101
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Liu J, Cremosnik GS, Otte F, Pahl A, Sievers S, Strohmann C, Waldmann H. Design, Synthesis, and Biological Evaluation of Chemically and Biologically Diverse Pyrroquinoline Pseudo Natural Products. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013731] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jie Liu
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Gregor S. Cremosnik
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Felix Otte
- Technical University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Compound Management and Screening Center Dortmund Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Compound Management and Screening Center Dortmund Germany
| | - Carsten Strohmann
- Technical University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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102
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Bogart JW, Cabezas MD, Vögeli B, Wong DA, Karim AS, Jewett MC. Cell-Free Exploration of the Natural Product Chemical Space. Chembiochem 2021; 22:84-91. [PMID: 32783358 PMCID: PMC8215586 DOI: 10.1002/cbic.202000452] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/07/2020] [Indexed: 01/24/2023]
Abstract
Natural products and secondary metabolites comprise an indispensable resource from living organisms that have transformed areas of medicine, agriculture, and biotechnology. Recent advances in high-throughput DNA sequencing and computational analysis suggest that the vast majority of natural products remain undiscovered. To accelerate the natural product discovery pipeline, cell-free metabolic engineering approaches used to develop robust catalytic networks are being repurposed to access new chemical scaffolds, and new enzymes capable of performing diverse chemistries. Such enzymes could serve as flexible biocatalytic tools to further expand the unique chemical space of natural products and secondary metabolites, and provide a more sustainable route to manufacture these molecules. Herein, we highlight select examples of natural product biosynthesis using cell-free systems and propose how cell-free technologies could facilitate our ability to access and modify these structures to transform synthetic and chemical biology.
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Affiliation(s)
- Jonathan W. Bogart
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Maria D. Cabezas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Bastian Vögeli
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Derek A. Wong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
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103
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Zubenko AA, Morkovnik AS, Divaeva LN, Demidov OP, Kartsev VG, Sochnev VS, Klimenko AI, Dobaeva NM, Borodkin GS, Bodryakov AN, Bodryakova MA, Fetisov LN. Thiourea assisted recyclization of 1-(chloromethyl)dihydroisoquinolines: a convenient route to β-(o-thiazolylaryl)ethylamines. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.01.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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104
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First discovery of pimprinine derivatives and analogs as novel potential herbicidal, insecticidal and nematicidal agents. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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105
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Lin S, Liu H, Svenningsen EB, Wollesen M, Jacobsen KM, Andersen FD, Moyano-Villameriel J, Pedersen CN, Nørby P, Tørring T, Poulsen TB. Expanding the antibacterial selectivity of polyether ionophore antibiotics through diversity-focused semisynthesis. Nat Chem 2020; 13:47-55. [PMID: 33353970 PMCID: PMC7610524 DOI: 10.1038/s41557-020-00601-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
Polyether ionophores are complex natural products capable of transporting cations across biological membranes. Many polyether ionophores possess potent antimicrobial activity and a few selected compounds have ability to target aggressive cancer cells. Nevertheless, ionophore function is believed to be associated with idiosyncratic cellu-lar toxicity and, consequently, human clinical development has not been pursued. Here, we demonstrate that structurally novel polyether ionophores can be efficiently constructed by recycling components of highly abundant polyethers to afford analogues with enhanced anti-bacterial selectivity compared to a panel of natural polyether ionophores. We used classic degradation reactions of the natural polyethers lasalocid and monensin and combined the resulting fragments with building blocks provided by total synthesis, including halogen-functionalized tetronic acids as cation-binding groups. Our results suggest that structural optimization of polyether ionophores is possible and that this area represents a potential opportunity for future methodological innovation.
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Affiliation(s)
- Shaoquan Lin
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Han Liu
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | | | | | - Frederikke D Andersen
- Department of Engineering-Microbial Biosynthesis, Aarhus University, Aarhus, Denmark
| | | | | | - Peter Nørby
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Thomas Tørring
- Department of Engineering-Microbial Biosynthesis, Aarhus University, Aarhus, Denmark
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106
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Begnini F, Poongavanam V, Over B, Castaldo M, Geschwindner S, Johansson P, Tyagi M, Tyrchan C, Wissler L, Sjö P, Schiesser S, Kihlberg J. Mining Natural Products for Macrocycles to Drug Difficult Targets. J Med Chem 2020; 64:1054-1072. [PMID: 33337880 PMCID: PMC7872424 DOI: 10.1021/acs.jmedchem.0c01569] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Lead
generation for difficult-to-drug targets that have large,
featureless, and highly lipophilic or highly polar and/or flexible
binding sites is highly challenging. Here, we describe how cores of
macrocyclic natural products can serve as a high-quality in
silico screening library that provides leads for difficult-to-drug
targets. Two iterative rounds of docking of a carefully selected set
of natural-product-derived cores led to the discovery of an uncharged
macrocyclic inhibitor of the Keap1-Nrf2 protein–protein interaction,
a particularly challenging target due to its highly polar binding
site. The inhibitor displays cellular efficacy and is well-positioned
for further optimization based on the structure of its complex with
Keap1 and synthetic access. We believe that our work will spur interest
in using macrocyclic cores for in silico-based lead
generation and also inspire the design of future macrocycle screening
collections.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Björn Over
- Department of Medicinal Chemistry, Research and Early Development, Early Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Marie Castaldo
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Patrik Johansson
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Mohit Tyagi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Christian Tyrchan
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Lisa Wissler
- Structure, Biophysics & Fragment-Based Lead Generation, Discovery Sciences, R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Peter Sjö
- Drugs for Neglected Diseases initiative (DNDi), 15 Chemin Louis Dunant, 1202 Geneva, Switzerland
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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107
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Wang Z, Liu J. All-carbon [3 + 2] cycloaddition in natural product synthesis. Beilstein J Org Chem 2020; 16:3015-3031. [PMID: 33363670 PMCID: PMC7736699 DOI: 10.3762/bjoc.16.251] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/21/2020] [Indexed: 12/28/2022] Open
Abstract
Many natural products possess interesting medicinal properties that arise from their intriguing chemical structures. The highly-substituted carbocycle is one of the most common structural features in many structurally complicated natural products. However, the construction of highly-substituted, stereo-congested, five-membered carbocycles containing all-carbon quaternary center(s) is, at present, a distinct challenge in modern synthetic chemistry, which can be accessed through the all-carbon [3 + 2] cycloaddition. More importantly, the all-carbon [3 + 2] cycloaddition can forge vicinal all-carbon quaternary centers in a single step and has been demonstrated in the synthesis of complex natural products. In this review, we present the development of all-carbon [3 + 2] cycloadditions and illustrate their application in natural product synthesis reported in the last decade covering 2011-2020 (inclusive).
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Affiliation(s)
- Zhuo Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Junyang Liu
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
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108
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Chen Y, Kirchmair J. Cheminformatics in Natural Product-based Drug Discovery. Mol Inform 2020; 39:e2000171. [PMID: 32725781 PMCID: PMC7757247 DOI: 10.1002/minf.202000171] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
This review seeks to provide a timely survey of the scope and limitations of cheminformatics methods in natural product-based drug discovery. Following an overview of data resources of chemical, biological and structural information on natural products, we discuss, among other aspects, in silico methods for (i) data curation and natural products dereplication, (ii) analysis, visualization, navigation and comparison of the chemical space, (iii) quantification of natural product-likeness, (iv) prediction of the bioactivities (virtual screening, target prediction), ADME and safety profiles (toxicity) of natural products, (v) natural products-inspired de novo design and (vi) prediction of natural products prone to cause interference with biological assays. Among the many methods discussed are rule-based, similarity-based, shape-based, pharmacophore-based and network-based approaches, docking and machine learning methods.
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Affiliation(s)
- Ya Chen
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
- Department of Pharmaceutical ChemistryFaculty of Life SciencesUniversity of Vienna1090ViennaAustria
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109
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Motika SE, Hergenrother PJ. Re-engineering natural products to engage new biological targets. Nat Prod Rep 2020; 37:1395-1403. [PMID: 33034322 PMCID: PMC7720426 DOI: 10.1039/d0np00059k] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2020 Natural products have a long history in drug discovery, with their inherent biological activity often tailored by medicinal chemists to arrive at the final drug product. This process is illustrated by numerous examples, including the conversion of epothilone to ixabepilone, erythromycin to azithromycin, and lovastatin to simvastatin. However, natural products are also fruitful starting points for the creation of complex and diverse compounds, especially those that are markedly different from the parent natural product and accordingly do not retain the biological activity of the parent. The resulting products have physiochemical properties that differ considerably when compared to traditional screening collections, thus affording an opportunity to discover novel biological activity. The synthesis of new structural frameworks from natural products thus yields value-added compounds, as demonstrated in the last several years with multiple biological discoveries emerging from these collections. This Highlight details a handful of these studies, describing new compounds derived from natural products that have biological activity and cellular targets different from those evoked/engaged by the parent. Such re-engineering of natural products offers the potential for discovering compounds with interesting and unexpected biological activity.
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Affiliation(s)
- Stephen E Motika
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA.
| | - Paul J Hergenrother
- Department of Chemistry, Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, Urbana-Champaign, USA.
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110
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Schneidewind T, Brause A, Pahl A, Burhop A, Mejuch T, Sievers S, Waldmann H, Ziegler S. Morphological Profiling Identifies a Common Mode of Action for Small Molecules with Different Targets. Chembiochem 2020; 21:3197-3207. [PMID: 32618075 PMCID: PMC7754162 DOI: 10.1002/cbic.202000381] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Unbiased morphological profiling of bioactivity, for example, in the cell painting assay (CPA), enables the identification of a small molecule's mode of action based on its similarity to the bioactivity of reference compounds, irrespective of the biological target or chemical similarity. This is particularly important for small molecules with nonprotein targets as these are rather difficult to identify with widely employed target-identification methods. We employed morphological profiling using the CPA to identify compounds that are biosimilar to the iron chelator deferoxamine. Structurally different compounds with different annotated cellular targets provoked a shared physiological response, thereby defining a cluster based on their morphological fingerprints. This cluster is based on a shared mode of action and not on a shared target, that is, cell-cycle modulation in the S or G2 phase. Hierarchical clustering of morphological fingerprints revealed subclusters that are based on the mechanism of action and could be used to predict target-related bioactivity.
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Affiliation(s)
- Tabea Schneidewind
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
- Technical University DortmundFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6Dortmund44227Germany
| | - Alexandra Brause
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Axel Pahl
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Annina Burhop
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Tom Mejuch
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Sonja Sievers
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
- Technical University DortmundFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6Dortmund44227Germany
| | - Slava Ziegler
- Max-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 11Dortmund44227Germany
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111
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Vonteddu NR, Solanke PR, Nayani K, Chandrasekhar S. Cation Triggered Domino Aza-Piancatelli Rearrangement/Friedel-Crafts Alkylation of Indole-Tethered Furfuyl Alcohols to Access Cycloocta[ b]indole Core of Alkaloids. Org Lett 2020; 22:8555-8560. [PMID: 33079545 DOI: 10.1021/acs.orglett.0c03155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A domino approach to bridged cycloocta[b]indolone through a cascade of aza-Piancatelli rearrangement/Friedel-Crafts alkylation is developed. This transformation has been realized by reaction of an indole-tethered 2-furylcarbinol and substituted aniline in the presence of a Lewis acid to initiate aza-Piancatelli rearrangement followed by an in situ intramolecular Friedel-Crafts alkylation to access bridged tetracyclic frameworks in one pot.
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Affiliation(s)
- Nagarjuna Reddy Vonteddu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.,Cipla Ltd, MIDC Patalganga, Rasayani, Maharashtra 410220, India
| | - Pooja R Solanke
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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112
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Abstract
Covering: 1986 to 2020Natural products are an enduring source of chemical information useful for probing biologically relevant chemical space. Toward gathering further structure-activity relationship (SAR) information for a particular natural product, synthetic chemists traditionally proceeded first by a total synthesis effort followed by the synthesis of simplified derivatives. While this approach has proven fruitful, it often does not incorporate hypotheses regarding structural features necessary for bioactivity at the synthetic planning stage, but rather focuses on the rapid assembly of the targeted natural product; a goal that often supersedes the opportunity to gather SAR information en route to the natural product. Furthermore, access to simplified variants of a natural product possessing only the proposed essential structural features necessary for bioactivity, typically at lower oxidation states overall, is sometimes non-trivial from the original established synthetic route. In recent years, several synthetic design strategies were described to streamline the process of finding bioactive molecules in concert with fathering further SAR studies for targeted natural products. This review article will briefly discuss traditional retrosynthetic strategies and contrast them to selected examples of recent synthetic strategies for the investigation of biologically relevant chemical space revealed by natural products. These strategies include: diversity-oriented synthesis (DOS), biology-oriented synthesis (BIOS), diverted-total synthesis (DTS), analogue-oriented synthesis (AOS), two-phase synthesis, function-oriented synthesis (FOS), and computed affinity/dynamically ordered retrosynthesis (CANDOR). Finally, a description of pharmacophore-directed retrosynthesis (PDR) developed in our laboratory and initial applications will be presented that was initially inspired by a retrospective analysis of our synthetic route to pateamine A completed in 1998.
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Affiliation(s)
- Nathanyal J Truax
- Department of Chemistry & Biochemistry, Baylor University, Waco, Texas 76710, USA.
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113
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Borquaye LS, Gasu EN, Ampomah GB, Kyei LK, Amarh MA, Mensah CN, Nartey D, Commodore M, Adomako AK, Acheampong P, Mensah JO, Mormor DB, Aboagye CI. Alkaloids from Cryptolepis sanguinolenta as Potential Inhibitors of SARS-CoV-2 Viral Proteins: An In Silico Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5324560. [PMID: 33029513 PMCID: PMC7512045 DOI: 10.1155/2020/5324560] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 01/18/2023]
Abstract
The ongoing global pandemic caused by the human coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions of people and claimed hundreds of thousands of lives. The absence of approved therapeutics to combat this disease threatens the health of all persons on earth and could cause catastrophic damage to society. New drugs are therefore urgently required to bring relief to people everywhere. In addition to repurposing existing drugs, natural products provide an interesting alternative due to their widespread use in all cultures of the world. In this study, alkaloids from Cryptolepis sanguinolenta have been investigated for their ability to inhibit two of the main proteins in SARS-CoV-2, the main protease and the RNA-dependent RNA polymerase, using in silico methods. Molecular docking was used to assess binding potential of the alkaloids to the viral proteins whereas molecular dynamics was used to evaluate stability of the binding event. The results of the study indicate that all 13 alkaloids bind strongly to the main protease and RNA-dependent RNA polymerase with binding energies ranging from -6.7 to -10.6 kcal/mol. In particular, cryptomisrine, cryptospirolepine, cryptoquindoline, and biscryptolepine exhibited very strong inhibitory potential towards both proteins. Results from the molecular dynamics study revealed that a stable protein-ligand complex is formed upon binding. Alkaloids from Cryptolepis sanguinolenta therefore represent a promising class of compounds that could serve as lead compounds in the search for a cure for the corona virus disease.
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Affiliation(s)
- Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gilbert Boadu Ampomah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lois Kwane Kyei
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Margaret Amerley Amarh
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Caleb Nketia Mensah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel Nartey
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Commodore
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Philipina Acheampong
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - David Batsa Mormor
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Caleb Impraim Aboagye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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114
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Kim Y, Heo J, Kim D, Chang S, Seo S. Ring-opening functionalizations of unstrained cyclic amines enabled by difluorocarbene transfer. Nat Commun 2020; 11:4761. [PMID: 32958762 PMCID: PMC7506026 DOI: 10.1038/s41467-020-18557-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Chemical synthesis based on the skeletal variation has been prolifically utilized as an attractive approach for modification of molecular properties. Given the ubiquity of unstrained cyclic amines, the ability to directly alter such motifs would grant an efficient platform to access unique chemical space. Here, we report a highly efficient and practical strategy that enables the selective ring-opening functionalization of unstrained cyclic amines. The use of difluorocarbene leads to a wide variety of multifaceted acyclic architectures, which can be further diversified to a range of distinctive homologative cyclic scaffolds. The virtue of this deconstructive strategy is demonstrated by successful modification of several natural products and pharmaceutical analogues.
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Affiliation(s)
- Youyoung Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Joon Heo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Dongwook Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Sukbok Chang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea. .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
| | - Sangwon Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea. .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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115
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Hill J, Hettikankanamalage AA, Crich D. Diversity-Oriented Synthesis of N, N, O-Trisubstituted Hydroxylamines from Alcohols and Amines by N-O Bond Formation. J Am Chem Soc 2020; 142:14820-14825. [PMID: 32803971 DOI: 10.1021/jacs.0c05991] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Magnesium dialkylamides react with alcohol-derived 2-methyl-2-tetrahydropyranyl alkyl peroxides (MTHPs) in tetrahydrofuran at 0 °C to give N,N,O-trisubstituted hydroxylamines suitable for medicinal chemistry purposes in good to excellent yields. A wide range of secondary alkyl and aryl amines and primary and secondary alcohol-derived MTHPs are compatible with the described reaction which, coupled with the enormous diversity of commercially available alcohols and secondary amines, suggests broad applicability of the reaction in fragment-based library design.
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Affiliation(s)
- Jarvis Hill
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States.,Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Asiri A Hettikankanamalage
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States.,Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - David Crich
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States.,Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States.,Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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116
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Hippman RS, Pavlinov I, Gao Q, Mavlyanova MK, Gerlach EM, Aldrich LN. Multiple Chemical Features Impact Biological Performance Diversity of a Highly Active Natural Product-Inspired Library. Chembiochem 2020; 21:3137-3145. [PMID: 32558167 DOI: 10.1002/cbic.202000356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 12/12/2022]
Abstract
A systematic, diversity-oriented synthesis approach was employed to access a natural product-inspired flavonoid library with diverse chemical features, including chemical properties, scaffold, stereochemistry, and appendages. Using Cell Painting, the effects of these diversity elements were evaluated, and multiple chemical features that predict biological performance diversity were identified. Scaffold identity appears to be the dominant predictor of performance diversity, but stereochemistry and appendages also contribute to a lesser degree. In addition, the diversity of chemical properties contributed to performance diversity, and the driving chemical property was dependent on the scaffold. These results highlight the importance of key chemical features that may inform the creation of small-molecule, performance-diverse libraries to improve the efficiency and success of high-throughput screening campaigns.
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Affiliation(s)
- Ryan S Hippman
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Ivan Pavlinov
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Qiwen Gao
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Michelle K Mavlyanova
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Erica M Gerlach
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
| | - Leslie N Aldrich
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, USA
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117
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Troelsen NS, Clausen MH. Library Design Strategies To Accelerate Fragment‐Based Drug Discovery. Chemistry 2020; 26:11391-11403. [DOI: 10.1002/chem.202000584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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118
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Foley DJ, Zinken S, Corkery D, Laraia L, Pahl A, Wu Y, Waldmann H. Phenotyping Reveals Targets of a Pseudo-Natural-Product Autophagy Inhibitor. Angew Chem Int Ed Engl 2020; 59:12470-12476. [PMID: 32108411 PMCID: PMC7383971 DOI: 10.1002/anie.202000364] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/25/2020] [Indexed: 12/26/2022]
Abstract
Pseudo-natural-product (NP) design combines natural product fragments to provide unprecedented NP-inspired compounds not accessible by biosynthesis, but endowed with biological relevance. Since the bioactivity of pseudo-NPs may be unprecedented or unexpected, they are best evaluated in target agnostic cell-based assays monitoring entire cellular programs or complex phenotypes. Here, the Cinchona alkaloid scaffold was merged with the indole ring system to synthesize indocinchona alkaloids by Pd-catalyzed annulation. Exploration of indocinchona alkaloid bioactivities in phenotypic assays revealed a novel class of azaindole-containing autophagy inhibitors, the azaquindoles. Subsequent characterization of the most potent compound, azaquindole-1, in the morphological cell painting assay, guided target identification efforts. In contrast to the parent Cinchona alkaloids, azaquindoles selectively inhibit starvation- and rapamycin-induced autophagy by targeting the lipid kinase VPS34.
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Affiliation(s)
- Daniel J. Foley
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Sarah Zinken
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundDortmundGermany
| | - Dale Corkery
- Department of ChemistryUmeå Centre for Microbial ResearchUmeå UniversityUmeåSweden
| | - Luca Laraia
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Current address: Department of ChemistryTechnical University of DenmarkCopenhagenDenmark
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Compound Management and Screening CentreDortmundGermany
| | - Yao‐Wen Wu
- Department of ChemistryUmeå Centre for Microbial ResearchUmeå UniversityUmeåSweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundDortmundGermany
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119
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Dhanju S, Upadhyaya K, Rice CA, Pegan SD, Media J, Valeriote FA, Crich D. Synthesis, Cytotoxicity, and Genotoxicity of 10-Aza-9-oxakalkitoxin, an N,N,O-Trisubstituted Hydroxylamine Analog, or Hydroxalog, of a Marine Natural Product. J Am Chem Soc 2020; 142:9147-9151. [DOI: 10.1021/jacs.0c03763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sandeep Dhanju
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Kapil Upadhyaya
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
| | - Christopher A. Rice
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
| | - Scott D. Pegan
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
| | - Joseph Media
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Cancer Institute, Detroit, Michigan 48202, United States
| | - Frederick A. Valeriote
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Cancer Institute, Detroit, Michigan 48202, United States
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 West Green Street, Athens, Georgia 30602, United States
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States,
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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120
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Foley DJ, Zinken S, Corkery D, Laraia L, Pahl A, Wu Y, Waldmann H. Phenotyping Reveals Targets of a Pseudo‐Natural‐Product Autophagy Inhibitor. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000364] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel J. Foley
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Current address: School of Physical and Chemical Sciences University of Canterbury Christchurch New Zealand
| | - Sarah Zinken
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Dortmund Germany
| | - Dale Corkery
- Department of Chemistry Umeå Centre for Microbial Research Umeå University Umeå Sweden
| | - Luca Laraia
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Current address: Department of Chemistry Technical University of Denmark Copenhagen Denmark
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Compound Management and Screening Centre Dortmund Germany
| | - Yao‐Wen Wu
- Department of Chemistry Umeå Centre for Microbial Research Umeå University Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Dortmund Germany
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121
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Cremosnik GS, Liu J, Waldmann H. Guided by evolution: from biology oriented synthesis to pseudo natural products. Nat Prod Rep 2020; 37:1497-1510. [DOI: 10.1039/d0np00015a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview and historical context to two concepts for the design of natural product-inspired compound libraries and highlights the used synthetic methodologies.
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Affiliation(s)
- Gregor S. Cremosnik
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
| | - Jie Liu
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
- Faculty of Chemistry and Chemical Biology
| | - Herbert Waldmann
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
- Faculty of Chemistry and Chemical Biology
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