1
|
Chen HW, Wu XY, Zhao ZY, Huang ZQ, Lei XS, Yang GX, Li J, Xiong J, Hu JF. Terricoxanthones A-E, unprecedented dihydropyran-containing dimeric xanthones from the endophytic fungus Neurospora terricola HDF-Br-2 associated with the vulnerable conifer Pseudotsuga gaussenii. PHYTOCHEMISTRY 2024; 219:113963. [PMID: 38171409 DOI: 10.1016/j.phytochem.2023.113963] [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: 10/15/2023] [Revised: 12/27/2023] [Accepted: 12/30/2023] [Indexed: 01/05/2024]
Abstract
An investigation on the secondary metabolites from a rice culture broth of the endophytic fungus Neurospora terricola HDF-Br-2 derived from the vulnerable conifer Pseudotsuga gaussenii led to the isolation and characterization of 34 structurally diverse polyketides (1-34). Seven of them are previously undescribed, including five unprecedented dihydropyran-containing (terricoxanthones A-E, 1-5, resp.) and one rare tetrahydrofuran-containing (terricoxanthone F, 6) dimeric xanthones. The structures were elucidated by spectroscopic methods and single-crystal X-ray diffraction analyses. Terricoxanthones each were obtained as a racemic mixture. Their plausible biosynthetic relationships were briefly proposed. Compounds 6, aspergillusone A (8), and alatinone (27) displayed considerable inhibition against Candida albicans with MIC values of 8-16 μg/mL. 4-Hydroxyvertixanthone (12) and 27 exhibited significant inhibitory activities against Staphylococcus aureus, with MIC values of 4-8 μg/mL. Furthermore, compounds 8 and 27 could disrupt biofilm of S. aureus and C. albicans at 128 μg/mL. The findings not only extend the skeletons of xanthone dimers and contribute to the diversity of metabolites of endophytes associated with the endangered Chinese conifer P. gaussenii, but could further reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics.
Collapse
Affiliation(s)
- Hao-Wei Chen
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xi-Ying Wu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ze-Yu Zhao
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Zi-Qi Huang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xin-Sheng Lei
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Guo-Xun Yang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Jiyang Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| | - Jin-Feng Hu
- School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, PR China; Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| |
Collapse
|
2
|
Lander A, Kong Y, Jin Y, Wu C, Luk LYP. Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery. ACS BIO & MED CHEM AU 2024; 4:68-76. [PMID: 38404743 PMCID: PMC10885103 DOI: 10.1021/acsbiomedchemau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 02/27/2024]
Abstract
Many cell-surface receptors are promising targets for chemical synthesis because of their critical roles in disease development. This synthetic approach enables investigations by racemic protein crystallography and ligand discovery by mirror-image methodologies. However, due to their complex nature, the chemical synthesis of a receptor can be a significant challenge. Here, we describe the chemical synthesis and folding of a central, cysteine-rich domain of the cell-surface receptor tumor necrosis factor 1 which is integral to binding of the cytokine TNF-α, namely, TNFR-1 CRD2. Racemic protein crystallography at 1.4 Å confirmed that the native binding conformation was preserved, and TNFR-1 CRD2 maintained its capacity to bind to TNF-α (KD ≈ 7 nM). Encouraged by this discovery, we carried out mirror-image phage display using the enantiomeric receptor mimic and identified a d-peptide ligand for TNFR-1 CRD2 (KD = 1 μM). This work demonstrated that cysteine-rich domains, including the central domains, can be chemically synthesized and used as mimics for investigations.
Collapse
Affiliation(s)
- Alexander
J. Lander
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Yifu Kong
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Yi Jin
- Manchester
Institute of Biotechnology, University of
Manchester, Manchester M1 7DN, U.K.
| | - Chuanliu Wu
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Louis Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| |
Collapse
|
3
|
Batista JM, Nicu VP. Simplified and enhanced VCD analysis of cyclic peptides guided by artificial intelligence. Phys Chem Chem Phys 2023; 25:22111-22116. [PMID: 37560904 DOI: 10.1039/d3cp01986a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Cyclic peptides are privileged structures in medicinal chemistry; however, their solution-state structure characterization is difficult. Vibrational circular dichroism (VCD) spectroscopy is a powerful alternative to NMR, but requires challenging calculations. We present a VCD approach guided by a genetic algorithm, which is simple, more effective, and has a higher conformer resolution.
Collapse
Affiliation(s)
- João M Batista
- Federal University of São Paulo, Institute of Science and Technology, R. Talim 330, 12231-280, São José dos Campos-SP, Brazil.
| | | |
Collapse
|
4
|
Chen HW, Jiang CX, Ma GL, Wu XY, Jiang W, Li J, Zang Y, Li J, Xiong J, Hu JF. Unprecedented spirodioxynaphthalenes from the endophytic fungus Phyllosticta ligustricola HDF-L-2 derived from the endangered conifer Pseudotsuga gaussenii. PHYTOCHEMISTRY 2023; 211:113687. [PMID: 37105348 DOI: 10.1016/j.phytochem.2023.113687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Four undescribed palmarumycin-type spirodioxynaphthalenes (phyligustricins A-D) and a known biogenetic precursor (palmarumycin BG1) were isolated from a solid fermentation of Phyllosticta ligustricola HDF-L-2, an endophyte associated with the endangered Chinese conifer Pseudotsuga gaussenii. The structures were elucidated by spectroscopic methods, single-crystal X-ray diffraction analyses, and electronic circular dichroism calculations. Both phyligustricins A and B have an unprecedented spirodioxynaphthalene-derived skeleton containing an extra 4H-furo [3,2-c]pyran-4-one moiety, while phyligustricins C and D are p-hydroxy-phenethyl substituted spirodioxynaphthalenes. The plausible biosynthetic relationships of the isolates were briefly proposed. Phyligustricins C and D and palmarumycin BG1 showed considerable antibacterial activity against Staphylococcus aureus, each with an MIC value of 16 μg/mL. Palmarumycin BG1 displayed significant inhibitory effects against ACL and ACC1, with IC50 values of 1.60 and 8.00 μM, respectively.
Collapse
Affiliation(s)
- Hao-Wei Chen
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Chun-Xiao Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, PR China
| | - Guang-Lei Ma
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Xi-Ying Wu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Wei Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Jiyang Li
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, 201203, PR China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China.
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai, 201203, PR China; School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, PR China.
| |
Collapse
|
5
|
Tyler TJ, Durek T, Craik DJ. Native and Engineered Cyclic Disulfide-Rich Peptides as Drug Leads. Molecules 2023; 28:molecules28073189. [PMID: 37049950 PMCID: PMC10096437 DOI: 10.3390/molecules28073189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Bioactive peptides are a highly abundant and diverse group of molecules that exhibit a wide range of structural and functional variation. Despite their immense therapeutic potential, bioactive peptides have been traditionally perceived as poor drug candidates, largely due to intrinsic shortcomings that reflect their endogenous heritage, i.e., short biological half-lives and poor cell permeability. In this review, we examine the utility of molecular engineering to insert bioactive sequences into constrained scaffolds with desired pharmaceutical properties. Applying lessons learnt from nature, we focus on molecular grafting of cyclic disulfide-rich scaffolds (naturally derived or engineered), shown to be intrinsically stable and amenable to sequence modifications, and their utility as privileged frameworks in drug design.
Collapse
Affiliation(s)
- Tristan J. Tyler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
6
|
Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
Collapse
Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| |
Collapse
|
7
|
Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [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: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
Collapse
Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| |
Collapse
|
8
|
Saemi Yokomichi MA, Leite Silva HR, Eivazian Vianna Nogueira Brandao L, Festozo Vicente E, Batista Junior JM. Conformational preferences induced by cyclization in orbitides: a vibrational CD study. Org Biomol Chem 2022; 20:1306-1314. [DOI: 10.1039/d1ob02170b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orbitides are bioactive head-to-tail natural cyclic peptides from plant species. Their bioactivity is intrinsically related to the main conformations adopted in solution, whose correct characterization represents an important bottleneck for...
Collapse
|
9
|
Payne CD, Fisher MF, Mylne JS, Rosengren KJ. Structural Characterization of the PawL-Derived Peptide Family, an Ancient Subfamily of Orbitides. JOURNAL OF NATURAL PRODUCTS 2021; 84:2914-2922. [PMID: 34672199 DOI: 10.1021/acs.jnatprod.1c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plants are an excellent source of bioactive peptides, often with disulfide bonds and/or a cyclic backbone. While focus has predominantly been directed at disulfide-rich peptides, a large family of small, cyclic plant peptides lacking disulfide bonds, known as orbitides, has been relatively ignored. A recently discovered subfamily of orbitides is the PawL-derived peptides (PLPs), produced during the maturation of precursors for seed storage albumins. Although their evolutionary origins have been dated, in-depth exploration of the family's structural characteristics and potential bioactivities remains to be conducted. Here we present an extensive and systematic characterization of the PLP family. Nine PLPs were chosen and prepared by solid phase peptide synthesis. Their structural features were studied using solution NMR spectroscopy, and seven were found to possess regions of backbone order. Ordered regions consist of β-turns, with some PLPs adopting two well-defined β-turns within sequences as short as seven residues, which are largely the result of side chain interactions. Our data highlight that the sequence diversity within this family results in equally diverse structures. None of these nine PLPs showed antibacterial or antifungal activity.
Collapse
Affiliation(s)
- Colton D Payne
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark F Fisher
- School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Joshua S Mylne
- School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
10
|
Fisher MF, Payne CD, Rosengren KJ, Mylne JS. An Orbitide from Ratibida columnifera Seed Containing 16 Amino Acid Residues. JOURNAL OF NATURAL PRODUCTS 2019; 82:2152-2158. [PMID: 31392883 DOI: 10.1021/acs.jnatprod.9b00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cyclic peptides are abundant in plants and have attracted interest due to their bioactivity and potential as drug scaffolds. Orbitides are head-to-tail cyclic peptides that are ribosomally synthesized, post-translationally modified, and lack disulfide bonds. All known orbitides contain 5-12 amino acid residues. Here we describe PLP-53, a novel orbitide from the seed of Ratibida columnifera. PLP-53 consists of 16 amino acids, four residues larger than any known orbitide. NMR structural studies showed that, compared to previously characterized orbitides, PLP-53 is more flexible and, under the studied conditions, did not adopt a single ordered conformation based on analysis of NOEs and chemical shifts.
Collapse
Affiliation(s)
- Mark F Fisher
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| | - Colton D Payne
- Faculty of Medicine, School of Biomedical Sciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - K Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Joshua S Mylne
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| |
Collapse
|
11
|
Wang CK, Craik DJ. Toward Structure Determination of Disulfide-Rich Peptides Using Chemical Shift-Based Methods. J Phys Chem B 2019; 123:1903-1912. [PMID: 30730741 DOI: 10.1021/acs.jpcb.8b10649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide-rich peptides are a class of molecules for which NMR spectroscopy has been the primary tool for structural characterization. Here, we explore whether the process can be achieved by using structural information encoded in chemical shifts. We examine (i) a representative set of five cyclic disulfide-rich peptides that have high-resolution NMR and X-ray structures and (ii) a larger set of 100 disulfide-rich peptides from the PDB. Accuracy of the calculated structures was dependent on the methods used for searching through conformational space and for identifying native conformations. Although Hα chemical shifts could be predicted reasonably well using SHIFTX, agreement between predicted and experimental chemical shifts was sufficient for identifying native conformations for only some peptides in the representative set. Combining chemical shift data with the secondary structure information and potential energy calculations improved the ability to identify native conformations. Additional use of sparse distance restraints or homology information to restrict the search space also improved the resolution of the calculated structures. This study demonstrates that abbreviated methods have potential for elucidation of peptide structures to high resolution and further optimization of these methods, e.g., improvement in chemical shift prediction accuracy, will likely help transition these methods into the mainstream of disulfide-rich peptide structural biology.
Collapse
Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| |
Collapse
|