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Liu M, Karuso P, Feng Y, Kellenberger E, Liu F, Wang C, Quinn RJ. Is it time for artificial intelligence to predict the function of natural products based on 2D-structure. MEDCHEMCOMM 2019; 10:1667-1677. [PMID: 31803392 PMCID: PMC6836574 DOI: 10.1039/c9md00128j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022]
Abstract
Currently, there is no established technique that allows the function of a compound produced by nature to be predicted by looking at its 2-dimensional chemical structure. One of chemistry's grand challenges: to find a function for every known metabolite. We explore the opportunity for Artificial Intelligence to provide rationale interrogation of metabolites to predict their function.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery , Griffith University , Brisbane , Qld 4111 , Australia . ; Tel: +61 7 3735 6006
| | - Peter Karuso
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery , Griffith University , Brisbane , Qld 4111 , Australia . ; Tel: +61 7 3735 6006
| | - Esther Kellenberger
- Laboratory of Therapeutic Innovation , Medalis Drug Discovery Center , University of Strasbourg , Illkirch , France
| | - Fei Liu
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Can Wang
- School of Information and Communication Technology , Griffith University , Gold Coast campus , Qld 4222 , Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery , Griffith University , Brisbane , Qld 4111 , Australia . ; Tel: +61 7 3735 6006
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2
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Biogenetic Relationships of Bioactive Sponge Merotriterpenoids. Mar Drugs 2017; 15:md15090285. [PMID: 28891968 PMCID: PMC5618424 DOI: 10.3390/md15090285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 02/01/2023] Open
Abstract
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied. In this review, an in depth structural analysis of sponge merotriterpenoids, including the adociasulfate family of kinesin motor protein inhibitors, provides insight into their biosynthesis. Several key structural features provide clues to the relationships between compounds. All adociasulfates appear to be derived from only four different hydroquinone hexaprenyl diphosphate precursors, each varying in the number and position of epoxidations. Proton-initiated cyclization of these precursors can lead to all carbon skeletons observed amongst sponge merotriterpenoids. Consideration of the enzymes involved in the proposed biosynthetic route suggests a bacterial source, and a hypothetical gene cluster was constructed that may facilitate discovery of the authentic pathway from the sponge metagenome. A similar rationale can be extended to other sponge meroterpenoids, for which no biosynthetic pathways have yet been identified.
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Moosmann P, Ueoka R, Grauso L, Mangoni A, Morinaka BI, Gugger M, Piel J. Cyanobacterial ent
-Sterol-Like Natural Products from a Deviated Ubiquinone Pathway. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Philipp Moosmann
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Reiko Ueoka
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Laura Grauso
- Dipartimento di Farmacia Università di Napoli Federico II; Università di Napoli Federico II; via D. Montesano 49 80131 Napoli Italy
- Current address: Stazione Zoologica Anton Dohrn; Villa Comunale 80121 Napoli Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia Università di Napoli Federico II; Università di Napoli Federico II; via D. Montesano 49 80131 Napoli Italy
| | - Brandon I. Morinaka
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Muriel Gugger
- Institut Pasteur; Collection des Cyanobactéries; Département de Microbiologie; 75015 Paris France
| | - Jörn Piel
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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Moosmann P, Ueoka R, Grauso L, Mangoni A, Morinaka BI, Gugger M, Piel J. Cyanobacterial ent
-Sterol-Like Natural Products from a Deviated Ubiquinone Pathway. Angew Chem Int Ed Engl 2017; 56:4987-4990. [DOI: 10.1002/anie.201611617] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/19/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Philipp Moosmann
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Reiko Ueoka
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Laura Grauso
- Dipartimento di Farmacia Università di Napoli Federico II; Università di Napoli Federico II; via D. Montesano 49 80131 Napoli Italy
- Current address: Stazione Zoologica Anton Dohrn; Villa Comunale 80121 Napoli Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia Università di Napoli Federico II; Università di Napoli Federico II; via D. Montesano 49 80131 Napoli Italy
| | - Brandon I. Morinaka
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Muriel Gugger
- Institut Pasteur; Collection des Cyanobactéries; Département de Microbiologie; 75015 Paris France
| | - Jörn Piel
- Institut für Mikrobiologie; Eidgenössiche Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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Czajkowska-Szczykowska D, Morzycki JW, Wojtkielewicz A. Pd-catalyzed steroid reactions. Steroids 2015; 97:13-44. [PMID: 25173819 DOI: 10.1016/j.steroids.2014.07.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/07/2014] [Accepted: 07/30/2014] [Indexed: 01/17/2023]
Abstract
We review the most important achievements of the last decade in the field of steroid synthesis in the presence of palladium catalysts. Various palladium-catalyzed cross-coupling reactions, including Heck, Suzuki, Stille, Sonogashira, Negishi and others, are exemplified with steroid transformations.
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Affiliation(s)
| | - Jacek W Morzycki
- Institute of Chemistry, University of Białystok, Hurtowa 1, 15-399 Białystok, Poland.
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Kulcitki V, Harghel P, Ungur N. Unusual cyclic terpenoids with terminal pendant prenyl moieties: from occurrence to synthesis. Nat Prod Rep 2015; 31:1686-720. [PMID: 25118808 DOI: 10.1039/c4np00081a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The paper reviews the known examples of cyclic terpenoids produced from open chain polyenic precursors by an "unusual" biosynthetic pathway, involving selective electrophilic attack on an internal double bond followed by cyclization. The resulting compounds possess cyclic backbones with pendant terminal prenyl groups. Synthetic approaches applied for the synthesis of such specifically functionalized compounds are also discussed, as well as biological activity of reported representatives.
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Affiliation(s)
- Veaceslav Kulcitki
- Institute of Chemistry, Moldova Academy of Sciences, Academiei str. 3, MD-2028, Chişinău, Republic of Moldova.
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Single-molecule inhibition of human kinesin by adociasulfate-13 and -14 from the sponge Cladocroce aculeata. Proc Natl Acad Sci U S A 2013; 110:18880-5. [PMID: 24191039 DOI: 10.1073/pnas.1314132110] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two merotriterpenoid hydroquinone sulfates designated adociasulfate-13 (1) and adociasulfate-14 (2) were purified from Cladocroce aculeata (Chalinidae) along with adociasulfate-8. All three compounds were found to inhibit microtubule-stimulated ATPase activity of kinesin at 15 µM by blocking both the binding of microtubules and the processive motion of kinesin along microtubules. These findings directly show that substitution of the 5'-sulfate in 1 for a glycolic acid moiety in 2 maintains kinesin inhibition. Nomarski imaging and bead diffusion assays in the presence of adociasulfates showed no signs of either free-floating or bead-bound adociasulfate aggregates. Single-molecule biophysical experiments also suggest that inhibition of kinesin activity does not involve adociasulfate aggregation. Furthermore, both mitotic and nonmitotic kinesins are inhibited by adociasulfates to a significantly different extent. We also report evidence that microtubule binding of nonkinesin microtubule binding domains may be affected by adociasulfates.
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Meroterpenes from marine invertebrates: structures, occurrence, and ecological implications. Mar Drugs 2013; 11:1602-43. [PMID: 23685889 PMCID: PMC3707164 DOI: 10.3390/md11051602] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 04/07/2013] [Accepted: 05/07/2013] [Indexed: 11/29/2022] Open
Abstract
Meroterpenes are widely distributed among marine organisms; they are particularly abundant within brown algae, but other important sources include microorganisms and invertebrates. In the present review the structures and bioactivities of meroterpenes from marine invertebrates, mainly sponges and tunicates, are summarized. More than 300 molecules, often complex and with unique skeletons originating from intra- and inter-molecular cyclizations, and/or rearrangements, are illustrated. The reported syntheses are mentioned. The issue of a potential microbial link to their biosynthesis is also shortly outlined.
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Bioactive Marine Prenylated Quinones/Quinols. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-444-53836-9.00023-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Good JAD, Skoufias DA, Kozielski F. Elucidating the functionality of kinesins: an overview of small molecule inhibitors. Semin Cell Dev Biol 2011; 22:935-45. [PMID: 22001111 DOI: 10.1016/j.semcdb.2011.09.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 09/30/2011] [Indexed: 12/19/2022]
Abstract
Kinesin motor proteins are ubiquitously involved in multiple fundamental cellular processes, coordinating transport and mediating changes to cellular architecture. Thus, specific small molecule kinesin inhibitors can shed new light on the functions of kinesins and the dynamic roles in which they participate. Here we review the range of known inhibitors, their key characteristics, and specificity, and discuss their potential suitability for chemical genetics as starting points to further investigate complex kinesin-mediated processes.
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Affiliation(s)
- James A D Good
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, Scotland, UK.
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Nakao Y, Fusetani N. Enzyme inhibitors from marine invertebrates. JOURNAL OF NATURAL PRODUCTS 2007; 70:689-710. [PMID: 17362037 DOI: 10.1021/np060600x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Marine invertebrates are rich sources of small molecules with unique chemical skeletons and potent bioactivities. Historically, such compounds were discovered mainly through the use of assays for phenotype-oriented activities, such as cytotoxicity or antimicrobial effects. More recently, target-oriented searches for bioactive substances, as exemplified by enzyme inhibitors, have become much more common, given a growing need for small-molecule inhibitors essential for studies of complex processes at the interface of chemistry and biology. In this review, selected enzyme inhibitors from marine invertebrates are presented.
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Affiliation(s)
- Yoichi Nakao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Brier S, Carletti E, DeBonis S, Hewat E, Lemaire D, Kozielski F. The Marine Natural Product Adociasulfate-2 as a Tool To Identify the MT-Binding Region of Kinesins. Biochemistry 2006; 45:15644-53. [PMID: 17176086 DOI: 10.1021/bi061395n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kinesins are molecular motors that transport cargo along microtubules (MTs). To move forward the motor must attach to the MT in a defined orientation and detach from it in a process that is driven by ATP hydrolysis. The knowledge of the motor-MT interface is essential for a detailed understanding of how kinesins move along MTs and how they are related to other molecular motors such as myosins or dyneins. We have used the marine natural product adociasulfate-2 (AS-2), previously identified as a MT-competitive inhibitor of conventional kinesin, to infer the secondary structure elements forming the MT interface of two human mitotic kinesins, namely, CENP-E and Eg5. AS-2 inhibits both basal and MT-stimulated ATPase activities of CENP-E (IC50 of 8.6 and 1.3 microM, respectively) and Eg5 (IC50 of 3.5 and 5.3 microM, respectively) and is a MT-competitive inhibitor of CENP-E with a Ki of 0.35 microM. Binding of AS-2 to CENP-E also stimulates the ADP release from the nucleotide-binding pocket. AS-2 is a nonspecific kinesin inhibitor targeting several superfamily members including KHC, MPP1, MKLP1, RabK6, KIFC1, KIFC3, CENP-E, and Eg5. By measuring hydrogen/deuterium exchange with mass spectrometry we have shown that the formation of the CENP-E/AS-2 complex decreases the solvent accessibility of three neighboring peptides on the same face of CENP-E. We deduce that this is the site of MT attachment and conclude that loop L11, helix alpha4, loop L12, helix alpha5, loop L8, and strand beta5 constitute the main MT interface of the CENP-E motor domain. Similarly for Eg5/AS-2, a region of increased solvent accessibility locates the MT interface of Eg5.
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Affiliation(s)
- Sébastien Brier
- Laboratoire de Spectrométrie de Masse des Protéines (LSMP), Institut de Biologie Structurale (CEA-CNRS-UJF), 41, rue Jules Horowitz, 38027 Grenoble Cedex 1, France.
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Abstract
Abstract17-Thienyl-and 17-benzo[b]thienyl-3-hydroxyestra-1,3,5(10),16-tetraenes were synthesized by either sequential or one-pot Suzuki cross-coupling and Wittig olefination reactions. At 160 °C, heteroaryl substituted steroids were observed to undergo thermal intramolecular cyclization to produce E-ring heteroareno-annelated estranes.
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West LM, Faulkner DJ. Hexaprenoid hydroquinones from the sponge Haliclona (aka Adocia) sp. JOURNAL OF NATURAL PRODUCTS 2006; 69:1001-4. [PMID: 16872132 DOI: 10.1021/np050459c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Three new hexaprenoid hydroquinones, adociaquinol (1), adociasulfate 11 (2), and adociasulfate 12 (3), together with the known adociasulfates 2, 4, and 6, were isolated from the marine sponge Haliclona (aka Adocia) sp. The structures of these compounds were elucidated by interpretation of spectroscopic data.
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Affiliation(s)
- Lyndon M West
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0212F, USA.
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Prinsep MR. Sulfur-Containing Natural Products from Marine Invertebrates. BIOACTIVE NATURAL PRODUCTS (PART I) 2003. [DOI: 10.1016/s1572-5995(03)80151-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Blackburn CL, Faulkner D. Adociasulfate 10, A New Merohexaprenoid Sulfate from the Sponge Haliclona (aka Adocia) sp. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00786-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bogenstätter M, Limberg A, Overman LE, Tomasi AL. Enantioselective Total Synthesis of the Kinesin Motor Protein Inhibitor Adociasulfate 1. J Am Chem Soc 1999. [DOI: 10.1021/ja9934091] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Bogenstätter
- Department of Chemistry, 516 Rowland Hall University of California, Irvine Irvine, California 92697-2025
| | - Anja Limberg
- Department of Chemistry, 516 Rowland Hall University of California, Irvine Irvine, California 92697-2025
| | - Larry E. Overman
- Department of Chemistry, 516 Rowland Hall University of California, Irvine Irvine, California 92697-2025
| | - Adam L. Tomasi
- Department of Chemistry, 516 Rowland Hall University of California, Irvine Irvine, California 92697-2025
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