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Irie R, Hitora Y, Watanabe R, Clark H, Suyama Y, Sekiya S, Suzuki T, Takada K, Matsunaga S, Hosokawa S, Oikawa M. Stereochemical Assignment of the 36-Membered Macrolide Ring Portion of Poecillastrin C. Org Lett 2024; 26:5290-5294. [PMID: 38864719 DOI: 10.1021/acs.orglett.4c01632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Absolute configuration at 12 stereocenters in the 36-membered macrocyclic ring portion of poecillastrin C (1) was disclosed by chemical degradation and NMR analyses of 1, chemical synthesis, and molecular modeling techniques.
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Affiliation(s)
- Raku Irie
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Yuki Hitora
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryuichi Watanabe
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Japan
| | - Hugh Clark
- Department of Applied Chemistry, Faculty of Advanced Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yu Suyama
- Department of Applied Chemistry, Faculty of Advanced Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Shinji Sekiya
- Department of Applied Chemistry, Faculty of Advanced Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Toshiyuki Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Seijiro Hosokawa
- Department of Applied Chemistry, Faculty of Advanced Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Masato Oikawa
- Yokohama City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
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Suresh P, Gupta S, Anmol, Sharma U. Insight into coronaviruses and natural products-based approach for COVID-19 treatment. BIOACTIVE NATURAL PRODUCTS 2022. [PMCID: PMC9294970 DOI: 10.1016/b978-0-323-91099-6.00005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
There is a deep-rooted belief in mankind that for every illness, somewhere in the world, there exists a botanical-based healing agent in nature in the form of a natural product. Natural products are better equipped to become successful drugs because of their million years of coevolution in a biological milieu. Generally, most herbal formulations and natural products obtained from traditionally used medicinal plants are nontoxic and have rarely shown any adverse side effects on humans. Plants synthesize secondary metabolites primarily for their defense against microbes and herbivores, and because of this, these metabolites have good specificity and potency against harmful pathogens. Nowadays, mankind is facing the contagion effect of SARS-CoV-2 that has caused the ongoing pandemic of COVID-19, which has no specific and effective treatment. Hence this is the time to explore nature for effective, safe, and affordable remedies against this disease. This chapter includes an overview of coronaviruses, their therapeutic targets, and the progress made in identifying lead natural products against the coronaviruses. Additionally, molecular docking and pharmacokinetics analysis of anticoronaviral natural products have been performed to narrow down the possible lead molecules.
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3
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Scheeff S, Rivière S, Ruiz J, Dedenbach S, Menche D. Modular Total Synthesis of iso-Archazolids and Archazologs. J Org Chem 2021; 86:10190-10223. [PMID: 34293866 DOI: 10.1021/acs.joc.1c00946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Full details on the design, development, and successful implementation of suitable synthetic strategies directed toward the total synthesis of iso-archazolids and archazologs are reported. Both a biomimetic and a multistep total synthesis of iso-archazolid B, the most potent and least abundant archazolid, are described. The bioinspired conversion from archazolid B was realized by a high-yielding 1,8-Diazabicyclo[5.4.0]undec-7-ene catalyzed one-step double-bond shift. A highly stereoselective total synthesis was accomplished in 25 steps, involving a sequence of highly stereoselective aldol reactions, an efficient aldol condensation to forge two elaborate fragments, and a challenging ring-closing metathesis macrocyclization with an unusual Stewart-Grubbs catalyst. These strategies proved to be generally useful and could be successfully implemented for the preparation of three novel iso-archazolids as well as five novel archazologs, lacking the thiazole side chain. A wide variety of further archazolids and archazologs may now be targeted for exploration of the promising anticancer potential of these polyketide macrolides.
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Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Solenne Rivière
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Johal Ruiz
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Simon Dedenbach
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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4
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Menche D. Design and Synthesis of Simplified Polyketide Analogs: New Modalities beyond the Rule of 5. ChemMedChem 2021; 16:2068-2074. [PMID: 33755304 PMCID: PMC8360190 DOI: 10.1002/cmdc.202100150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 12/29/2022]
Abstract
Natural products provide important lead structures for development of pharmaceutical agents or present attractive tools for medicinal chemistry. However, structurally complex and thus less accessible metabolites defying conventional drug-like properties, as expressed by Pfizer's rule of five, have received less attention as medicinal leads. Traditionally, research focus has been on realizing total syntheses rather than developing more readily available analogs to resolve the critical supply issue. However, very recent studies with complex myxobacterial polyketides have demonstrated that considerable structural simplification may be realized with retention of biological potencies. The context, underlying rationale and importance of tailored synthetic strategies of three such case studies are presented, which may inspire further related activities and may eventually help exploiting the largely untapped biological potential of complex metabolites in general.
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Affiliation(s)
- Dirk Menche
- Kekulé-Institut für Organische Chemie und BiochemieUniversität BonnGerhard-Domagk-Strasse 153121BonnGermany
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5
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Zhang W. Heck macrocyclization in natural product total synthesis. Nat Prod Rep 2021; 38:1109-1135. [PMID: 33662070 DOI: 10.1039/d0np00087f] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1981-2020 Heck macrocyclization is a logical extension of the award-winning Mizoroki-Heck reaction. Through covalent linking of two otherwise discrete coupling partners, the resultant chimeric substrate is transformed into a large ring with enhanced rigidity and unique functional group disposition. Pioneered in the early 1980s, this methodology has evolved into a competent option for creating diverse macrocycles. Despite its growing influence, hitherto no systematic survey has ever appeared in the literature. The present review delineates the state-of-the-art of Heck macrocyclization in the context of natural product synthesis. Sixteen selected cases, each examined from a different perspective, coalesce into the view that the title reaction is a viable tool for synthesis-enabled macrocycle research.
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Affiliation(s)
- Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, People's Republic of China.
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Scheeff S, Rivière S, Ruiz J, Abdelrahman A, Schulz-Fincke AC, Köse M, Tiburcy F, Wieczorek H, Gütschow M, Müller CE, Menche D. Synthesis of Novel Potent Archazolids: Pharmacology of an Emerging Class of Anticancer Drugs. J Med Chem 2020; 63:1684-1698. [DOI: 10.1021/acs.jmedchem.9b01887] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Solenne Rivière
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Johal Ruiz
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
| | - Aliaa Abdelrahman
- Pharmazeutisches Institut, Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | | | - Meryem Köse
- Pharmazeutisches Institut, Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Felix Tiburcy
- Fachbereich Biologie/Chemie, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - Helmut Wieczorek
- Fachbereich Biologie/Chemie, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - Michael Gütschow
- Pharmazeutisches Institut, Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Christa E. Müller
- Pharmazeutisches Institut, Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
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7
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Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
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8
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Scheeff S, Menche D. Total syntheses of the archazolids: an emerging class of novel anticancer drugs. Beilstein J Org Chem 2017; 13:1085-1098. [PMID: 28684988 PMCID: PMC5480361 DOI: 10.3762/bjoc.13.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
V-ATPase has recently emerged as a promising novel anticancer target based on extensive in vitro and in vivo studies with the archazolids, complex polyketide macrolides which present the most potent V-ATPase inhibitors known to date, rendering these macrolides important lead structures for the development of novel anticancer agents. The limited natural supply of these metabolites from their myxobacterial source renders total synthesis of vital importance for the further preclinical development. This review describes in detail the various tactics and strategies employed so far in archazolid syntheses that culminated in three total syntheses and discusses the future synthetic challenges that have to be addressed.
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Affiliation(s)
- Stephan Scheeff
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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9
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Gölz JP, Bockelmann S, Mayer K, Steinhoff HJ, Wieczorek H, Huss M, Klare JP, Menche D. EPR Studies of V-ATPase with Spin-Labeled Inhibitors DCC and Archazolid: Interaction Dynamics with Proton Translocating Subunit c. ChemMedChem 2015; 11:420-8. [DOI: 10.1002/cmdc.201500500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Jan Philipp Gölz
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Svenja Bockelmann
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Kerstin Mayer
- Institut für Organische Chemie; Ruprecht-Karls-Universität Heidelberg; INF 270; 69120 Heidelberg Germany
| | | | - Helmut Wieczorek
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Markus Huss
- Fachbereich Biologie/Chemie; Universität Osnabrück; 49069 Osnabrück Germany
| | - Johann P. Klare
- Fachbereich Physik; Universität Osnabrück; 49069 Osnabrück Germany
| | - Dirk Menche
- Kekulé-Institut für Organische Chemie und Biochemie; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Str. 1 53121 Bonn Germany
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10
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Machine learning estimates of natural product conformational energies. PLoS Comput Biol 2014; 10:e1003400. [PMID: 24453952 PMCID: PMC3894151 DOI: 10.1371/journal.pcbi.1003400] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/10/2013] [Indexed: 11/19/2022] Open
Abstract
Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP), mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures. Molecular dynamics simulations provide insight into the dynamic behavior of molecules, e.g., into the adopted spatial arrangements of its atoms over time. Methods differ in the approximations they employ, resulting in a trade-off between accuracy and speed that ranges from highly accurate but expensive quantum mechanical calculations to fast but more inaccurate molecular mechanics force fields. Machine learning, a sub-discipline of artificial intelligence, provides algorithms that learn from data, that is, make predictions based on previously seen examples. By starting with a few expensive quantum mechanical calculations, training a machine learning algorithm on them, and then using the resulting model to carry out the molecular dynamics simulation, one can improve the accuracy/speed trade-off. We have developed and applied such a hybrid quantum mechanics/machine learning approach to Archazolid A, a natural product from the myxobacterium Archangium gephyra and a potent inhibitor of vacuolar-type ATPase. By dynamically refining our model over the course of the simulation, we achieve errors of less than 1 kcal/mol while saving over 40% of the quantum mechanical calculations. Our study demonstrates the feasibility of predictive machine learning models for the dynamics of structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of even larger biomolecular structures.
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11
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Negishi EI, Xu S. Syntheses of Chiral Heterocyclic Compounds via Zirconium-Catalyzed Asymmetric Carboalumination of Alkynes (ZACA Reaction). HETEROCYCLES 2014. [DOI: 10.3987/rev-13-sr(s)5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Irschik H, Washausen P, Sasse F, Fohrer J, Huch V, Müller R, Prusov EV. Isolierung, Strukturaufklärung und biologische Untersuchung von Maltepoliden: bemerkenswerte Makrolide aus Myxobakterien. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Irschik H, Washausen P, Sasse F, Fohrer J, Huch V, Müller R, Prusov EV. Isolation, Structure Elucidation, and Biological Activity of Maltepolides: Remarkable Macrolides from Myxobacteria. Angew Chem Int Ed Engl 2013; 52:5402-5. [DOI: 10.1002/anie.201210113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Indexed: 11/12/2022]
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14
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Abstract
Polyketides are a very diverse family of natural products with an extremely broad range of biological activities and pharmacological properties, including antiproliferative, antibiotic, antifungal, or antiplasmodial activities, and in many cases specific targets are addressed at the molecular level. Their structures are characterized by diverse assemblies of methyl- and hydroxyl-bearing stereogenic centers enabling large numbers of stereochemical permutations, which are often embedded into macrolide rings. This complexity renders the stereochemical assignment and directed total synthesis challenging tasks. Within this review, we will detail practicable approaches for the stereochemical determination of diverse complex polyketides of myxobacterial origin by using computational and NMR methods in combination with novel procedures based on bioinformatics. Furthermore, we have developed efficient preparative strategies for the synthesis of these compounds, which have culminated in several first total syntheses. Key aspects of these various endeavors, which will also focus on the importance of conformational bias in complex polyketide analysis and synthesis, will be discussed within this review in the realm of the potent macrolide antibiotics etnangien and rhizopodin. Along these lines, we will also summarize novel methods for the rapid assembly of key structural elements of polyketides including a novel domino concept relying on a combination of a nucleophilic addition and a Tsuji–Trost reaction.
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Affiliation(s)
- Sebastian Essig
- 1Institut für Organische Chemie, Universität Heidelberg, INF 270, D-69120 Heidelberg, Germany
| | - Dirk Menche
- 2Kekulé-Institut für Organische Chemie und Biochemie der Universität Bonn, Gerhard-Domagk-Str. 1, D-53121 Bonn, Germany
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15
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Persch E, Basile T, Bockelmann S, Huss M, Wieczorek H, Carlomagno T, Menche D. Synthesis and biological evaluation of a water-soluble derivative of the potent V-ATPase inhibitor archazolid. Bioorg Med Chem Lett 2012; 22:7735-8. [DOI: 10.1016/j.bmcl.2012.09.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/19/2012] [Accepted: 09/22/2012] [Indexed: 10/27/2022]
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16
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Dreisigacker S, Latek D, Bockelmann S, Huss M, Wieczorek H, Filipek S, Gohlke H, Menche D, Carlomagno T. Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. J Chem Inf Model 2012; 52:2265-72. [DOI: 10.1021/ci300242d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandra Dreisigacker
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
- Institute of Organic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer
Feld 270, D-69120 Heidelberg, Germany
| | - Dorota Latek
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Svenja Bockelmann
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Markus Huss
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Helmut Wieczorek
- Department of Animal Physiology, Faculty of Biology and Chemistry, University of Osnabrück, Barbarastrasse 11, D-49069 Osnabrück, Germany
| | - Slawomir Filipek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Holger Gohlke
- Heinrich-Heine-University Düsseldorf,
Institute of Pharmaceutical and Medicinal Chemistry, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Dirk Menche
- Institute of Organic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer
Feld 270, D-69120 Heidelberg, Germany
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, EMBL, Mayerhofstrasse 1, D-69117 Heidelberg, Germany
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17
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Tello-Aburto R, Newar TD, Maio WA. Evolution of a protecting-group-free total synthesis: studies en route to the neuroactive marine macrolide (-)-palmyrolide A. J Org Chem 2012; 77:6271-89. [PMID: 22721171 DOI: 10.1021/jo301121f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A full account of our synthetic work toward the first total synthesis of the neuroactive marine macrolide (-)-palmyrolide A is described. Our first-generation approach aimed to unlock the unknown C(5)-C(7) stereochemical relationship via the synthesis of four diastereomers of palmyrolide A aldehyde, a known degradation product. When these efforts provided inconclusive results, recourse to synthesizing all possible stereocombinations of the 15-membered macrolide was undertaken. These studies were critical in confirming the absolute stereochemistry, yielding the first total synthesis of (+)-ent-palmyrolide A. Subsequent to this work, the first protecting-group-free total synthesis of natural (-)-palmyrolide A is also reported.
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Affiliation(s)
- Rodolfo Tello-Aburto
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, New Mexico 88003, USA
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18
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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19
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Horstmann N, Essig S, Bockelmann S, Wieczorek H, Huss M, Sasse F, Menche D. Archazolid A-15-O-β-D-glucopyranoside and iso-archazolid B: potent V-ATPase inhibitory polyketides from the myxobacteria Cystobacter violaceus and Archangium gephyra. JOURNAL OF NATURAL PRODUCTS 2011; 74:1100-1105. [PMID: 21513292 DOI: 10.1021/np200036v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Two structurally novel analogues of the macrolides archazolids A and B, archazolid A-15-O-β-D-glucopyranoside (archazolid E, 5) and iso-archazolid B (archazolid F, 6), were isolated from the myxobacterium Cystobacter violaceus and Archangium gephyra, respectively. Macrolactone 5 represents the first 15-O-glycoside of the archazolids. iso-Archazolid B (6) incorporates a C-3 alkene and presents the first constitutional isomer reported for this natural product class. The structures of these polyketides were determined by spectroscopic analysis, in particular by HMBC, HMQC, and ROESY NMR investigations and by chemical degradation. iso-Archazolid B (6) demonstrated extremely high antiproliferative and V-ATPase inhibitory effects, with IC(50) values in the picomolar range, while only moderate activity was observed for glycoside 5. iso-Archazolid B presents the most potent archazolid known.
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Affiliation(s)
- Nicole Horstmann
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
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Gagnepain J, Moulin E, Nevado C, Waser M, Maier A, Kelter G, Fiebig HH, Fürstner A. Molecular Editing and Assessment of the Cytotoxic Properties of Iejimalide and Progeny. Chemistry 2011; 17:6973-84. [DOI: 10.1002/chem.201100180] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Indexed: 01/21/2023]
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Ma B, Xiang Y, An L. Structural bases of physiological functions and roles of the vacuolar H(+)-ATPase. Cell Signal 2011; 23:1244-56. [PMID: 21397012 DOI: 10.1016/j.cellsig.2011.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/03/2011] [Indexed: 12/09/2022]
Abstract
Vacuolar-type H(+)-ATPases (V-ATPases) is a large multi-protein complex containing at least 14 different subunits, in which subunits A, B, C, D, E, F, G, and H compose the peripheral 500-kDa V(1) responsible for ATP hydrolysis, and subunits a, c, c', c″, and d assembly the 250-kDa membrane-integral V(0) harboring the rotary mechanism to transport protons across the membrane. The assembly of V-ATPases requires the presence of all V(1) and V(0) subunits, in which the V(1) must be completely assembled prior to association with the V(0), accordingly the V(0) failing to assemble cannot provide a membrane anchor for the V(1), thereby prohibiting membrane association of the V-ATPase subunits. The V-ATPase mediates acidification of intracellular compartments and regulates diverse critical physiological processes of cell for functions of its numerous functional subunits. The core catalytic mechanism of the V-ATPase is a rotational catalytic mechanism. The V-ATPase holoenzyme activity is regulated by the reversible assembly/disassembly of the V(1) and V(0), the targeting and recycling of V-ATPase-containing vesicles to and from the plasma membrane, the coupling ratio between ATP hydrolysis and proton pumping, ATP, Ca(2+), and its inhibitors and activators.
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Affiliation(s)
- Binyun Ma
- Key Laboratory of Arid and Grassland Agroecology of Ministry of Education, School of Life Sciences, Lanzhou University, 730000, Lanzhou, China
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Tran AB, Melly GC, Doucette R, Ashcraft B, Sebren LJ, Havko N, Young JC, O'Neil GW. Synthesis and activity of the archazolid western hemisphere. Org Biomol Chem 2011; 9:7671-4. [DOI: 10.1039/c1ob06446k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bockelmann S, Menche D, Rudolph S, Bender T, Grond S, von Zezschwitz P, Muench SP, Wieczorek H, Huss M. Archazolid A binds to the equatorial region of the c-ring of the vacuolar H+-ATPase. J Biol Chem 2010; 285:38304-14. [PMID: 20884613 DOI: 10.1074/jbc.m110.137539] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The macrolactone archazolid is a novel, highly specific V-ATPase inhibitor with an IC(50) value in the low nanomolar range. The binding site of archazolid is presumed to overlap with the binding site of the established plecomacrolide V-ATPase inhibitors bafilomycin and concanamycin in subunit c of the membrane-integral V(O) complex. Using a semi-synthetic derivative of archazolid for photoaffinity labeling of the V(1)V(O) holoenzyme we confirmed binding of archazolid to the V(O) subunit c. For the plecomacrolide binding site a model has been published based on mutagenesis studies of the c subunit of Neurospora crassa, revealing 11 amino acids that are part of the binding pocket at the interface of two adjacent c subunits (Bowman, B. J., McCall, M. E., Baertsch, R., and Bowman, E. J. (2006) J. Biol. Chem. 281, 31885-31893). To investigate the contribution of these amino acids to the binding of archazolid, we established in Saccharomyces cerevisiae mutations that in N. crassa had changed the IC(50) value for bafilomycin 10-fold or more and showed that out of the amino acids forming the plecomacrolide binding pocket only one amino acid (tyrosine 142) contributes to the binding of archazolid. Using a fluorescent derivative of N,N'-dicyclohexylcarbodiimide, we found that the binding site for archazolid comprises the essential glutamate within helix 4 of subunit c. In conclusion the archazolid binding site resides within the equatorial region of the V(O) rotor subunit c. This hypothesis was supported by an additional subset of mutations within helix 4 that revealed that leucine 144 plays a role in archazolid binding.
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Affiliation(s)
- Svenja Bockelmann
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Tierphysiologie, Barbarastrasse 11, 49069 Osnabrück, Germany
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Moulin E, Nevado C, Gagnepain J, Kelter G, Fiebig HH, Fürstner A. Synthesis and evaluation of an Iejimalide-archazolid chimera. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Pérez-Sayáns M, Somoza-Martín JM, Barros-Angueira F, Rey JMG, García-García A. V-ATPase inhibitors and implication in cancer treatment. Cancer Treat Rev 2009; 35:707-13. [PMID: 19758758 DOI: 10.1016/j.ctrv.2009.08.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 08/03/2009] [Accepted: 08/06/2009] [Indexed: 01/08/2023]
Abstract
Acidity is one of the main features of the tumors. The V-ATPase is the primary responsible for the control of tumor microenvironment by proton extrusion to the extracellular medium. The acid environment favors tissue damage, activation of destructive enzymes in the extracellular matrix, the acquisition of metastatic cell phenotypes as well as increasing the destructive capacity. The application of specific inhibitors of V-ATPases, can decrease the acidity of tumor and may allow the reduction of tumor metastasis, acting on the survival of tumor cells and prevent the phenomena of chemoresistance. Among the most important inhibitors can be distinguished benzolactone enamides (salicylihalamide), lobatamide A and B, apicularen, indolyls, oximidine, macrolactone archazolid, lobatamide C, and cruentaren. The latest generation of inhibitors includes NiK12192, FR202126, and PPI SB 242784. The purpose of this paper is to describe the latest advances in the field of V-ATPase inhibitors, describe further developments related to the classic inhibitors, and discuss new potential applications of these drugs in cancer treatment.
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Menche D, Hassfeld J, Li J, Mayer K, Rudolph S. Modular Total Synthesis of Archazolid A and B. J Org Chem 2009; 74:7220-9. [DOI: 10.1021/jo901565n] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dirk Menche
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Jorma Hassfeld
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Jun Li
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Kerstin Mayer
- Institut für Organische Chemie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg
| | - Sven Rudolph
- Helmholtz-Zentrum für Infektionsforschung, Medizinische Chemie, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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Abstract
V-ATPases constitute a ubiquitous family of heteromultimeric, proton translocating proteins. According to their localization in a multitude of eukaryotic endomembranes and plasma membranes, they energize many different transport processes. Currently, a handful of specific inhibitors of the V-ATPase are known, which represent valuable tools for the characterization of transport processes on the level of tissues, single cells or even purified proteins. The understanding of how these inhibitors function may provide a basis to develop new drugs for the benefit of patients suffering from diseases such as osteoporosis or cancer. For this purpose, it appears absolutely essential to determine the exact inhibitor binding site in a target protein on the one side and to uncover the crucial structural elements of an inhibitor on the other side. However, even for some of the most popular and long known V-ATPase inhibitors, such as bafilomycin or concanamycin, the authentic structures of their binding sites are elusive. The aim of this review is to summarize the recent advances for the old players in the inhibition game, the plecomacrolides bafilomycin and concanamycin, and to introduce some of the new players, the macrolacton archazolid, the benzolactone enamides salicylihalamide, lobatamide, apicularen, oximidine and cruentaren, and the indolyls.
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Affiliation(s)
- Markus Huss
- Department of Biology/Chemistry, University of Osnabrück, 49069 Osnabrück, Germany.
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Affiliation(s)
- Christina M. Thiele
- Technische Universität Darmstadt, Clemens‐Schöpf‐Institut für Organische Chemie und Biochemie, Petersenstr. 22, 64287 Darmstadt, Germany, Fax: +49‐6151‐165531
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Farès C, Hassfeld J, Menche D, Carlomagno T. Simultaneous Determination of the Conformation and Relative Configuration of Archazolide A by Using Nuclear Overhauser Effects,J Couplings, and Residual Dipolar Couplings. Angew Chem Int Ed Engl 2008; 47:3722-6. [DOI: 10.1002/anie.200800225] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Farès C, Hassfeld J, Menche D, Carlomagno T. Simultaneous Determination of the Conformation and Relative Configuration of Archazolide A by Using Nuclear Overhauser Effects,J Couplings, and Residual Dipolar Couplings. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800225] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Menche D. New methods for stereochemical determination of complex polyketides: configurational assignment of novel metabolites from myxobacteria. Nat Prod Rep 2008; 25:905-18. [DOI: 10.1039/b707989n] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Huang Z, Negishi EI. Highly stereo- and regioselective synthesis of (Z)-trisubstituted alkenes via 1-bromo-1-alkyne hydroboration-migratory insertion-Zn-promoted iodinolysis and Pd-catalyzed organozinc cross-coupling. J Am Chem Soc 2007; 129:14788-92. [PMID: 17985915 PMCID: PMC3891656 DOI: 10.1021/ja0772039] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroboration of 1-bromo-1-alkynes with dibromoborane followed by addition of 3 or 4 equiv of Me2Zn provides an efficient and selective route to (Z)-2-alkenyldimethylboranes (3) or (Z)-2-alkenylmethylzincs (4), respectively, which have been successfully applied to one-pot Suzuki (B-I) or Negishi (Zn-I) coupling in some less demanding cases. However, in more demanding cross-coupling reactions, only the use of either (Z)-2-alkenyliodides (5) or the alkenylzincs prepared from lithiation and then zincation of 5 proves to be highly satisfactory (Zn-II or Zn-III protocol). On the contrary, the corresponding organoboron coupling under B-II or B-III protocol appears to be less satisfactory. Preliminary studies indicate that certain substituents proximal to trisubstituted alkenes seriously affect the course of the desired alkenylboron cross-coupling.
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Affiliation(s)
- Zhihong Huang
- Herbert C. Brown Laboratories of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
| | - Ei-ichi Negishi
- Herbert C. Brown Laboratories of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084
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Bifulco G, Dambruoso P, Gomez-Paloma L, Riccio R. Determination of relative configuration in organic compounds by NMR spectroscopy and computational methods. Chem Rev 2007; 107:3744-79. [PMID: 17649982 DOI: 10.1021/cr030733c] [Citation(s) in RCA: 452] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Giuseppe Bifulco
- Dipartimento di Scienze Farmaceutiche, University of Salerno, Via Ponte Don Melillo, 84084 Fisciano, Salerno, Italy.
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Affiliation(s)
- Paul A Roethle
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, USA
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Janssen D, Albert D, Jansen R, Müller R, Kalesse M. Chivosazol A – Aufklärung der absoluten und relativen Konfiguration. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605198] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Janssen D, Albert D, Jansen R, Müller R, Kalesse M. Chivosazole A—Elucidation of the Absolute and Relative Configuration. Angew Chem Int Ed Engl 2007; 46:4898-901. [PMID: 17506055 DOI: 10.1002/anie.200605198] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dominic Janssen
- Zentrum für Biomolekulare Wirkstoffe (BMWZ), Leibniz Universität Hannover, Schneiderberg 1B, 30167 Hannover, Germany
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Menche D, Hassfeld J, Steinmetz H, Huss M, Wieczorek H, Sasse F. The First Hydroxylated Archazolid from the Myxobacterium Cystobacter violaceus: Isolation, Structural Elucidation and V-ATPase Inhibition. J Antibiot (Tokyo) 2007; 60:328-31. [PMID: 17551213 DOI: 10.1038/ja.2007.43] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The novel macrocyclic polyketide, 10-hydroxymethyl-archazolid-7-O-beta-D-glucopyranoside (archazolid D), was obtained from the myxobacterium Cystobacter violaceus. The structure of this first hydroxylated archazolid was determined by spectroscopic analysis, in particular by HMBC, HMQC, and ROESY NMR investigations, and by degradation. This novel metabolite was evaluated for growth inhibition of murine connective tissue cells and V-ATPase inhibition in comparison to other known archazolids.
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Affiliation(s)
- Dirk Menche
- Helmholtz-Zentrum für Infektionsforschung GmbH, Medicinal Chemistry and Chemical Biology, Braunschweig, Germany.
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Affiliation(s)
- Dirk Menche
- Helmholtz-Zentrum für Infektionsforschung, Medicinal Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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Archazolid-7-O-β-D-glucopyranoside – Isolation, Structural Elucidation and Solution Conformation of a Novel V-ATPase Inhibitor from the MyxobacteriumCystobacter violaceus. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600912] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Menche D, Hassfeld J, Sasse F, Huss M, Wieczorek H. Design, synthesis, and biological evaluation of novel analogues of archazolid: A highly potent simplified V-ATPase inhibitor. Bioorg Med Chem Lett 2007; 17:1732-5. [PMID: 17239591 DOI: 10.1016/j.bmcl.2006.12.073] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 12/14/2006] [Accepted: 12/17/2006] [Indexed: 11/17/2022]
Abstract
Novel analogues of the V-ATPase inhibitors archazolid A and B with modifications of the free hydroxyl groups and the side chain were designed by molecular modeling, synthesized by derivatization of the parent natural product and evaluated for V-ATPase inhibition and growth inhibition of murine connective tissue cells.
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Affiliation(s)
- Dirk Menche
- Helmholtz-Zentrum für Infektionsforschung GmbH, Medizinische Chemie, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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