1
|
Kiganda I, Bogaerts J, Wieske LHE, Deyou T, Atilaw Y, Uwamariya C, Miah M, Said J, Ndakala A, Akala HM, Herrebout W, Trybala E, Bergström T, Yenesew A, Erdelyi M. Antiviral Rotenoids and Isoflavones Isolated from Millettia oblata ssp. teitensis. JOURNAL OF NATURAL PRODUCTS 2024; 87:1003-1012. [PMID: 38579352 PMCID: PMC11061832 DOI: 10.1021/acs.jnatprod.3c01288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024]
Abstract
Three new (1-3) and six known rotenoids (5-10), along with three known isoflavones (11-13), were isolated from the leaves of Millettia oblata ssp. teitensis. A new glycosylated isoflavone (4), four known isoflavones (14-18), and one known chalcone (19) were isolated from the root wood extract of the same plant. The structures were elucidated by NMR and mass spectrometric analyses. The absolute configuration of the chiral compounds was established by a comparison of experimental ECD and VCD data with those calculated for the possible stereoisomers. This is the first report on the use of VCD to assign the absolute configuration of rotenoids. The crude leaves and root wood extracts displayed anti-RSV (human respiratory syncytial virus) activity with IC50 values of 0.7 and 3.4 μg/mL, respectively. Compounds 6, 8, 10, 11, and 14 showed anti-RSV activity with IC50 values of 0.4-10 μM, while compound 3 exhibited anti-HRV-2 (human rhinovirus 2) activity with an IC50 of 4.2 μM. Most of the compounds showed low cytotoxicity for laryngeal carcinoma (HEp-2) cells; however compounds 3, 11, and 14 exhibited low cytotoxicity also in primary lung fibroblasts. This is the first report on rotenoids showing antiviral activity against RSV and HRV viruses.
Collapse
Affiliation(s)
- Ivan Kiganda
- Department
of Chemistry, University of Nairobi, P.O. Box 30197, 00100 Nairobi, Kenya
- Department
of Chemistry − BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Jonathan Bogaerts
- Department
of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Tsegaye Deyou
- Department
of Chemistry, Salale University, P.O. Box 245, QPVQ+6C7, Fitche, Ethiopia
| | - Yoseph Atilaw
- Department
of Chemistry − BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Colores Uwamariya
- Department
of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Masum Miah
- Department
of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Joanna Said
- Department
of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Albert Ndakala
- Department
of Chemistry, University of Nairobi, P.O. Box 30197, 00100 Nairobi, Kenya
| | - Hoseah M. Akala
- Walter
Reed Army Institute of Research - Africa (WRAIR-A), Kenya Medical Research Institute (KEMRI), P.O. Box 54, 40100 Kisumu, Kenya
| | - Wouter Herrebout
- Department
of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
| | - Edward Trybala
- Department
of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Tomas Bergström
- Department
of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska
Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
| | - Abiy Yenesew
- Department
of Chemistry, University of Nairobi, P.O. Box 30197, 00100 Nairobi, Kenya
| | - Mate Erdelyi
- Department
of Chemistry − BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| |
Collapse
|
2
|
Aerts R, Bogaerts J, Johannessen C, Herrebout WA. Vibrational Optical Activity Study of Four Antibiotic (Lipo)glycopeptides: Vancomycin, Oritavancin, Dalbavancin, and Teicoplanin. ACS OMEGA 2022; 7:43657-43664. [PMID: 36506196 PMCID: PMC9730478 DOI: 10.1021/acsomega.2c04584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
The antibiotic glycopeptide class, of which vancomycin is the original compound, has received due attention over the past few decades in search of antibiotics to overcome resistances developed by bacteria. Crucial for the understanding and further development of glycopeptides that possess desired antibacterial effects is the determination of their conformational behavior, as this sheds light on the mechanism of action of the compound. Among others, vibrational optical activity (VOA) techniques (vibrational circular dichroism and Raman optical activity) can be deployed for this, but the question remains to what extent these spectroscopic techniques can provide information concerning the molecular class under investigation. This contribution takes the last hurdle in the search for the capabilities of the VOA techniques in the conformational analysis of the antibiotic glycopeptide class by extending research that was previously conducted for vancomycin toward its three derivatives: oritavancin, dalbavancin, and teicoplanin. The principal information that can be drawn from VOA spectra is the conformation of the rigid cyclic parts of the glycopeptides and the aromatic rings that are part hereof. The addition or removal of carbohydrates does not induce noticeable VOA spectral responses, preventing the determination of the conformation they adopt.
Collapse
|
3
|
Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
Collapse
Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
| |
Collapse
|
4
|
Aerts R, Bogaerts J, Herrebout W, Johannessen C. Insights in the vibrational optical activity spectra of the antibiotic vancomycin in DMSO. Phys Chem Chem Phys 2022; 24:9619-9625. [PMID: 35403645 DOI: 10.1039/d2cp00746k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vibrational circular dichroism (VCD) and Raman optical activity (ROA) are two spectroscopic techniques that are sensitive towards the conformational behaviour of molecules, and are often complementary herein. In this work we pursue the determination of the conformational ensemble of the antibiotic glycopeptide vancomycin in DMSO through comparison of experimental and computational spectra, both for VCD and ROA. ROA is found to be highly suitable for the task, identifying an ensemble that strongly resembles the NMR conformation. In the case of VCD, however, a too high sensitivity of the intensities with respect to minor conformational changes hampers a reliable conformational analysis. Whence attempting to improve the match between the VCD experiment and calculations by any means - e.g., by inducing minor conformational changes or including solvent effects in the calculations - we show that there is the risk of going down the rabbit hole. In conclusion, this work contributes to the broader understanding of where, when and how VCD and ROA can be deployed as techniques for conformational analysis.
Collapse
Affiliation(s)
- Roy Aerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Jonathan Bogaerts
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium.
| |
Collapse
|
5
|
Bogaerts J, Aerts R, Vermeyen T, Johannessen C, Herrebout W, Batista JM. Tackling Stereochemistry in Drug Molecules with Vibrational Optical Activity. Pharmaceuticals (Basel) 2021; 14:877. [PMID: 34577577 PMCID: PMC8468215 DOI: 10.3390/ph14090877] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/29/2022] Open
Abstract
Chirality plays a crucial role in drug discovery and development. As a result, a significant number of commercially available drugs are structurally dissymmetric and enantiomerically pure. The determination of the exact 3D structure of drug candidates is, consequently, of paramount importance for the pharmaceutical industry in different stages of the discovery pipeline. Traditionally the assignment of the absolute configuration of druggable molecules has been carried out by means of X-ray crystallography. Nevertheless, not all molecules are suitable for single-crystal growing. Additionally, valuable information about the conformational dynamics of drug candidates is lost in the solid state. As an alternative, vibrational optical activity (VOA) methods have emerged as powerful tools to assess the stereochemistry of drug molecules directly in solution. These methods include vibrational circular dichroism (VCD) and Raman optical activity (ROA). Despite their potential, VCD and ROA are still unheard of to many organic and medicinal chemists. Therefore, the present review aims at highlighting the recent use of VOA methods for the assignment of the absolute configuration of chiral small-molecule drugs, as well as for the structural analysis of biologics of pharmaceutical interest. A brief introduction on VCD and ROA theory and the best experimental practices for using these methods will be provided along with selected representative examples over the last five years. As VCD and ROA are commonly used in combination with quantum calculations, some guidelines will also be presented for the reliable simulation of chiroptical spectra. Special attention will be paid to the complementarity of VCD and ROA to unambiguously assess the stereochemical properties of pharmaceuticals.
Collapse
Affiliation(s)
- Jonathan Bogaerts
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (R.A.); (T.V.); (C.J.); (W.H.)
| | - Roy Aerts
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (R.A.); (T.V.); (C.J.); (W.H.)
| | - Tom Vermeyen
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (R.A.); (T.V.); (C.J.); (W.H.)
- Department of Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Christian Johannessen
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (R.A.); (T.V.); (C.J.); (W.H.)
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (R.A.); (T.V.); (C.J.); (W.H.)
| | - Joao M. Batista
- Institute of Science and Technology, Federal University of Sao Paulo, Sao Jose dos Campos 12231-280, SP, Brazil
| |
Collapse
|