in these target-agnostic efflux studies and provide guidance for the conversion of non-BBB-penetrant drugs into versions that are BBB-penetrant and efficacious.
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Affiliation(s)
- Aya M Kelly
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew R Berry
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sarah Z Tasker
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sydney A McKee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Timothy M Fan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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33
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Zhou YF, Yan BC, Yang Q, Long XY, Zhang DQ, Luo RH, Wang HY, Sun HD, Xue XS, Zheng YT, Puno PT. Harnessing Natural Products by a Pharmacophore-Oriented Semisynthesis Approach for the Discovery of Potential Anti-SARS-CoV-2 Agents. Angew Chem Int Ed Engl 2022; 61:e202201684. [PMID: 35484726 PMCID: PMC9074085 DOI: 10.1002/anie.202201684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Indexed: 12/11/2022]
Abstract
Natural products possessing unique scaffolds may have antiviral activity but their complex structures hinder facile synthesis. A pharmacophore‐oriented semisynthesis approach was applied to (−)‐maoelactone A (1) and oridonin (2) for the discovery of anti‐SARS‐CoV‐2 agents. The Wolff rearrangement/lactonization cascade (WRLC) reaction was developed to construct the unprecedented maoelactone‐type scaffold during semisynthesis of 1. Further mechanistic study suggested a concerted mechanism for Wolff rearrangement and a water‐assisted stepwise process for lactonization. The WRLC reaction then enabled the creation of a novel family by assembly of the maoelactone‐type scaffold and the pharmacophore of 2, whereby one derivative inhibited SARS‐CoV‐2 replication in HPA EpiC cells with a low EC50 value (19±1 nM) and a high TI value (>1000), both values better than those of remdesivir.
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Affiliation(s)
- Yuan-Fei Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing-Chao Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xin-Yan Long
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Dan-Qi Zhang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Han-Yu Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
| | - Han-Dong Sun
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiao-Song Xue
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Pema-Tenzin Puno
- State Key Laboratory of Phytochemistry and Plant Resources in West China, and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming, 650201, China
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34
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Combining visible-light induction and copper catalysis for chemo-selective nitrene transfer for late-stage amination of natural products. Commun Chem 2022; 5:79. [PMID: 36697627 PMCID: PMC9814389 DOI: 10.1038/s42004-022-00692-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/22/2022] [Indexed: 01/28/2023] Open
Abstract
Nitrene transfer chemistry is an effective strategy for introducing C-N bonds, which are ubiquitous in pharmaceuticals, agrochemicals and diverse bioactive natural products. The development of chemical methodology that can functionalize unique sites within natural products through nitrene transfer remains a challenge in the field. Herein, we developed copper catalyzed chemoselective allylic C-H amination and catalyst-free visible-light induced aziridination of alkenes through nitrene transfer. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Furthermore, combination of these two methods enable the intermolecular chemo-selective late-stage amination of biologically active natural products, leading to C-H amination or C=C aziridination products in a tunable way. A series of control experiments indicate two-step radical processes were involved in both reaction systems.
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35
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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36
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Zhou YF, Yan BC, Yang Q, Long XY, Zhang DQ, Luo RH, Wang HY, Sun HD, Xue XS, Zheng YT, Puno PT. Harnessing Natural Products by a Pharmacophore‐Oriented Semisynthesis Approach for the Discovery of Potential Anti‐SARS‐CoV‐2 Agents. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuan-Fei Zhou
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Bing-Chao Yan
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Qian Yang
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Xin-Yan Long
- Kunming Institute of Zoology Chinese Academy of Sciences Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences CHINA
| | - Dan-Qi Zhang
- Nankai University State Key Laboratory of Elemento-organic Chemistry CHINA
| | - Rong-Hua Luo
- Kunming Institute of Zoology Chinese Academy of Sciences Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences CHINA
| | - Han-Yu Wang
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Han-Dong Sun
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Xiao-Song Xue
- Nankai University State Key Laboratory of Elemento-organic Chemistry CHINA
| | - Yong-Tang Zheng
- Kunming Institute of Zoology Chinese Academy of Sciences Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences CHINA
| | - Pema-Tenzin Puno
- Kunming Institute of Botany Chinese Academy of Sciences State Key Laboratory of Phytochemistry and Plant Resources in West China No. 132, Lanhei Road 650201 Kunming CHINA
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37
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Recent Advances in Divergent Synthetic Strategies for Indole-Based Natural Product Libraries. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072171. [PMID: 35408569 PMCID: PMC9000743 DOI: 10.3390/molecules27072171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/26/2023]
Abstract
Considering the potential bioactivities of natural product and natural product-like compounds with highly complex and diverse structures, the screening of collections and small-molecule libraries for high-throughput screening (HTS) and high-content screening (HCS) has emerged as a powerful tool in the development of novel therapeutic agents. Herein, we review the recent advances in divergent synthetic approaches such as complexity-to-diversity (Ctd) and biomimetic strategies for the generation of structurally complex and diverse indole-based natural product and natural product-like small-molecule libraries.
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38
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Dethe DH, Beeralingappa NC, Siddiqui SA, Chavan PN. Asymmetric Ru/Cinchonine Dual Catalysis for the One-Pot Synthesis of Optically Active Phthalides from Benzoic Acids and Acrylates. J Org Chem 2022; 87:4617-4630. [PMID: 35266689 DOI: 10.1021/acs.joc.1c02961] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Herein, we report the asymmetric Ru/cinchonine dual catalysis that provides straightforward access to enantioselective synthesis of C-3 substituted phthalides via tandem C-H activation/Michael addition cascade. The use of readily accessible and less expensive [RuCl2(p-cym)]2 and cinchonine catalyst for the one-pot assembly of chiral phthalides greatly overcomes the present trend of using highly sophisticated catalysts. The developed method provides access to both enantiomers of a product using pseudoenantiomeric cinchona alkaloids as catalysts streamlining the synthesis of phthalide in both the optically active forms.
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Affiliation(s)
- Dattatraya H Dethe
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | | | - Salman A Siddiqui
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Prakash N Chavan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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39
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Abstract
![]()
Natural products
are the result of Nature’s exploration
of biologically relevant chemical space through evolution and an invaluable
source of bioactive small molecules for chemical biology and medicinal
chemistry. Novel concepts for the discovery of new bioactive compound
classes based on natural product structure may enable exploration
of wider biologically relevant chemical space. The pseudo-natural
product concept merges the relevance of natural product structure
with efficient exploration of chemical space by means of fragment-based
compound development to inspire the discovery of new bioactive chemical
matter through de novo combination of natural product
fragments in unprecedented arrangements. The novel scaffolds retain
the biological relevance of natural products but are not obtainable
through known biosynthetic pathways which can lead to new chemotypes
that may have unexpected or unprecedented bioactivities. Herein, we
cover the workflow of pseudo-natural product design and development,
highlight recent examples, and discuss a cheminformatic analysis in
which a significant portion of biologically active synthetic compounds
were found to be pseudo-natural products. We compare the concept to
natural evolution and discuss pseudo-natural products as the human-made
equivalent, i.e. the chemical evolution of natural product structure.
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Affiliation(s)
- Michael Grigalunas
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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40
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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41
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Srinivasulu V, Srikanth G, Khanfar MA, Abu-Yousef IA, Majdalawieh AF, Mazitschek R, Setty SC, Sebastian A, Al-Tel TH. Stereodivergent Complexity-to-Diversity Strategy en Route to the Synthesis of Nature-Inspired Skeleta. J Org Chem 2022; 87:1377-1397. [PMID: 35014258 DOI: 10.1021/acs.joc.1c02698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The complexity-to-diversity (CtD) strategy has become one of the most powerful tools used to transform complex natural products into diverse skeleta. However, the reactions utilized in this process are often limited by their compatibility with existing functional groups, which in turn restricts access to the desired skeletal diversity. In the course of employing a CtD strategy en route to the synthesis of natural product-inspired compounds, our group has developed several stereodivergent strategies employing indoloquinolizine natural product analogues as starting materials. These transformations led to the rapid and diastereoselective synthesis of diverse classes of natural product-like architectures, including camptothecin-inspired analogues, azecane medium-sized ring systems, arborescidine-inspired systems, etc. This manifestation required a drastic modification of the synthetic design that ultimately led to modular and diastereoselective access to a diverse collection of various classes of biologically significant natural product analogues. The reported strategies provide a unique platform that will be broadly applicable to other late-stage natural product transformation approaches.
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Affiliation(s)
- Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Gourishetty Srikanth
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Monther A Khanfar
- College of Science, Department of Chemistry, Pure and Applied Chemistry Group, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Subbaiah Chennam Setty
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE.,College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
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42
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Yoneda T, Kojima N, Matsumoto T, Imahori D, Ohta T, Yoshida T, Watanabe T, Matsuda H, Nakamura S. Construction of sulfur-containing compounds with anti-cancer stem cell activity using thioacrolein derived from garlic based on nature-inspired scaffolds. Org Biomol Chem 2021; 20:196-207. [PMID: 34878480 DOI: 10.1039/d1ob01992a] [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
Sulfur-containing compounds, such as cyclic compounds with a vinyl sulfane structure, exhibit a wide range of biological activities including anticancer activity. Therefore, the development of efficient strategies to synthesize such compounds is a remarkable achievement. We have developed a unique approach for the rapid and modular preparation of nature-inspired cyclic and acyclic sulfur-containing compounds using thioacrolein, a naturally occurring chemically unstable intermediate. We constructed thiopyranone derivatives through the regioselective sequential double Diels-Alder reaction of thioacrolein produced by allicin, a major component in garlic, and two molecules of silyl enol ether as the diene partner. The cytotoxicity toward cancer stem cells of the thiopyranones was equal to or higher than that of (Z)-ajoene (positive control) derived from garlic, and the thiopyranones had higher chemical stability than (Z)-ajoene.
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Affiliation(s)
- Taichi Yoneda
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Naoto Kojima
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Takahiro Matsumoto
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Daisuke Imahori
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Tomoe Ohta
- Faculty of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch-Cho, Sasebo, Nagasaki 859-3298, Japan
| | - Tatsusada Yoshida
- Faculty of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch-Cho, Sasebo, Nagasaki 859-3298, Japan
| | - Tetsushi Watanabe
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Hisashi Matsuda
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Seikou Nakamura
- Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
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43
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Whitmarsh-Everiss T, Olsen AH, Laraia L. Identification of Inhibitors of Cholesterol Transport Proteins Through the Synthesis of a Diverse, Sterol-Inspired Compound Collection. Angew Chem Int Ed Engl 2021; 60:26755-26761. [PMID: 34626154 DOI: 10.1002/anie.202111639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/26/2022]
Abstract
Cholesterol transport proteins regulate a vast array of cellular processes including lipid metabolism, vesicular and non-vesicular trafficking, organelle contact sites, and autophagy. Despite their undoubted importance, the identification of selective modulators of this class of proteins has been challenging due to the structural similarities in the cholesterol-binding site. Herein we report a general strategy for the identification of selective inhibitors of cholesterol transport proteins via the synthesis of a diverse sterol-inspired compound collection. Fusion of a primary sterol fragment to an array of secondary privileged scaffolds led to the identification of potent and selective inhibitors of the cholesterol transport protein Aster-C, which displayed a surprising preference for the unnatural-sterol AB-ring stereochemistry and new inhibitors of Aster-A. We propose that this strategy can and should be applied to any therapeutically relevant sterol-binding protein.
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Affiliation(s)
- Thomas Whitmarsh-Everiss
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
| | - Asger Hegelund Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800, Kongens Lyngby, Denmark
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44
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Whitmarsh‐Everiss T, Olsen AH, Laraia L. Identification of Inhibitors of Cholesterol Transport Proteins Through the Synthesis of a Diverse, Sterol‐Inspired Compound Collection. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111639] [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)
- Thomas Whitmarsh‐Everiss
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Asger Hegelund Olsen
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Luca Laraia
- Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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45
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Lim H, Seong S, Kim Y, Seo S, Han S. Biopatterned Reorganization of Alkaloids Enabled by Ring-Opening Functionalization of Tertiary Amines. J Am Chem Soc 2021; 143:19966-19974. [PMID: 34784466 DOI: 10.1021/jacs.1c10205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Biosynthetic processes often involve reorganization of one family of natural products to another. Chemical emulation of nature's rearrangement-based structural diversification strategy would enable the conversion of readily available natural products to other value-added secondary metabolites. However, the development of a chemical method that can be universally applied to structurally diverse natural products is nontrivial. Key to the successful reorganization of complex molecules is a versatile and mild bond-cleaving method that correctly places desired functionality, facilitating the target synthesis. Here, we report a ring-opening functionalization of a tertiary amine that can introduce desired functionalities in the context of alkaloids reorganization. The semistability of the difluoromethylated ammonium salt, accessed by the reaction of tertiary amine and in situ generated difluorocarbene, enabled the attack at the α-position by various external nucleophiles. The utility and generality of the method is highlighted by its applications in the transformation of securinega, iboga, and sarpagine alkaloids to neosecurinega, chippiine/dippinine, and vobasine-type bisindole alkaloids, respectively. During the course of these biosynthetically inspired reorganizations, we could explore chemical reactivities of biogenetically relevant precursors.
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Affiliation(s)
- Hyeonggeun Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sikwang Seong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Youyoung Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Sangwon Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
| | - Sunkyu Han
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
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46
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Hostetler MA, Smith C, Nelson S, Budimir Z, Modi R, Woolsey I, Frerk A, Baker B, Gantt J, Parkinson EI. Synthetic Natural Product Inspired Cyclic Peptides. ACS Chem Biol 2021; 16:2604-2611. [PMID: 34699170 PMCID: PMC8610019 DOI: 10.1021/acschembio.1c00641] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Natural products
are a bountiful source of bioactive molecules.
Unfortunately, discovery of novel bioactive natural products is challenging
due to cryptic biosynthetic gene clusters, low titers, and arduous
purifications. Herein, we describe SNaPP (Synthetic Natural Product
Inspired Cyclic Peptides), a method for identifying
NP-inspired bioactive peptides. SNaPP expedites bioactive molecule
discovery by combining bioinformatics predictions of nonribosomal
peptide synthetases with chemical synthesis of the predicted natural
products (pNPs). SNaPP utilizes a recently discovered cyclase, the
penicillin binding protein-like cyclase, as the lynchpin for the development
of a library of head-to-tail cyclic peptide pNPs. Analysis of 500
biosynthetic gene clusters allowed for identification of 131 novel
pNPs. Fifty-one diverse pNPs were synthesized using solid phase peptide
synthesis and solution-phase cyclization. Antibacterial testing revealed
14 pNPs with antibiotic activity, including activity against multidrug-resistant
Gram-negative bacteria. Overall, SNaPP demonstrates the power of combining
bioinformatics predictions with chemical synthesis to accelerate the
discovery of bioactive molecules.
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Affiliation(s)
- Matthew A. Hostetler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chloe Smith
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samantha Nelson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zachary Budimir
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ramya Modi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ian Woolsey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Autumn Frerk
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Braden Baker
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jessica Gantt
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Elizabeth I. Parkinson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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47
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Zhang X, Zhang S, Zhao S, Wang X, Liu B, Xu H. Click Chemistry in Natural Product Modification. Front Chem 2021; 9:774977. [PMID: 34869223 PMCID: PMC8635925 DOI: 10.3389/fchem.2021.774977] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
Click chemistry is perhaps the most powerful synthetic toolbox that can efficiently access the molecular diversity and unique functions of complex natural products up to now. It enables the ready synthesis of diverse sets of natural product derivatives either for the optimization of their drawbacks or for the construction of natural product-like drug screening libraries. This paper showcases the state-of-the-art development of click chemistry in natural product modification and summarizes the pharmacological activities of the active derivatives as well as the mechanism of action. The aim of this paper is to gain a deep understanding of the fruitful achievements and to provide perspectives, trends, and directions regarding further research in natural product medicinal chemistry.
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Affiliation(s)
- Xiang Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Songfeng Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xuan Wang
- The Second Clinical Medical College, Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bo Liu
- The Second Clinical Medical College, Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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48
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Berger KJ, Driscoll JL, Yuan M, Dherange BD, Gutierrez O, Levin MD. Direct Deamination of Primary Amines via Isodiazene Intermediates. J Am Chem Soc 2021; 143:17366-17373. [PMID: 34637305 PMCID: PMC8892627 DOI: 10.1021/jacs.1c09779] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report here a reaction that selectively deaminates primary amines and anilines under mild conditions and with remarkable functional group tolerance including a range of pharmaceutical compounds, amino acids, amino sugars, and natural products. An anomeric amide reagent is uniquely capable of facilitating the reaction through the intermediacy of an unprecedented monosubstituted isodiazene intermediate. In addition to dramatically simplifying deamination compared to existing protocols, our approach enables strategic applications of iminium and amine-directed chemistries as traceless methods. Mechanistic and computational studies support the intermedicacy of a primary isodiazene which exhibits an unexpected divergence from previously studied secondary isodiazenes, leading to cage-escaping, free radical species that engage in a chain, hydrogen-atom transfer process involving aliphatic and diazenyl radical intermediates.
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Affiliation(s)
- Kathleen J. Berger
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Julia L. Driscoll
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mingbin Yuan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Balu D. Dherange
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Osvaldo Gutierrez
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States; Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Mark D. Levin
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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49
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Bhuyan S, Das D, Chakraborty A, Mandal S, Dhanabal K, Roy BG. A Carbohydrate-based Synthetic Approach to Diverse Structurally and Stereochemically Complex Chiral Polyheterocycles. Chem Asian J 2021; 16:4108-4121. [PMID: 34706155 DOI: 10.1002/asia.202101123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 10/22/2021] [Indexed: 12/27/2022]
Abstract
Chiral polyheterocycles are one of the most frequently encountered scaffolds in natural products and in current drugs repertoire. A carbohydrate-based diversity oriented synthetic (DOS) approach has been employed for gaining access to many structurally diverse and stereochemically complex rigid polyheterocyclic molecules with multiple chiral hydroxyl groups to enhance aqueous solubility. Inexpensive chiral pool of D-Glucose has been judiciously exploited to get access of complex chiral polyheterocyclic structures using inexpensive, common achiral reagents and domino-Knoevenagel hetero-Diels-Alder (DKHDA) reaction as one of the key synthetic tools. Stereochemistry of newly generated stereocenters of polycyclic structures are unambiguously determined through NMR and X-ray crystallographic study. A chemoinformatic comparison (PCA and PMI) with 40 branded blockbuster drugs showed that newly generated polyheterocycles have good three-dimensional scaffold diversity and most of these pass the Lipinski filter of drug-likeness.
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Affiliation(s)
- Samuzal Bhuyan
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Dharmendra Das
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Amit Chakraborty
- Department of Mathematics, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Susanta Mandal
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | | | - Biswajit Gopal Roy
- Department of Chemistry, Sikkim University, 6th Mile, Tadong, Gangtok, Sikkim, 737102, India
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50
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Kim KE, Kim AN, McCormick CJ, Stoltz BM. Late-Stage Diversification: A Motivating Force in Organic Synthesis. J Am Chem Soc 2021; 143:16890-16901. [PMID: 34614361 PMCID: PMC9285880 DOI: 10.1021/jacs.1c08920] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interest in therapeutic discovery typically drives the preparation of natural product analogs, but these undertakings contribute significant advances for synthetic chemistry as well. The need for a highly efficient and scalable synthetic route to a complex molecular scaffold for diversification frequently inspires new methodological development or unique application of existing methods on structurally intricate systems. Additionally, synthetic planning with an aim toward late-stage diversification can provide access to otherwise unavailable compounds or facilitate preparation of complex molecules with diverse patterns of substitution around a shared carbon framework. For these reasons among others, programs dedicated to the diversification of natural product frameworks and other complex molecular scaffolds have been increasing in popularity, a trend likely to continue given their fruitfulness and breadth of impact. In this Perspective, we discuss our experience using late-stage diversification as a guiding principle for the synthesis of natural product analogs and reflect on the impact such efforts have on the future of complex molecule synthesis.
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Affiliation(s)
- Kelly E Kim
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, Washington 98402, United States
| | - Alexia N Kim
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Carter J McCormick
- Sciences and Mathematics Division, School of Interdisciplinary Arts and Sciences, University of Washington, Tacoma, Washington 98402, United States
| | - Brian M Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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