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Kong Y, Liu Y, Wang K, Wang T, Wang C, Ai B, Jia H, Pan G, Yin M, Xu Z. Confirmation of the stereochemistry of spiroviolene. Beilstein J Org Chem 2024; 20:852-858. [PMID: 38655555 PMCID: PMC11035986 DOI: 10.3762/bjoc.20.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
We confirm the previously revised stereochemistry of spiroviolene by X-ray crystallographically characterizing a hydrazone derivative of 9-oxospiroviolane, which is synthesized by hydroboration/oxidation of spiroviolene followed by oxidation of the resultant hydroxy group. An unexpected thermal boron migration occurred during the hydroboration process of spiroviolene that resulted in the production of a mixture of 1α-hydroxyspiroviolane, 9α- and 9β-hydroxyspiroviolane after oxidation. The assertion of the cis-orientation of the 19- and 20-methyl groups provided further support for the revised cyclization mechanism of spiroviolene.
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Affiliation(s)
- Yao Kong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Yuanning Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Kaibiao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Tao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Chen Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Ben Ai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Hongli Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yin
- School of Medicine, Yunnan University, 2 North Cui Hu Road, Kunming 650091, China
| | - Zhengren Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; Ningbo Institute of Marine Medicine, Peking University, Ningbo 315010, China
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2
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Taizoumbe KA, Goldfuss B, Dickschat JS. The Diterpenoid Substrate Analogue 19-nor-GGPP Reveals Pronounced Methyl Group Effects in Diterpene Cyclisations. Angew Chem Int Ed Engl 2024; 63:e202318375. [PMID: 38117607 DOI: 10.1002/anie.202318375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/22/2023]
Abstract
The substrate analogue 19-nor-geranylgeranyl diphosphate (19-nor-GGPP) was synthesised and incubated with 20 diterpene synthases, resulting in the formation of diterpenoids in all cases. A total of 23 different compounds were isolated from these enzyme reactions and structurally characterised, if possible including the experimental determination of absolute configurations through a stereoselective deuteration approach. In several cases the missing 19-Me group in the substrate analogue resulted in opening of completely new reaction paths towards compounds with novel skeletons. DFT calculations were applied to gain a deeper understanding of these observed methyl group effects in diterpene biosynthesis.
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Affiliation(s)
- Kizerbo A Taizoumbe
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department of Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jeroen S Dickschat
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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3
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Klucznik T, Syntrivanis LD, Baś S, Mikulak-Klucznik B, Moskal M, Szymkuć S, Mlynarski J, Gadina L, Beker W, Burke MD, Tiefenbacher K, Grzybowski BA. Computational prediction of complex cationic rearrangement outcomes. Nature 2024; 625:508-515. [PMID: 37967579 PMCID: PMC10864989 DOI: 10.1038/s41586-023-06854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.
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Affiliation(s)
- Tomasz Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Leonidas-Dimitrios Syntrivanis
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Basel, Basel, Switzerland.
| | - Sebastian Baś
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Barbara Mikulak-Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Louis Gadina
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Beker
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Martin D Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Bartosz A Grzybowski
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- IBS Center for Algorithmic and Robotized Synthesis, CARS, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
- Department of Chemistry, UNIST, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
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4
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Sato H. Theoretical Study of Natural Product Biosynthesis Using Computational Chemistry. Chem Pharm Bull (Tokyo) 2024; 72:524-528. [PMID: 38825452 DOI: 10.1248/cpb.c24-00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The biosynthetic pathways of natural products are complicated, and it is difficult to fully elucidate their details using experimental chemistry alone. In recent years, efforts have been made to elucidate the biosynthetic reaction mechanisms by combining computational and experimental methods. In this review, we will discuss the biosynthetic studies using computational chemistry for various terpene compounds such as cyclooctatin, sesterfisherol, quiannulatene, trichobrasilenol, asperterpenol, preasperterpenoid, spiroviolene, and mangicol.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
- PRESTO, Japan Science and Technology Agency
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5
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Gu B, Goldfuss B, Schnakenburg G, Dickschat JS. Subrutilane-A Hexacyclic Sesterterpene from Streptomyces subrutilus. Angew Chem Int Ed Engl 2023; 62:e202313789. [PMID: 37846897 DOI: 10.1002/anie.202313789] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
Mining of a terpene synthase from Streptomyces subrutilus resulted in the identification of the hexacyclic sesterterpene subrutilane, besides eight pentacyclic side products. Subrutilane represents the first case of a saturated sesterterpene hydrocarbon. Its structure, including the absolute configuration, was unambiguously determined through X-ray crystallographic analysis and stereoselective deuteration. The cyclisation mechanism to subrutilane and its side products was investigated in all detail by isotopic labelling experiments and DFT calculations. The subrutilane synthase (SrS) also converted (2Z)-GFPP into one major product. Additional compounds were obtained from the substrate analogues (7R)-6,7-dihydro-GFPP and (2Z,7R)-6,7-dihydro-GFPP with blocked reactivity at the C6-C7 bond. Interestingly, the early steps of the cyclisation cascade with (2Z)-GFPP and the saturated substrate analogues were analogous to those of GFPP, but then deviations from the natural cyclisation mode occur.
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Affiliation(s)
- Binbin Gu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department for Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Gregor Schnakenburg
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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6
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Nakano M, Gemma R, Sato H. Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B. Beilstein J Org Chem 2023; 19:1503-1510. [PMID: 37799177 PMCID: PMC10548252 DOI: 10.3762/bjoc.19.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023] Open
Abstract
Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.
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Affiliation(s)
- Moe Nakano
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Rintaro Gemma
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332–0012, Japan
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7
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Matsuyama T, Togashi K, Nakano M, Sato H, Uchiyama M. Revision of the Peniroquesine Biosynthetic Pathway by Retro-Biosynthetic Theoretical Analysis: Ring Strain Controls the Unique Carbocation Rearrangement Cascade. JACS AU 2023; 3:1596-1603. [PMID: 37388688 PMCID: PMC10301677 DOI: 10.1021/jacsau.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023]
Abstract
Peniroquesine, a sesterterpenoid featuring a unique 5/6/5/6/5 fused pentacyclic ring system, has been known for a long time, but its biosynthetic pathway/mechanism remains elusive. Based on isotopic labeling experiments, a plausible biosynthetic pathway to peniroquesines A-C and their derivatives was recently proposed, in which the characteristic peniroquesine-type 5/6/5/6/5 pentacyclic skeleton is synthesized from geranyl-farnesyl pyrophosphate (GFPP) via a complex concerted A/B/C-ring formation, repeated reverse-Wagner-Meerwein alkyl shifts, three successive secondary (2°) carbocation intermediates, and a highly distorted trans-fused bicyclo[4.2.1]nonane intermediate. However, our density functional theory calculations do not support this mechanism. By applying a retro-biosynthetic theoretical analysis strategy, we were able to find a preferred pathway for peniroquesine biosynthesis, involving a multistep carbocation cascade including triple skeletal rearrangements, trans-cis isomerization, and 1,3-H shift. This pathway/mechanism is in good agreement with all of the reported isotope-labeling results.
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Affiliation(s)
- Taro Matsuyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Togashi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Moe Nakano
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials (RISM), Shinshu
University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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8
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Sato H, Nakano M. Concertedness and Activation Energy Control by Distal Methyl Group during Ring Contraction/Expansion in Scalarane-Type Sesterterpenoid Biosynthesis. Chemistry 2023; 29:e202203076. [PMID: 36411271 DOI: 10.1002/chem.202203076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Salmahyritisol A, similan A, and hippospongide A, which are scalarane-type sesterterpenoids, feature 6/6/5/7/5 pentacyclic skeletons. Although their biosyntheses have been previously proposed to involve a unique skeletal rearrangement reaction, the detailed reaction mechanism remains unclear as none of the corresponding biosynthetic enzymes for this reaction have been reported. Herein, this skeletal rearrangement reaction was investigated using computational techniques, which revealed the following four key features: (i) the distal 24-Me substituent controls both the concertedness and activation energy of this transformation, (ii) enzymes are not responsible for the observed regioselectivity of C12-C20 bond formation, (iii) stereoselectivity is enzyme-regulated, and (iv) protonation is a key step in this skeletal rearrangement process. These new findings provide insight into the C-ring-contraction and D-ring-expansion mechanisms in scalarane-type sesterterpenoid biosyntheses.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Moe Nakano
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
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Sakamoto K, Sato H, Uchiyama M. DFT Study on the Biosynthesis of Asperterpenol and Preasperterpenoid Sesterterpenoids: Exclusion of Secondary Carbocation Intermediates and Origin of Structural Diversification. J Org Chem 2022; 87:6432-6437. [PMID: 35467870 DOI: 10.1021/acs.joc.2c00291] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic pathway to asperterpenol, a sesterterpenoid featuring a 6/6/8/5 tetracyclic ring system, was proposed to involve three secondary (2°) carbocation intermediates (B, D, and I), but it remains controversial whether or not these are viable. Further, the proposed 11/6/5 tricyclic intermediate C has the same "ChemDraw" structure as an intermediate in the biosynthesis of preasperterpenoid, which has a very different 5/7/(3)6/5 pentacyclic skeleton. Here, we present a detailed scrutiny of the asperterpenol/preasperterpenoid biosynthetic pathways based on comprehensive DFT calculations.
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Affiliation(s)
- Kyoka Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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