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Xu Z, Zhang X, Pal C, Rozners E, Callahan BP. Enzyme Fragment Complementation Driven by Nucleic Acid Hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572427. [PMID: 38187717 PMCID: PMC10769296 DOI: 10.1101/2023.12.19.572427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A modified protein fragment complementation assay has been designed and validated as a gain-of-signal biosensor for nucleic acid:nucleic acid interactions. The assay uses fragments of NanoBiT, the split luciferase reporter enzyme, that are esterified at their C-termini to steramers, sterol-modified oligodeoxynucleotides. The Drosophila hedgehog autoprocessing domain, DHhC, served as a self-cleaving catalyst for these bioconjugations. In the presence of ssDNA or RNA with segments complementary to the steramers and adjacent to one another, the two NanoBiT fragments productively associate, reconstituting NanoBiT enzyme activity. NanoBiT luminescence in samples containing nM ssDNA or RNA template exceeded background by 30-fold and as high as 120-fold depending on assay conditions. A unique feature of this detection system is the absence of a self-labeling domain in the NanoBiT bioconjugates. Eliminating that extraneous bulk broadens the detection range from short oligos to full-length mRNA.
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Affiliation(s)
- Zihan Xu
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Xiaoyu Zhang
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Chandan Pal
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
| | - Brian P. Callahan
- Department of Chemistry, Binghamton University, The State University of New York, 4400 Vestal Parkway East Binghamton, New York, 13902, USA
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2
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Ciulla DA, Xu Z, Pezzullo JL, Dranchak P, Wang C, Giner JL, Inglese J, Callahan BP. Paracatalytic induction: Subverting specificity in hedgehog protein autoprocessing with small molecules. Methods Enzymol 2023; 685:1-41. [PMID: 37245899 PMCID: PMC10294009 DOI: 10.1016/bs.mie.2023.03.001] [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] [Indexed: 05/30/2023]
Abstract
Paracatalytic inducers are antagonists that shift the specificity of biological catalysts, resulting in non-native transformations. In this Chapter we describe methods to discover paracatalytic inducers of Hedgehog (Hh) protein autoprocessing. Native autoprocessing uses cholesterol as a substrate nucleophile to assist in cleaving an internal peptide bond within a precursor form of Hh. This unusual reaction is brought about by HhC, an enzymatic domain that resides within the C-terminal region of Hh precursor proteins. Recently, we reported paracatalytic inducers as a novel class of Hh autoprocessing antagonists. These small molecules bind HhC and tilt the substrate specificity away from cholesterol in favor of solvent water. The resulting cholesterol-independent autoproteolysis of the Hh precursor generates a non-native Hh side product with substantially reduced biological signaling activity. Protocols are provided for in vitro FRET-based and in-cell bioluminescence assays to discover and characterize paracatalytic inducers of Drosophila and human hedgehog protein autoprocessing, respectively.
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Affiliation(s)
- Daniel A Ciulla
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY, United States
| | - John L Pezzullo
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - José-Luis Giner
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY, United States
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3
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Callahan BP, Xu Z. There's more to enzyme antagonism than inhibition. Bioorg Med Chem 2023; 82:117231. [PMID: 36893527 PMCID: PMC10228466 DOI: 10.1016/j.bmc.2023.117231] [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: 12/19/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
A native enzyme's usual assurance in recognizing their physiological substrate(s) at the ground state and on going to the transition state can be undermined by interactions with selected small molecule antagonists, leading to the generation of abnormal products. We classify this mode of enzyme antagonism resulting in the gain-of-nonnative-function as paracatalytic induction. Enzymes bound by paracatalytic inducers exhibit new or enhanced activity toward transformations that appear aberrant or erroneous. The enzyme/ paracatalytic inducer complex may take up native substrate but then bring about a transformation that is chemically distinct from the normal reaction. Alternatively, the enzyme / paracatalytic inducer complex may exhibit abnormal ground state selectivity, preferentially interacting with and transforming a molecule outside the physiological substrate scope. Paracatalytic inducers can be cytotoxic, while in other cases they divert enzyme activity toward transformations that appear adaptive and even therapeutically useful. In this perspective, we highlight two noteworthy examples from recent literature.
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Affiliation(s)
- Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY 13902, United States
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4
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Ciulla DA, Dranchak P, Pezzullo JL, Mancusi RA, Psaras AM, Rai G, Giner JL, Inglese J, Callahan BP. A cell-based bioluminescence reporter assay of human Sonic Hedgehog protein autoprocessing to identify inhibitors and activators. J Biol Chem 2022; 298:102705. [PMID: 36400200 PMCID: PMC9772569 DOI: 10.1016/j.jbc.2022.102705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
The Sonic Hedgehog (SHh) precursor protein undergoes biosynthetic autoprocessing to cleave off and covalently attach cholesterol to the SHh signaling ligand, a vital morphogen and oncogenic effector protein. Autoprocessing is self-catalyzed by SHhC, the SHh precursor's C-terminal enzymatic domain. A method to screen for small molecule regulators of this process may be of therapeutic value. Here, we describe the development and validation of the first cellular reporter to monitor human SHhC autoprocessing noninvasively in high-throughput compatible plates. The assay couples intracellular SHhC autoprocessing using endogenous cholesterol to the extracellular secretion of the bioluminescent nanoluciferase enzyme. We developed a WT SHhC reporter line for evaluating potential autoprocessing inhibitors by concentration response-dependent suppression of extracellular bioluminescence. Additionally, a conditional mutant SHhC (D46A) reporter line was developed for identifying potential autoprocessing activators by a concentration response-dependent gain of extracellular bioluminescence. The D46A mutation removes a conserved general base that is critical for the activation of the cholesterol substrate. Inducibility of the D46A reporter was established using a synthetic sterol, 2-α carboxy cholestanol, designed to bypass the defect through intramolecular general base catalysis. To facilitate direct nanoluciferase detection in the cell culture media of 1536-well plates, we designed a novel anionic phosphonylated coelenterazine, CLZ-2P, as the nanoluciferase substrate. This new reporter system offers a long-awaited resource for small molecule discovery for cancer and for developmental disorders where SHh ligand biosynthesis is dysregulated.
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Affiliation(s)
- Daniel A Ciulla
- Chemistry Department, Binghamton University, Binghamton, New York, USA
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - John L Pezzullo
- State University of New York, College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Rebecca A Mancusi
- Chemistry Department, Binghamton University, Binghamton, New York, USA
| | | | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - José-Luis Giner
- State University of New York, College of Environmental Science and Forestry, Syracuse, New York, USA.
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | - Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, New York, USA.
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5
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Tharappel AM, Li Z, Zhu YC, Wu X, Chaturvedi S, Zhang QY, Li H. Calcimycin Inhibits Cryptococcus neoformans In Vitro and In Vivo by Targeting the Prp8 Intein Splicing. ACS Infect Dis 2022; 8:1851-1868. [PMID: 35948057 PMCID: PMC9464717 DOI: 10.1021/acsinfecdis.2c00137] [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] [Indexed: 01/29/2023]
Abstract
Drug resistance is a significant concern in the treatment of diseases, including cryptococcosis caused by Cryptococcus neoformans (Cne) and Cryptococcus gattii (Cga). Alternative drug targets are necessary to overcome drug resistance before it attains a critical stage. Splicing of inteins from pro-protein precursors is crucial for activities of essential proteins hosting intein elements in many organisms, including human pathogens such as Cne and Cga. Through a high-throughput screening, we identified calcimycin (CMN) as a potent Prp8 intein splicing inhibitor with a minimum inhibitory concentration (MIC) of 1.5 μg/mL against the wild-type Cne-H99 (Cne-WT or Cne). In contrast, CMN inhibited the intein-less mutant strain (Cne-Mut) with a 16-fold higher MIC. Interestingly, Aspergillus fumigatus and a few Candida species were resistant to CMN. Further studies indicated that CMN reduced virulence factors such as urease activity, melanin production, and biofilm formation in Cne. CMN also inhibited Cne intracellular infection in macrophages. In a target-specific split nanoluciferase assay, the IC50 of CMN was 4.6 μg/mL. Binding of CMN to recombinant Prp8 intein was demonstrated by thermal shift assay and microscale thermophoresis. Treating Cne cells with CMN reduced intein splicing. CMN was fungistatic and showed a synergistic effect with the known antifungal drug amphotericin B. Finally, CMN treatment at 20 mg/kg body weight led to 60% reduction in lung fungal load in a cryptococcal pulmonary infection mouse model. Overall, CMN represents a potent antifungal with a novel mechanism of action to treat Cne and possibly Cga infections.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Yan Chun Zhu
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
| | - Sudha Chaturvedi
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson Arizona 85721-0207, United States
- Wadsworth Center, New York State Department of Health, Albany, New York 12208, United States
- The BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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6
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Wagner AG, Stagnitta RT, Xu Z, Pezzullo JL, Kandel N, Giner JL, Covey DF, Wang C, Callahan BP. Nanomolar, Noncovalent Antagonism of Hedgehog Cholesterolysis: Exception to the "Irreversibility Rule" for Protein Autoprocessing Inhibition. Biochemistry 2022; 61:1022-1028. [PMID: 34941260 PMCID: PMC9382716 DOI: 10.1021/acs.biochem.1c00697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hedgehog (Hh) signaling ligands undergo carboxy terminal sterylation through specialized autoprocessing, called cholesterolysis. Sterylation is brought about intramolecularly in a single turnover by an adjacent enzymatic domain, called HhC, which is found in precursor Hh proteins only. Previous attempts to identify antagonists of the intramolecular activity of HhC have yielded inhibitors that bind HhC irreversibly through covalent mechanisms, as is common for protein autoprocessing inhibitors. Here, we report an exception to the "irreversibility rule" for autoprocessing inhibition. Using a fluorescence resonance energy transfer-based activity assay for HhC, we screened a focused library of sterol-like analogues for noncovalent inhibitors and identified and validated four structurally related molecules, which were then used for structure-activity relationship studies. The most effective derivative, tBT-HBT, inhibits HhC noncovalently with an IC50 of 300 nM. An allosteric binding site for tBT-HBT, encompassing residues from the two subdomains of HhC, is suggested by kinetic analysis, mutagenesis studies, and photoaffinity labeling. The inhibitors described here resemble a family of noncovalent, allosteric inducers of HhC paracatalysis which we have described previously. The inhibition and the induction appear to be mediated by a shared allosteric site on HhC.
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Affiliation(s)
- Andrew G Wagner
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Robert T Stagnitta
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Zihan Xu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - John L Pezzullo
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, United States
| | - Nabin Kandel
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - José-Luis Giner
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, United States
| | - Douglas F Covey
- Department of Developmental Biology, Taylor Family Institute for Innovative Psychiatric Research, 660 South Euclid Avenue, St. Louis, Missouri 63110, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Brian P Callahan
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
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7
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Kandel N, Wang C. Hedgehog Autoprocessing: From Structural Mechanisms to Drug Discovery. Front Mol Biosci 2022; 9:900560. [PMID: 35669560 PMCID: PMC9163320 DOI: 10.3389/fmolb.2022.900560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Hedgehog (Hh) signaling plays pivotal roles in embryonic development. In adults, Hh signaling is mostly turned off but its abnormal activation is involved in many types of cancer. Hh signaling is initiated by the Hh ligand, generated from the Hh precursor by a specialized autocatalytic process called Hh autoprocessing. The Hh precursor consists of an N-terminal signaling domain (HhN) and a C-terminal autoprocessing domain (HhC). During Hh autoprocessing, the precursor is cleaved between N- and C-terminal domain followed by the covalent ligation of cholesterol to the last residue of HhN, which subsequently leads to the generation of Hh ligand for Hh signaling. Hh autoprocessing is at the origin of canonical Hh signaling and precedes all downstream signaling events. Mutations in the catalytic residues in HhC can lead to congenital defects such as holoprosencephaly (HPE). The aim of this review is to provide an in-depth summary of the progresses and challenges towards an atomic level understanding of the structural mechanisms of Hh autoprocessing. We also discuss drug discovery efforts to inhibit Hh autoprocessing as a new direction in cancer therapy.
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Affiliation(s)
- Nabin Kandel
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- *Correspondence: Chunyu Wang,
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8
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Tharappel AM, Li Z, Li H. Inteins as Drug Targets and Therapeutic Tools. Front Mol Biosci 2022; 9:821146. [PMID: 35211511 PMCID: PMC8861304 DOI: 10.3389/fmolb.2022.821146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Multidrug-resistant pathogens are of significant concern in recent years. Hence new antifungal and anti-bacterial drug targets are urgently needed before the situation goes beyond control. Inteins are polypeptides that self-splice from exteins without the need for cofactors or external energy, resulting in joining of extein fragments. Inteins are present in many organisms, including human pathogens such as Mycobacterium tuberculosis, Cryptococcus neoformans, C. gattii, and Aspergillus fumigatus. Because intein elements are not present in human genes, they are attractive drug targets to develop antifungals and antibiotics. Thus far, a few inhibitors of intein splicing have been reported. Metal-ions such as Zn2+ and Cu2+, and platinum-containing compound cisplatin inhibit intein splicing in M. tuberculosis and C. neoformans by binding to the active site cysteines. A small-molecule inhibitor 6G-318S and its derivative 6G-319S are found to inhibit intein splicing in C. neoformans and C. gattii with a MIC in nanomolar concentrations. Inteins have also been used in many other applications. Intein can be used in activating a protein inside a cell using small molecules. Moreover, split intein can be used to deliver large genes in experimental gene therapy and to kill selected species in a mixed population of microbes by taking advantage of the toxin-antitoxin system. Furthermore, split inteins are used in synthesizing cyclic peptides and in developing cell culture model to study infectious viruses including SARS-CoV-2 in the biosafety level (BSL) 2 facility. This mini-review discusses the recent research developments of inteins in drug discovery and therapeutic research.
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Affiliation(s)
- Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, United States
- BIO5 Institute, The University of Arizona, Tucson, AZ, United States
- *Correspondence: Hongmin Li,
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9
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Wall DA, Tarrant SP, Wang C, Mills KV, Lennon CW. Intein Inhibitors as Novel Antimicrobials: Protein Splicing in Human Pathogens, Screening Methods, and Off-Target Considerations. Front Mol Biosci 2021; 8:752824. [PMID: 34692773 PMCID: PMC8529194 DOI: 10.3389/fmolb.2021.752824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/24/2021] [Indexed: 01/20/2023] Open
Abstract
Protein splicing is a post-translational process by which an intervening polypeptide, or intein, catalyzes its own removal from the flanking polypeptides, or exteins, concomitant with extein ligation. Although inteins are highly abundant in the microbial world, including within several human pathogens, they are absent in the genomes of metazoans. As protein splicing is required to permit function of essential proteins within pathogens, inteins represent attractive antimicrobial targets. Here we review key proteins interrupted by inteins in pathogenic mycobacteria and fungi, exciting discoveries that provide proof of concept that intein activity can be inhibited and that this inhibition has an effect on the host organism's fitness, and bioanalytical methods that have been used to screen for intein activity. We also consider potential off-target inhibition of hedgehog signaling, given the similarity in structure and function of inteins and hedgehog autoprocessing domains.
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Affiliation(s)
- Diana A Wall
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Seanan P Tarrant
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross, Worcester, MA, United States
| | - Christopher W Lennon
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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10
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Abstract
Self-splicing proteins, called inteins, are present in many human pathogens, including the emerging fungal threats Cryptococcus neoformans (Cne) and Cryptococcus gattii (Cga), the causative agents of cryptococcosis. Inhibition of protein splicing in Cryptococcus sp. interferes with activity of the only intein-containing protein, Prp8, an essential intron splicing factor. Here, we screened a small-molecule library to find addititonal, potent inhibitors of the Cne Prp8 intein using a split-GFP splicing assay. This revealed the compound 6G-318S, with IC50 values in the low micromolar range in the split-GFP assay and in a complementary split-luciferase system. A fluoride derivative of the compound 6G-318S displayed improved cytotoxicity in human lung carcinoma cells, although there was a slight reduction in the inhibition of splicing. 6G-318S and its derivative inhibited splicing of the Cne Prp8 intein in vivo in Escherichia coli and in C. neoformans Moreover, the compounds repressed growth of WT C. neoformans and C. gattii In contrast, the inhibitors were less potent at inhibiting growth of the inteinless Candida albicans Drug resistance was observed when the Prp8 intein was overexpressed in C. neoformans, indicating specificity of this molecule toward the target. No off-target activity was observed, such as inhibition of serine/cysteine proteases. The inhibitors bound covalently to the Prp8 intein and binding was reduced when the active-site residue Cys1 was mutated. 6G-318S showed a synergistic effect with amphotericin B and additive to indifferent effects with a few other clinically used antimycotics. Overall, the identification of these small-molecule intein-splicing inhibitors opens up prospects for a new class of antifungals.
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11
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Banavali NK. The Mechanism of Cholesterol Modification of Hedgehog Ligand. J Comput Chem 2020; 41:520-527. [PMID: 31823413 DOI: 10.1002/jcc.26097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/06/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022]
Abstract
Hedgehog (Hh) proteins are important components of signal transduction pathways involved in animal development, and their defects are implicated in carcinogenesis. Their N-terminal domain (HhN) acts as a signaling ligand, and their C-terminal domain (HhC) performs an autocatalytic function of cleaving itself away, while adding a cholesterol moiety to HhN. HhC has two sub-domains: a hedgehog/intein (hint) domain that primarily performs the autocatalytic activity, and a sterol-recognition region (SRR) that binds to cholesterol and properly positions it with respect to HhN. The three-dimensional details of this autocatalytic mechanism remain unknown, as does the structure of the precursor Hh protein. In this study, a complete cholesterol-bound precursor form of the drosophila Hh precursor is modeled using known crystal structures of HhN and the hint domain, and a hypothesized similarity of SRR to an unrelated but similar-sized cholesterol binding protein. The restrained geometries and topology switching (RGATS) strategy is then used to predict atomic-detail pathways for the full autocatalytic reaction starting from the precursor and ending in a cholesterol-linked HhN domain and a cleaved HhC domain. The RGATS explicit solvent simulations indicate the roles of individual HhC residues in facilitating the reaction, which can be confirmed through mutational experiments. These simulations also provide plausible structural models for the N/S acyl transfer intermediate and the product states of this reaction. This study thus provides a good framework for future computational and experimental studies to develop a full structural and dynamic understanding of Hh autoprocessing. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Nilesh K Banavali
- Laboratory of Cellular and Molecular Basis of Diseases, Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, USA
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12
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Smith CJ, Wagner AG, Stagnitta RT, Xu Z, Pezzullo JL, Giner JL, Xie J, Covey DF, Wang C, Callahan BP. Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis. Biochemistry 2020; 59:736-741. [PMID: 32013401 PMCID: PMC7031038 DOI: 10.1021/acs.biochem.0c00013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hedgehog proteins, a family of vital cell signaling factors, are expressed in precursor form, which requires specialized autoprocessing, called cholesterolysis, for full biological activity. Cholesterolysis occurs in cis through the action of the precursor's C-terminal enzymatic domain, HhC. In this work, we describe HhC activator compounds (HACs), a novel class of noncovalent modulators that induce autoprocessing infidelity, diminishing native cholesterolysis in favor of precursor autoproteolysis, an otherwise minor and apparently nonphysiological side reaction. HAC-induced autoproteolysis generates hedgehog protein that is cholesterol free and hence signaling deficient. The most effective HAC has an AC50 of 9 μM, accelerates HhC autoproteolytic activity by 225-fold, and functions in the presence and absence of cholesterol, the native substrate. HACs join a rare class of "antagonists" that suppress native enzymatic activity by subverting mechanistic fidelity.
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Affiliation(s)
- Carl J Smith
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Andrew G Wagner
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Robert T Stagnitta
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - Zihan Xu
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
| | - John L Pezzullo
- Department of Chemistry , State University of New York College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - José-Luis Giner
- Department of Chemistry , State University of New York College of Environmental Science and Forestry , Syracuse , New York 13210 , United States
| | - Jian Xie
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Douglas F Covey
- Department of Developmental Biology , Taylor Family Institute for Innovative Psychiatric Research , 660 South Euclid Avenue , St. Louis , Missouri 63110 , United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , 110 8th Street , Troy , New York 12180 , United States
| | - Brian P Callahan
- Department of Chemistry , Binghamton University, State University of New York , 4400 Vestal Parkway East , Binghamton , New York 13902 , United States
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13
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Zhao J, Ciulla DA, Xie J, Wagner AG, Castillo DA, Zwarycz AS, Lin Z, Beadle S, Giner JL, Li Z, Li H, Banavali N, Callahan BP, Wang C. General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing. J Am Chem Soc 2019; 141:18380-18384. [PMID: 31682419 PMCID: PMC7106946 DOI: 10.1021/jacs.9b08914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hedgehog (Hh) autoprocessing converts Hh precursor protein to cholesterylated Hh ligand for downstream signaling. A conserved active-site aspartate residue, D46, plays a key catalytic role in Hh autoprocessing by serving as a general base to activate substrate cholesterol. Here we report that a charge-altering Asp-to-His mutant (D46H) expands native cholesterylation activity and retains active-site conformation. Native activity toward cholesterol was established for D46H in vitro using a continuous FRET-based autoprocessing assay and in cellulo with stable expression in human 293T cells. The catalytic efficiency of cholesterylation with D46H is similar to that with wild type (WT), with kmax/KM = 2.1 × 103 and 3.7 × 103 M-1 s-1, respectively, and an identical pKa = 5.8 is obtained for both residues by NMR. To our knowledge this is the first example where a general base substitution of an Asp for His preserves both the structure and activity as a general base. Surprisingly, D46H exhibits increased catalytic efficiency toward non-native substrates, especially coprostanol (>200-fold) and epicoprostanol (>300-fold). Expanded substrate tolerance is likely due to stabilization by H46 of the negatively charged tetrahedral intermediate using electrostatic interactions, which are less constrained by geometry than H-bond stabilization by D46. In addition to providing fundamental insights into Hh autoprocessing, our findings have important implications for protein engineering and enzyme design.
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Affiliation(s)
- Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Daniel A. Ciulla
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Jian Xie
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Andrew G. Wagner
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Drew A. Castillo
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Allison S. Zwarycz
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Zhongqian Lin
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Seth Beadle
- Department of Chemistry, State University of New York-ESF, Syracuse, New York 13210, United States
| | - José-Luis Giner
- Department of Chemistry, State University of New York-ESF, Syracuse, New York 13210, United States
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, United States
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12222, United States
| | - Nilesh Banavali
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12222, United States
| | - Brian P. Callahan
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, United States
| | - Chunyu Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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14
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Zhang X, Xu Z, Moumin DS, Ciulla DA, Owen TS, Mancusi RA, Giner JL, Wang C, Callahan BP. Protein-Nucleic Acid Conjugation with Sterol Linkers Using Hedgehog Autoprocessing. Bioconjug Chem 2019; 30:2799-2804. [PMID: 31600061 PMCID: PMC7045895 DOI: 10.1021/acs.bioconjchem.9b00550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Hedgehog (Hh) precursor proteins contain an autoprocessing domain called HhC whose native function is protein cleavage and C-terminal glycine sterylation. The transformation catalyzed by HhC occurs in cis from a precursor protein and exhibits wide tolerance toward both sterol and protein substrates. Here, we repurpose HhC as a 1:1 protein-nucleic acid ligase, with the sterol serving as a molecular linker. A procedure is described for preparing HhC-active sterylated DNA, called steramers, using aqueous compatible chemistry and commercial reagents. Steramers have KM values of 7-11 μM and reaction t1/2 values of ∼10 min. Modularity of the HhC/steramer method is demonstrated using four different proteins along with structured and unstructured sterylated nucleic acids. The resulting protein-DNA conjugates retain the native solution properties and biochemical function. Unlike self-tagging domains, HhC does not remain fused to the conjugate; rather, enzymatic activity is mechanistically coupled to conjugate release. That unique feature of HhC, coupled with efficient kinetics and substrate tolerance, may ease access and open new applications for these suprabiological chimeras.
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Affiliation(s)
- Xiaoyu Zhang
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Dina S. Moumin
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Daniel A. Ciulla
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Timothy S. Owen
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - Rebecca A. Mancusi
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
| | - José-Luis Giner
- Department of Chemistry, State University of New York - ESF, Syracuse, New York 13210, United States
| | - Chunyu Wang
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Brian P. Callahan
- Chemistry Department, Binghamton University, Binghamton, New York 13902, United States
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15
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Ciulla DA, Wagner AG, Xinyue L, Cooper CL, Jorgensen MT, Wang C, Goyal P, Banavali NK, Pezzullo J, Giner JL, Callahan BP. Sterol A-ring plasticity in hedgehog protein cholesterolysis supports a primitive substrate selectivity mechanism. Chem Commun (Camb) 2019; 55:1829-1832. [PMID: 30672911 PMCID: PMC6365966 DOI: 10.1039/c8cc09729a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cholesterolysis of Hedgehog family proteins couples endoproteolysis to protein C-terminal sterylation. The transformation is self-catalyzed by HhC, a partially characterized enzymatic domain found in precursor forms of Hedgehog. Here we explore spatial ambiguity in sterol recognition by HhC, using a trio of derivatives where the sterol A-ring is contracted, fused, or distorted. Sterylation assays indicate that these geometric variants react as substrates with relative activity: cholesterol, 1.000 > A-ring contracted, 0.100 > A-ring fused, 0.020 > A-ring distorted, 0.005. Experimental results and computational sterol docking into the first HhC homology model suggest a partially unstructured binding site with substrate recognition governed in large part by hydrophobic interactions.
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Affiliation(s)
- Daniel A. Ciulla
- Chemistry Department, Binghamton University, Binghamton, New York 13902, USA
| | - Andrew G. Wagner
- Chemistry Department, Binghamton University, Binghamton, New York 13902, USA
| | - Liu Xinyue
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Courtney L. Cooper
- Chemistry Department, Binghamton University, Binghamton, New York 13902, USA
| | | | - Chunyu Wang
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Puja Goyal
- Chemistry Department, Binghamton University, Binghamton, New York 13902, USA
| | - Nilesh K. Banavali
- NYS Department of Health, ESP C419B, Biggs Laboratory, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
| | - John Pezzullo
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, USA
| | - José-Luis Giner
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, USA
| | - Brian P. Callahan
- Chemistry Department, Binghamton University, Binghamton, New York 13902, USA
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16
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Ciulla DA, Jorgensen MT, Giner JL, Callahan BP. Chemical Bypass of General Base Catalysis in Hedgehog Protein Cholesterolysis Using a Hyper-Nucleophilic Substrate. J Am Chem Soc 2018; 140:916-918. [PMID: 28930454 PMCID: PMC6054137 DOI: 10.1021/jacs.7b05161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Proteins in the hedgehog family undergo self-catalyzed endoproteolysis involving nucleophilic attack by a molecule of cholesterol. Recently, a conserved aspartate residue (D303, or D46) of hedgehog was identified as the general base that activates cholesterol during this unusual autoprocessing event; mutation of the catalyzing functional group (D303A) reduces activity by >104-fold. Here we report near total rescue of this ostensibly dead general base mutant by a synthetic substrate, 3β-hydroperoxycholestane (3HPC) in which the sterol -OH group is replaced by the hyper nucleophilic -OOH group. Other hedgehog point mutants at D303, also unreactive with cholesterol, accepted 3HPC as a substrate with the rank order: WT > D303A ≈ D303N ≫ D303R, D303E. We attribute the revived activity with 3-HPC to the α-effect, where tandem electronegative atoms exhibit exceptionally high nucleophilicity despite relatively low basicity.
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Affiliation(s)
- Daniel A. Ciulla
- Chemistry Department, Binghamton University (SUNY), Binghamton, New York 13902, United States
| | | | - José-Luis Giner
- Department of Chemistry, SUNY-ESF, Syracuse, New York 13210, United States
| | - Brian P. Callahan
- Chemistry Department, Binghamton University (SUNY), Binghamton, New York 13902, United States
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17
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Xie J, Owen T, Xia K, Callahan B, Wang C. A Single Aspartate Coordinates Two Catalytic Steps in Hedgehog Autoprocessing. J Am Chem Soc 2016; 138:10806-9. [PMID: 27529645 PMCID: PMC5589136 DOI: 10.1021/jacs.6b06928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hedgehog (Hh) signaling is driven by the cholesterol-modified Hh ligand, generated by autoprocessing of Hh precursor protein. Two steps in Hh autoprocessing, N-S acyl shift and transesterification, must be coupled for efficient Hh cholesteroylation and downstream signal transduction. In the present study, we show that a conserved aspartate residue, D46 of the Hh autoprocessing domain, coordinates these two catalytic steps. Mutagenesis demonstrated that D46 suppresses non-native Hh precursor autoprocessing and is indispensable for transesterification with cholesterol. NMR measurements indicated that D46 has a pKa of 5.6, ∼2 units above the expected pKa of aspartate, due to a hydrogen-bond between protonated D46 and a catalytic cysteine residue. However, the deprotonated form of D46 side chain is also essential, because a D46N mutation cannot mediate cholesteroylation. On the basis of these data, we propose that the proton shuttling of D46 side chain mechanistically couples the two steps of Hh cholesteroylation.
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Affiliation(s)
- Jian Xie
- Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Timothy Owen
- Department of Chemistry, Binghamton University, State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Brian Callahan
- Department of Chemistry, Binghamton University, State University of New York, 4400 Vestal Parkway East, Binghamton, New York 13902, United States
| | - Chunyu Wang
- Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
- Department of Biological Sciences, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
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18
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Bordeau BM, Ciulla DA, Callahan BP. Hedgehog Proteins Consume Steroidal CYP17A1 Antagonists: Potential Therapeutic Significance in Advanced Prostate Cancer. ChemMedChem 2016; 11:1983-6. [PMID: 27435344 DOI: 10.1002/cmdc.201600238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/29/2016] [Indexed: 12/21/2022]
Abstract
Abiraterone, a potent inhibitor of the human enzyme CYP17A1 (cytochrome P450c17), provides a last line of defense against ectopic androgenesis in advanced prostate cancer. Herein we report an unprecedented off-target interaction between abiraterone and oncogenic hedgehog proteins. Our experiments indicate that abiraterone and its structural congener, galeterone, can replace cholesterol as a substrate in a specialized biosynthetic event of hedgehog proteins, known as cholesterolysis. The off-target reaction generates covalent hedgehog-drug conjugates. Cell-based reporter assays indicate that these conjugates activate hedgehog signaling when present in the low nanomolar range. Because hedgehog signaling is implicated in prostate cancer progression, and abiraterone is administered to treat advanced stages of the disease, this off-target interaction may have therapeutic significance.
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Affiliation(s)
- Brandon M Bordeau
- Chemistry Department, State University of New York at Binghamton, 4400 Vestal Parkway East, Binghamton, NY, 13902, USA
| | - Daniel A Ciulla
- Chemistry Department, State University of New York at Binghamton, 4400 Vestal Parkway East, Binghamton, NY, 13902, USA
| | - Brian P Callahan
- Chemistry Department, State University of New York at Binghamton, 4400 Vestal Parkway East, Binghamton, NY, 13902, USA.
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19
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Callahan BP, Wang C. Hedgehog Cholesterolysis: Specialized Gatekeeper to Oncogenic Signaling. Cancers (Basel) 2015; 7:2037-53. [PMID: 26473928 PMCID: PMC4695875 DOI: 10.3390/cancers7040875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
Discussions of therapeutic suppression of hedgehog (Hh) signaling almost exclusively focus on receptor antagonism; however, hedgehog's biosynthesis represents a unique and potentially targetable aspect of this oncogenic signaling pathway. Here, we review a key biosynthetic step called cholesterolysis from the perspectives of structure/function and small molecule inhibition. Cholesterolysis, also called cholesteroylation, generates cholesterol-modified Hh ligand via autoprocessing of a hedgehog precursor protein. Post-translational modification by cholesterol appears to be restricted to proteins in the hedgehog family. The transformation is essential for Hh biological activity and upstream of signaling events. Despite its decisive role in generating ligand, cholesterolysis remains conspicuously unexplored as a therapeutic target.
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Affiliation(s)
- Brian P Callahan
- Chemistry Department, Binghamton University 4400 Vestal Parkway East, Binghamton, NY 13902, USA.
| | - Chunyu Wang
- Biology Department, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
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