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Thompson T, Pewklang T, Piyanuch P, Wanichacheva N, Kamkaew A, Burgess K. A fluorescent electrophile for CLIPS: self indicating TrkB binders. Org Biomol Chem 2024; 22:506-512. [PMID: 38111346 PMCID: PMC10863675 DOI: 10.1039/d3ob01654d] [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] [Indexed: 12/20/2023]
Abstract
Combination of cysteine-containing peptides with electrophiles provides efficient access to cyclo-organopeptides. However, there are no routes to intrinsically fluorescent cyclo-organopeptides containing robust, brilliant fluorophores emitting at wavelengths longer than cellular autofluorescence. We show such fluorescent cyclo-organopeptides can be made via SNAr reactions of cysteine-containing peptides with a BODIPY system. Seven compounds of this type were prepared to test as probes; six contained peptide sequences corresponding to loop regions in brain-derived neurotrophic factor and neurotrophic factor 4 (BDNF and NT-4) which bind tropomyocin receptor kinase B (TrkB). Cellular assays in serum-free media indicated two of the six key compounds induced survival of HEK293 cells stably transfected with TrkB whereas a control did not. The two compounds inducing cell survival bound TrkB on those cells (Kd ∼40 and 47 nM), illustrating how intrinsically fluorescent cyclo-organopeptides can be assayed for quantifiable binding to surface receptors in cell membrane environments.
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Affiliation(s)
- Tye Thompson
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
| | - Thitima Pewklang
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Pornthip Piyanuch
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Nantanit Wanichacheva
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom 73000, Thailand
| | - Anyanee Kamkaew
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
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Vandborg B, Holroyd DL, Pukala T, Bruning JB. Production of recombinant human proliferating cellular nuclear antigen (PCNA) for structural and biophysical characterization. Protein Expr Purif 2023; 212:106353. [PMID: 37597793 DOI: 10.1016/j.pep.2023.106353] [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] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023]
Abstract
Human proliferating cell nuclear antigen (hPCNA) is a DNA replication processivity factor, which acts as a docking platform, allowing proteins to have access to the replication fork and increasing the affinity of DNA interacting proteins, making it critical for cell survival. The trimer forms a ring-shaped oligomer allowing DNA to pass through the middle and interacting proteins to dock on the outside of the ring. Without this structural formation, there is a loss of DNA replication and repair in the cell. Due to the location of subunit-subunit termini, the addition of a purification tag can hamper crystallography and biophysical experiments, as the trimer complex folding can be impeded. To avoid these complications, a tag-less, step-wise purification was implemented, which resulted in 17.6 mg from 2 L culture of pure hPCNA with a 260 nm/280 nm value of 0.43. The produced crystal structure reveals a correctly formed oligomer. The clear depletion of the tracer binding and probe protein interaction in a fluorescence polarisation competition-based assay demonstrates the purification method produces a protein structure with a functional binding site. This purification method presents a reliable and simple method for producing hPCNA for biophysical characterisation.
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Affiliation(s)
- B Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - D L Holroyd
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - T Pukala
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - J B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia; School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
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Vandborg BC, Horsfall AJ, Pederick JL, Abell AD, Bruning JB. Towards a High-Affinity Peptidomimetic Targeting Proliferating Cell Nuclear Antigen from Aspergillus fumigatus. J Fungi (Basel) 2023; 9:1098. [PMID: 37998903 PMCID: PMC10672205 DOI: 10.3390/jof9111098] [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: 10/11/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Invasive fungal infections (IFIs) are prevalent in immunocompromised patients. Due to alarming levels of increasing resistance in clinical settings, new drugs targeting the major fungal pathogen Aspergillus fumigatus are required. Attractive drug targets are those involved in essential processes like DNA replication, such as proliferating cell nuclear antigens (PCNAs). PCNA has been previously studied in cancer research and presents a viable target for antifungals. Human PCNA interacts with the p21 protein, outcompeting binding proteins to halt DNA replication. The affinity of p21 for hPCNA has been shown to outcompete other associating proteins, presenting an attractive scaffold for peptidomimetic design. p21 has no A. fumigatus homolog to our knowledge, yet our group has previously demonstrated that human p21 can interact with A. fumigatus PCNA (afumPCNA). This suggests that a p21-based inhibitor could be designed to outcompete the native binding partners of afumPCNA to inhibit fungal growth. Here, we present an investigation of extensive structure-activity relationships between designed p21-based peptides and afumPCNA and the first crystal structure of a p21 peptide bound to afumPCNA, demonstrating that the A. fumigatus replication model uses a PIP-box sequence as the method for binding to afumPCNA. These results inform the new optimized secondary structure design of a potential peptidomimetic inhibitor of afumPCNA.
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Affiliation(s)
- Bethiney C. Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Aimee J. Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide 5005, Australia
| | - Jordan L. Pederick
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Andrew D. Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide 5005, Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
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Horsfall AJ, Chav T, Pederick JL, Kikhtyak Z, Vandborg BC, Kowalczyk W, Scanlon DB, Tilley WD, Hickey TE, Abell AD, Bruning JB. Designing Fluorescent Nuclear Permeable Peptidomimetics to Target Proliferating Cell Nuclear Antigen. J Med Chem 2023; 66:10354-10363. [PMID: 37489955 DOI: 10.1021/acs.jmedchem.3c00471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Human proliferating cell nuclear antigen (PCNA) is a critical mediator of DNA replication and repair, acting as a docking platform for replication proteins. Disrupting these interactions with a peptidomimetic agent presents as a promising avenue to limit proliferation of cancerous cells. Here, a p21-derived peptide was employed as a starting scaffold to design a modular peptidomimetic that interacts with PCNA and is cellular and nuclear permeable. Ultimately, a peptidomimetic was produced which met these criteria, consisting of a fluorescein tag and SV40 nuclear localization signal conjugated to the N-terminus of a p21 macrocycle derivative. Attachment of the fluorescein tag was found to directly affect cellular uptake of the peptidomimetic, with fluorescein being requisite for nuclear permeability. This work provides an important step forward in the development of PCNA targeting peptidomimetics for use as anti-cancer agents or as cancer diagnostics.
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Affiliation(s)
- Aimee J Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Theresa Chav
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bethiney C Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Denis B Scanlon
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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