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Huynh TH, Bae ES, Heo BE, Lee J, An JS, Kwon Y, Nam SJ, Oh KB, Jang J, Lee SK, Oh DC. Tandocyclinones A and B, Ether Bridged C-Glycosyl Benz[ a]anthracenes from an Intertidal Zone Streptomyces sp. Mar Drugs 2023; 21:500. [PMID: 37755113 PMCID: PMC10533038 DOI: 10.3390/md21090500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
Two new proton-deficient metabolites, tandocyclinones A and B (1 and 2), were discovered via the chemical profiling of the Streptomyces sp. strain TDH03, which was isolated from a marine sediment sample collected from the intertidal mudflat in Tando Port, the Republic of Korea. The structures of 1 and 2 were elucidated as new ether-bridged C-glycosyl benz[a]anthracenes by using a combination of spectroscopic analyses of ultraviolet (UV) and mass spectrometry (MS) data, along with nuclear magnetic resonance (NMR) spectra, which were acquired in tetrahydrofuran (THF)-d8 selected after an extensive search for a solvent, resulting in mostly observable exchangeable protons in the 1H NMR spectrum. Their configurations were successfully assigned by applying a J-based configuration analysis, rotating-frame Overhauser enhancement spectroscopy (ROESY) NMR correlations, chemical derivatization methods based on NMR (a modified version of Mosher's method) and circular dichroism (CD) (Snatzke's method using Mo2(OAc)4-induced CD), as well as quantum-mechanics-based computational methods, to calculate the electronic circular dichroism (ECD). Tandocyclinones A and B (1 and 2) were found to have weak antifungal activity against Trichophyton mentagrophytes IFM40996 with an MIC value of 128 μg/mL (244 and 265 μM for 1 and 2, respectively). A further biological evaluation revealed that tandocyclinone A (1) displayed inhibitory activity against Mycobacterium avium (MIC50 = 40.8 μM) and antiproliferative activity against SNU638 and HCT116 cancer cells, with IC50 values of 31.9 µM and 49.4 µM, respectively.
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Affiliation(s)
- Thanh-Hau Huynh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (T.-H.H.); (E.S.B.); (J.S.A.); (S.K.L.)
| | - Eun Seo Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (T.-H.H.); (E.S.B.); (J.S.A.); (S.K.L.)
| | - Bo Eun Heo
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (B.E.H.); (J.J.)
| | - Jayho Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences and Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea; (J.L.); (K.-B.O.)
| | - Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (T.-H.H.); (E.S.B.); (J.S.A.); (S.K.L.)
| | - Yun Kwon
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea;
| | - Ki-Bong Oh
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences and Natural Products Research Institute, Seoul National University, Seoul 08826, Republic of Korea; (J.L.); (K.-B.O.)
| | - Jichan Jang
- Division of Life Science, Department of Bio & Medical Big Data (BK21 Four Program), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (B.E.H.); (J.J.)
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (T.-H.H.); (E.S.B.); (J.S.A.); (S.K.L.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; (T.-H.H.); (E.S.B.); (J.S.A.); (S.K.L.)
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2
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DiBello M, Healy AR, Nikolayevskiy H, Xu Z, Herzon SB. Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls. Acc Chem Res 2023; 56:1656-1668. [PMID: 37220079 PMCID: PMC10468810 DOI: 10.1021/acs.accounts.3c00183] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.
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Affiliation(s)
- Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alan R Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Herman Nikolayevskiy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Zhi Xu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Departments of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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Wang Y, Fan A, Cohen RD, Dal Poggetto G, Huang Z, Yang H, Martin GE, Sherer EC, Reibarkh M, Wang X. Unequivocal identification of two-bond heteronuclear correlations in natural products at nanomole scale by i-HMBC. Nat Commun 2023; 14:1842. [PMID: 37012241 PMCID: PMC10070429 DOI: 10.1038/s41467-023-37289-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
HMBC is an essential NMR experiment for determining multiple bond heteronuclear correlations in small to medium-sized organic molecules, including natural products, yet its major limitation is the inability to differentiate two-bond from longer-range correlations. There have been several attempts to address this issue, but all reported approaches suffer various drawbacks, such as restricted utility and poor sensitivity. Here we present a sensitive and universal methodology to identify two-bond HMBC correlations using isotope shifts, referred to as i-HMBC (isotope shift detection HMBC). Experimental utility was demonstrated at the sub-milligram / nanomole scale with only a few hours of acquisition time required for structure elucidation of several complex proton-deficient natural products, which could not be fully elucidated by conventional 2D NMR experiments. Because i-HMBC overcomes the key limitation of HMBC without significant reduction in sensitivity or performance, i-HMBC can be used as a complement to HMBC when unambiguous identifications of two-bond correlations are needed.
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Affiliation(s)
- Yunyi Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Ryan D Cohen
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | | | - Zheng Huang
- Process Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Haifeng Yang
- Process Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Gary E Martin
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, 07079, USA
| | - Edward C Sherer
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA.
| | - Xiao Wang
- Analytical Research & Development, Merck & Co. Inc, Rahway, NJ, 07065, USA.
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Abstract
Glycans, carbohydrate molecules in the realm of biology, are present as biomedically important glycoconjugates and a characteristic aspect is that their structures in many instances are branched. In determining the primary structure of a glycan, the sugar components including the absolute configuration and ring form, anomeric configuration, linkage(s), sequence, and substituents should be elucidated. Solution state NMR spectroscopy offers a unique opportunity to resolve all these aspects at atomic resolution. During the last two decades, advancement of both NMR experiments and spectrometer hardware have made it possible to unravel carbohydrate structure more efficiently. These developments applicable to glycans include, inter alia, NMR experiments that reduce spectral overlap, use selective excitations, record tilted projections of multidimensional spectra, acquire spectra by multiple receivers, utilize polarization by fast-pulsing techniques, concatenate pulse-sequence modules to acquire several spectra in a single measurement, acquire pure shift correlated spectra devoid of scalar couplings, employ stable isotope labeling to efficiently obtain homo- and/or heteronuclear correlations, as well as those that rely on dipolar cross-correlated interactions for sequential information. Refined computer programs for NMR spin simulation and chemical shift prediction aid the structural elucidation of glycans, which are notorious for their limited spectral dispersion. Hardware developments include cryogenically cold probes and dynamic nuclear polarization techniques, both resulting in enhanced sensitivity as well as ultrahigh field NMR spectrometers with a 1H NMR resonance frequency higher than 1 GHz, thus improving resolution of resonances. Taken together, the developments have made and will in the future make it possible to elucidate carbohydrate structure in great detail, thereby forming the basis for understanding of how glycans interact with other molecules.
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Affiliation(s)
- Carolina Fontana
- Departamento
de QuÃmica del Litoral, CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden,
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Bence Farkas L, Timári I, Kövér KE, Sørensen OW. Four-in-one: HSQC, HSQC-TOCSY (or H2BC), TOCSY, and enhanced HMBC spectra integrated into a single NO Relaxation Delay (NORD) NMR experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 343:107297. [PMID: 36174396 DOI: 10.1016/j.jmr.2022.107297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
The NMR pulse sequence design strategy of NORD (NO Relaxation Delay) is extended to design of two new three-module experiments, NORD {HMBC}-{HSQC-TOCSY}-{TOCSY} and NORD {HMBC}-{2BOB}-{TOCSY}, each delivering four spectra - HMBC, HSQC, TOCSY, and either HSQC-TOCSY or H2BC. Compared to individual recording of these spectra particularly the sensitivity of the least sensitive module, HMBC, is enhanced by designing the homonuclear TOCSY module to allow buildup of magnetization pertinent to HMBC during its execution. Effectively, the sensitivity of the heteronuclear modules is boosted at the expense of the inherently much higher TOCSY sensitivity, thus resulting in a significant saving in spectrometer time.
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Affiliation(s)
- László Bence Farkas
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - István Timári
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Hungary.
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6
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Nagy TM, Kövér KE, Sørensen OW. NORD: NO Relaxation Delay NMR Spectroscopy. Angew Chem Int Ed Engl 2021; 60:13587-13590. [PMID: 33783935 PMCID: PMC8252012 DOI: 10.1002/anie.202102487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 12/16/2022]
Abstract
The novel concept of NORD (NO relaxation delay) NMR spectroscopy is introduced. The idea is to design concatenated experiments in a way that the magnetization used in the first relaxes toward equilibrium during the second and vice versa, thus saving instrument time. Applications include complete well-resolved 1 H-1 H and 1 H-13 C one-bond and long-range correlation maps of an 80 mM solution of a trisaccharide recorded in less than two minutes and hydrocortisone with extensive spectral overlap.
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Affiliation(s)
- Tamás Milán Nagy
- Department of Inorganic and Analytical ChemistryUniversity of DebrecenEgyetem tér 14032DebrecenHungary
| | - Katalin E. Kövér
- Department of Inorganic and Analytical ChemistryUniversity of DebrecenEgyetem tér 14032DebrecenHungary
- MTA-DE Molecular Recognition and Interaction Research GroupUniversity of DebrecenHungary
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7
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Nagy TM, Kövér KE, Sørensen OW. NORD: NO Relaxation Delay NMR Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tamás Milán Nagy
- Department of Inorganic and Analytical Chemistry University of Debrecen Egyetem tér 1 4032 Debrecen Hungary
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry University of Debrecen Egyetem tér 1 4032 Debrecen Hungary
- MTA-DE Molecular Recognition and Interaction Research Group University of Debrecen Hungary
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Nagy TM, Kövér KE, Sørensen OW. Double and adiabatic BANGO for concatenating two NMR experiments relying on the same pool of magnetization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 316:106767. [PMID: 32540729 DOI: 10.1016/j.jmr.2020.106767] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/20/2020] [Accepted: 06/01/2020] [Indexed: 05/22/2023]
Abstract
It is shown how the same pool of magnetization can be tapped twice in two different concatenations of three experiments into a single pulse sequence with only one relaxation delay. This is accomplished by using the BANGO pulse sequence element twice for independent rotations of 1H magnetization attached or not attached to 13C and it includes a refinement of BANGO with an adiabatic 13C inversion pulse resulting in improved tolerance to a spread in 1JCH coupling constants that translates directly into improved sensitivity of the modular experiment relying on 1H magnetization attached to 13C. The two new pulse sequences are SEA XLOC-HMBC-H2OBC/2BOB and SEA XLOC(ZQ)-SEA XLOC(2Q)-H2OBC/2BOB which both represent a rapid route to complete heteronuclear one-bond and long-range JCH correlation maps for small molecules, as is demonstrated on ibuprofen and prednisolone.
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Affiliation(s)
- Tamás Milán Nagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Hungary.
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Gyöngyösi T, Kövér KE, Sørensen OW. Resolution Enhancement in SEA XLOC for Heteronuclear NMR Long-Range Correlation. ChemistryOpen 2019; 8:1048-1051. [PMID: 31463169 PMCID: PMC6709521 DOI: 10.1002/open.201900136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/26/2019] [Indexed: 11/18/2022] Open
Abstract
It is shown how the resolution in SEA XLOC NMR spectra for distinguishing between heteronuclear two- and three-bond correlations for all 13C multiplicities can be improved by a modified experiment delivering absorptive profiles in the indirect dimension. The method is demonstrated with applications to ibuprofen and strychnine.
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Affiliation(s)
- Tamás Gyöngyösi
- Department of Inorganic and Analytical ChemistryUniversity of DebrecenEgyetem tér 1H-4032DebrecenHungary
| | - Katalin E. Kövér
- Department of Inorganic and Analytical ChemistryUniversity of DebrecenEgyetem tér 1H-4032DebrecenHungary
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Nagy TM, Gyöngyösi T, Kövér KE, Sørensen OW. BANGO SEA XLOC/HMBC–H2OBC: complete heteronuclear correlation within minutes from one NMR pulse sequence. Chem Commun (Camb) 2019; 55:12208-12211. [DOI: 10.1039/c9cc06253j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Novel NMR experiments, BANGO SEA XLOC–H2OBC or BANGO HMBC–H2OBC, deliver complete heteronuclear correlations and assignments on a time scale of minutes on small molecules.
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Affiliation(s)
- Tamás Milán Nagy
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- H-4032 Debrecen
- Hungary
| | - Tamás Gyöngyösi
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- H-4032 Debrecen
- Hungary
- MTA-DE Molecular Recognition and Interaction Research Group
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry
- University of Debrecen
- H-4032 Debrecen
- Hungary
- MTA-DE Molecular Recognition and Interaction Research Group
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