1
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Kim YY, Gryder BE, Sinniah R, Peach ML, Shern JF, Abdelmaksoud A, Pomella S, Woldemichael GM, Stanton BZ, Milewski D, Barchi JJ, Schneekloth JS, Chari R, Kowalczyk JT, Shenoy SR, Evans JR, Song YK, Wang C, Wen X, Chou HC, Gangalapudi V, Esposito D, Jones J, Procter L, O'Neill M, Jenkins LM, Tarasova NI, Wei JS, McMahon JB, O'Keefe BR, Hawley RG, Khan J. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nat Commun 2024; 15:1703. [PMID: 38402212 PMCID: PMC10894237 DOI: 10.1038/s41467-024-45902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.
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Affiliation(s)
| | - Berkley E Gryder
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Girma M Woldemichael
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Nationwide Children's Hospital, Center for Childhood Cancer Research, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, FNLCR, Frederick, MD, USA
| | | | - Shilpa R Shenoy
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Jason R Evans
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | | | - Chaoyu Wang
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Jane Jones
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Lauren Procter
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, FNLCR, NIH, Frederick, MD, USA
| | | | | | - Jun S Wei
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Barry R O'Keefe
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | - Robert G Hawley
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Anatomy and Cell Biology, George Washington University, Washington, DC, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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2
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Barchi JJ, De Meo C, Mootoo DR. Editorial: Tribute to Professor B. Fraser Reid. Carbohydr Res 2023; 526:108795. [PMID: 37002031 DOI: 10.1016/j.carres.2023.108795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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3
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Barchi JJ, Strain CN. The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation. Front Mol Biosci 2023; 10:1117850. [PMID: 36845552 PMCID: PMC9950641 DOI: 10.3389/fmolb.2023.1117850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.
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Affiliation(s)
| | - Caitlin N. Strain
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute at Frederick, Frederick, MD, United States
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4
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Mondal UK, Barchi JJ. Isolipoic acid-linked gold nanoparticles bearing the thomsen friedenreich tumor-associated carbohydrate antigen: Stability and in vitro studies. Front Chem 2022; 10:1002146. [PMID: 36300019 PMCID: PMC9588967 DOI: 10.3389/fchem.2022.1002146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
We have previously prepared gold nanoparticles (AuNPs) bearing the Thomsen-Friedenreich antigen disaccharide (TFag), a pan-carcinoma, Tumor-Associated Carbohydrate Antigen (TACA), as tools for various assays and biological applications. Conjugation to AuNPs typically involves the use of thiols due to the affinity of sulfur for the gold surface of the nanoparticle. While a use of a single thiol-containing ligand bound to the gold surface is standard practice, several studies have shown that ligands bearing multiple thiols can enhance the strength of the conjugation in a nearly linear fashion. (R)-(+)-α-Lipoic acid (LA), a naturally occurring disulfide-containing organic acid that is used as a cofactor in many enzymatic reactions, has been used as a linker to conjugate various molecules to AuNPs through its branched di-thiol system to enhance nanoparticle stability. We sought to use a similar system to increase nanoparticle stability that was devoid of the chiral center in (R)-(+)-α-lipoic acid. Isolipoic acid, an isomer of LA, where the exocyclic pentanoic acid chain is shifted by one carbon on the dithiolane ring to produce an achiral acid, was thought to act similarly as LA without the risk of any contaminating (L)-(−) isomer. We synthesized AuNPs with ligands of both serine and threonine glycoamino acids bearing the TFag linked to isolipoic acid and examined their stability under various conditions. In addition, these particles were shown to bind to Galectin-3 and inhibit the interaction of Galectin-3 with a protein displaying copies of the TFag. These agents should prove useful in the design of potential antimetastatic therapeutics that would benefit from achiral linkers that are geometrically linear and achiral.
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5
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Barchi JJ. Glycoconjugate Nanoparticle-Based Systems in Cancer Immunotherapy: Novel Designs and Recent Updates. Front Immunol 2022; 13:852147. [PMID: 35432351 PMCID: PMC9006936 DOI: 10.3389/fimmu.2022.852147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 11/15/2022] Open
Abstract
For many years, cell-surface glycans (in particular, Tumor-Associated Carbohydrate Antigens, TACAs) have been the target of both passive and active anticancer immunotherapeutic design. Recent advances in immunotherapy as a treatment for a variety of malignancies has revolutionized anti-tumor treatment regimens. Checkpoint inhibitors, Chimeric Antigen Receptor T-cells, Oncolytic virus therapy, monoclonal antibodies and vaccines have been developed and many approvals have led to remarkable outcomes in a subset of patients. However, many of these therapies are very selective for specific patient populations and hence the search for improved therapeutics and refinement of techniques for delivery are ongoing and fervent research areas. Most of these agents are directed at protein/peptide epitopes, but glycans–based targets are gaining in popularity, and a handful of approved immunotherapies owe their activity to oligosaccharide targets. In addition, nanotechnology and nanoparticle-derived systems can help improve the delivery of these agents to specific organs and cell types based on tumor-selective approaches. This review will first outline some of the historical beginnings of this research area and subsequently concentrate on the last 5 years of work. Based on the progress in therapeutic design, predictions can be made as to what the future holds for increasing the percentage of positive patient outcomes for optimized systems.
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Affiliation(s)
- Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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6
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Trabbic KR, Kleski KA, Barchi JJ. A Stable Gold Nanoparticle-Based Vaccine for the Targeted Delivery of Tumor-Associated Glycopeptide Antigens. ACS Bio Med Chem Au 2021; 1:31-43. [PMID: 34927166 PMCID: PMC8675876 DOI: 10.1021/acsbiomedchemau.1c00021] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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We
have developed a novel antigen delivery system based on polysaccharide-coated
gold nanoparticles (AuNPs) targeted to antigen-presenting cells (APCs)
expressing Dectin-1. AuNPs were synthesized de novo using yeast-derived
β-1,3-glucans (B13G) as the reductant and passivating agent
in a microwave-catalyzed procedure, yielding highly uniform and serum-stable
particles. These were further functionalized with both a peptide and
a specific glycosylated form from the tandem repeat sequence of mucin
4 (MUC4), a glycoprotein overexpressed in pancreatic tumors. The glycosylated
sequence contained the Thomsen–Friedenreich disaccharide, a
pan-carcinoma, tumor-associated carbohydrate antigen (TACA), which
has been a traditional target for antitumor vaccine design. These
motifs were prepared with a cathepsin B protease cleavage site (Gly-Phe-Leu-Gly),
loaded on the B13G-coated particles, and these constructs were examined
for Dectin-1 binding, APC processing, and presentation in a model
in vitro system and for immune responses in mice. We showed that these
particles elicit strong in vivo immune responses through the production
of both high-titer antibodies and priming of antigen-recognizing T-cells.
Further examination showed that a favorable antitumor balance of expressed
cytokines was generated, with limited expression of immunosuppressive
Il-10. This system is modular in that any range of antigens can be
conjugated to our particles and efficiently delivered to APCs expressing
Dectin-1.
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Affiliation(s)
- Kevin R Trabbic
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Kristopher A Kleski
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
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7
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Trabbic KR, Whalen K, Abarca-Heideman K, Xia L, Temme JS, Edmondson EF, Gildersleeve JC, Barchi JJ. A Tumor-Selective Monoclonal Antibody from Immunization with a Tumor-Associated Mucin Glycopeptide. Sci Rep 2019; 9:5662. [PMID: 30952968 PMCID: PMC6450958 DOI: 10.1038/s41598-019-42076-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
We have previously studied the generation of immune responses after vaccination with tumor-associated carbohydrate antigen (TACA)-containing glycopeptides from the tandem repeat (TR) sequence of MUC4, an aberrantly expressed mucin in pancreatic adenocarcinomas. A specific lead antigen from that study containing the Thomsen-Friedenreich TACA disaccharide facilitated the pursuit of a monoclonal antibody to this synthetic hapten. Initial evaluation of polyclonal antiserum resulting from immunization with a KLH conjugate of this glycopeptide into rabbits showed high titer antibodies by ELISA assays, and selective immunoreactivity with MUC4+ cells by western blot and flow cytometry techniques. Glycan microarray analysis showed an intriguing binding pattern where the antiserum showed near complete specificity for MUC4 TR glycopeptides and peptides, relative to all components on the array. Tissue staining also showed distinct tumor specificity to pancreatic tumor tissue in relation to normal pancreatic tissue, with a preference for more aggressive tumor foci. Based on this data, we produced a monoclonal antibody whose binding and reactivity profile was similar to that of the polyclonal serum, with the added benefit of being more specific for the N-terminal glycosylated peptide domain. This epitope represents a novel immunogen to potentially develop diagnostic antibodies or immunotherapies against various MUC4-positive cancers.
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Affiliation(s)
- Kevin R Trabbic
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | | | - Li Xia
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - J Sebastian Temme
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Elijah F Edmondson
- Pathology and Histotechnology Lab, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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8
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Siddiqui M, Ambre S, Keay SK, Rhyne JM, Zhang CO, Barchi JJ. Glycoamino Acid Analogues of the Thomsen-Friedenreich Tumor-Associated Carbohydrate Antigen: Synthesis and Evaluation of Novel Antiproliferative Factor Glycopeptides. ACS Omega 2017; 2:5618-5632. [PMID: 28983523 PMCID: PMC5623948 DOI: 10.1021/acsomega.7b01018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 08/24/2017] [Indexed: 05/21/2023]
Abstract
Glycoamino acid analogues of the Thomsen-Friedenreich antigen disaccharide, where the 4' and 4″ hydroxyl groups were substituted with fluorine or hydrogen, were synthesized and incorporated into the asialylated antiproliferative factor (as-APF), a biologically active form of APF, a glycopeptide found in the urine of patients with interstitial cystitis. Various strategies were employed to incorporate the fluorine atom at the 4-positions of either the galactose or N-acetylgalactosamine unit of the disaccharide antigen, based on stereochemistry and reactivity. These glycopeptides were evaluated in antiproliferative assays on both primary normal bladder epithelial cells and T24 bladder carcinoma cells. Unlike many previously published substitutions to APF, mono-4'-fluorination of the GalNAc residue did not affect the activity, whereas fluoro-derivatives of the galactose 4″-position or both 4' and 4″ hydroxyls showed a reduced potency relative to the monosubstituted GalNAc derivative. A fourth compound where the 4″ position of galactose was deoxygenated showed a lower potency than the parent and monosubstituted compounds. These results suggest that specific substitutions in the sugar moieties in the APF can be tolerated, and the glycomimetic design of APF analogues can include fluorine in the GalNAc sugar of the disaccharide.
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Affiliation(s)
- Maqbool
A. Siddiqui
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Shailesh Ambre
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Susan K. Keay
- Medical
Service, Veterans Administration Maryland Health Care System, Baltimore, Maryland 21201, United States
- Baltimore
Research and Education Foundation, Baltimore, Maryland 21201, United States
- Department of Medicine and Department of
Pathology, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
| | - Jeffrey M. Rhyne
- Department of Medicine and Department of
Pathology, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
| | - Chen-Ou Zhang
- Department of Medicine and Department of
Pathology, University of Maryland School
of Medicine, Baltimore, Maryland 21201, United States
| | - Joseph J. Barchi
- Chemical
Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- E-mail: . Phone: 301-846-5905. Fax: 301-846-6033 (J.J.B.)
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9
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Gibadullin R, Farnsworth DW, Barchi JJ, Gildersleeve JC. GalNAc-Tyrosine Is a Ligand of Plant Lectins, Antibodies, and Human and Murine Macrophage Galactose-Type Lectins. ACS Chem Biol 2017. [PMID: 28644609 DOI: 10.1021/acschembio.7b00471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In 2011, a new type of protein O-glycosylation was discovered in which N-acetylgalactosamine is attached to the side chain of tyrosine (GalNAc-Tyr). While present on dozens of proteins, the biological roles of GalNAc-Tyr are unknown. To gain insight into this new type of modification, we synthesized a group of GalNAc-Tyr glycopeptides, constructed microarrays, and evaluated potential recognition of GalNAc-Tyr by a series of glycan-binding proteins. Through a series of >150 microarray experiments, we assessed binding properties of a variety of plant lectins, monoclonal antibodies, and endogenous lectins. VVL, HPA, and SBA were all found to bind tightly to GalNAc-Tyr, and several Tn binding antibodies and blood group A antibodies were found to cross-react with GalNAc-Tyr. Thus, detection of GalNAc-Tyr modified proteins is an important consideration when analyzing results from these reagents. Additionally, we evaluated potential recognition by two mammalian lectins, human (hMGL) and murine (mMGL-2) macrophage galactose type C-type lectins. Both hMGL and mMGL-2 bound tightly to GalNAc-Tyr determinants. The apparent Kd values (∼1-40 nM) were on par with some of the best known ligands for MGL, such as the Tn antigen. hMGL also bound the natural beta-amyloid peptide containing a GalNAc-Tyr epitope. STD NMR experiments provided structural insights into the molecular basis of recognition. Finally, GalNAc-Tyr was selectively captured by mMGL-2 positive dendritic cells. These results provide the first evidence that GalNAc-Tyr modified proteins and/or peptides may be ligands for hMGL and mMGL-2 and offer unique structures for the design of MGL targeting agents.
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Affiliation(s)
- Ruslan Gibadullin
- Chemical
Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles St., Frederick, Maryland 21702, United States
| | - David Wayne Farnsworth
- Chemical
Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles St., Frederick, Maryland 21702, United States
| | - Joseph J. Barchi
- Chemical
Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles St., Frederick, Maryland 21702, United States
| | - Jeffrey C. Gildersleeve
- Chemical
Biology Laboratory, National Cancer Institute, National Institutes of Health, 376 Boyles St., Frederick, Maryland 21702, United States
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10
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Zlotkowski K, Hewitt WM, Sinniah RS, Tropea JE, Needle D, Lountos GT, Barchi JJ, Waugh DS, Schneekloth JS. A Small-Molecule Microarray Approach for the Identification of E2 Enzyme Inhibitors in Ubiquitin-Like Conjugation Pathways. SLAS Discov 2017; 22:760-766. [PMID: 28346086 DOI: 10.1177/2472555216683937] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
E2 enzymes in ubiquitin-like conjugation pathways are important, highly challenging pharmacological targets, and despite significant efforts, few noncovalent modulators have been discovered. Small-molecule microarray (SMM)-based screening was employed to identify an inhibitor of the "undruggable" small ubiquitin-like modifier (SUMO) E2 enzyme Ubc9. The inhibitor, a degradation product from a commercial screening collection, was chemically synthesized and evaluated in biochemical, mechanistic, and structure-activity relationship studies. Binding to Ubc9 was confirmed through the use of ligand-detected nuclear magnetic resonance, and inhibition of sumoylation in a reconstituted enzymatic cascade was found to occur with an IC50 of 75 µM. This work establishes the utility of the SMM approach for identifying inhibitors of E2 enzymes, targets with few known small-molecule modulators.
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Affiliation(s)
- Katherine Zlotkowski
- 1 Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - William M Hewitt
- 1 Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Ranu S Sinniah
- 1 Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Joseph E Tropea
- 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Danielle Needle
- 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - George T Lountos
- 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.,3 Basic Science Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph J Barchi
- 1 Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - David S Waugh
- 2 Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - John S Schneekloth
- 1 Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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11
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Guasch L, Yapamudiyansel W, Peach ML, Kelley JA, Barchi JJ, Nicklaus MC. Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples. J Chem Inf Model 2016; 56:2149-2161. [PMID: 27669079 PMCID: PMC5129033 DOI: 10.1021/acs.jcim.6b00338] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
We
investigated how many cases of the same chemical sold as different
products (at possibly different prices) occurred in a prototypical
large aggregated database and simultaneously tested the tautomerism
definitions in the chemoinformatics toolkit CACTVS. We applied the
standard CACTVS tautomeric transforms plus a set of recently developed
ring–chain transforms to the Aldrich Market Select (AMS) database
of 6 million screening samples and building blocks. In 30 000
cases, two or more AMS products were found to be just different tautomeric
forms of the same compound. We purchased and analyzed 166 such tautomer
pairs and triplets by 1H and 13C NMR to determine
whether the CACTVS transforms accurately predicted what is the same
“stuff in the bottle”. Essentially all prototropic transforms
with examples in the AMS were confirmed. Some of the ring–chain
transforms were found to be too “aggressive”, i.e. to
equate structures with one another that were different compounds.
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Affiliation(s)
- Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Waruna Yapamudiyansel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
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12
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Biswas S, Medina SH, Barchi JJ. Synthesis and cell-selective antitumor properties of amino acid conjugated tumor-associated carbohydrate antigen-coated gold nanoparticles. Carbohydr Res 2015; 405:93-101. [PMID: 25556664 PMCID: PMC4354769 DOI: 10.1016/j.carres.2014.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 11/26/2022]
Abstract
The Thomsen Friedenreich antigen (TFag) disaccharide is a tumor-associated carbohydrate antigen (TACA) found primarily on carcinoma cells and rarely expressed in normal tissue. The TFag has been shown to interact with Galectin-3 (Gal-3), one in a family of β-galactoside binding proteins. Galectins have a variety of cellular functions, and Gal-3 has been shown to be the sole galectin with anti-apoptotic activity. We have previously prepared gold nanoparticles (AuNP) coated with the TFag in various presentations as potential anti-adhesive therapeutic tools or antitumor vaccine platforms. Here we describe the synthesis of TFag-glycoamino acid conjugates attached to gold nanoparticles through a combined alkane/PEG linker, where the TFag was attached to either a serine or threonine amino acid. Particles were fully characterized by a host of biophysical techniques, and along with a control particle carrying hydroxyl-terminated linker units, were evaluated in both Gal-3 positive and negative cell lines. We show that the particles bearing the saccharides selectively inhibited tumor cell growth of the Gal-3 positive cells significantly more than the Gal-3 negative cells. In addition, the threonine-attached TF particles were more potent than the serine-attached constructs. These results support the use of AuNP as antitumor therapeutic platforms, targeted against cell lines that express specific lectins that interact with TFag.
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Affiliation(s)
- Souvik Biswas
- Chemical Biology Laboratory, The Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Scott H Medina
- Chemical Biology Laboratory, The Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Joseph J Barchi
- Chemical Biology Laboratory, The Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States.
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13
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14
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Glinskii OV, Li F, Wilson LS, Barnes S, Rittenhouse-Olson K, Barchi JJ, Pienta KJ, Glinsky VV. Endothelial integrin α3β1 stabilizes carbohydrate-mediated tumor/endothelial cell adhesion and induces macromolecular signaling complex formation at the endothelial cell membrane. Oncotarget 2015; 5:1382-9. [PMID: 24675526 PMCID: PMC4012737 DOI: 10.18632/oncotarget.1837] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Blood borne metastatic tumor cell adhesion to endothelial cells constitutes a critical rate-limiting step in hematogenous cancer metastasis. Interactions between cancer associated carbohydrate Thomsen-Friedenreich antigen (TF-Ag) and endothelium-expressed galectin-3 (Gal-3) have been identified as the leading molecular mechanism initiating tumor/endothelial cell adhesion in several types of cancer. However, it is unknown how these rather weak and transient carbohydrate/lectin mediated interactions are stabilized. Here, using Western blot and LC tandem mass spectrometry analyses of pull-downs utilizing TF-Ag loaded gold nanoparticles, we identified Gal-3, endothelial integrin α3β1, Src kinase, as well as 5 additional molecules mapping onto focal adhesion pathway as parts of the macromolecular complexes formed at the endothelial cell membranes downstream of TF-Ag/Gal-3 interactions. In a modified parallel flow chamber assay, inhibiting α3β1 integrin greatly reduced the strength of tumor/endothelial cell interactions without affecting the initial cancer cell adhesion. Further, the macromolecular complex induced by TF-Ag/Gal-3/α3β1 interactions activates Src kinase, p38, and ERK1/2, pathways in endothelial cells in a time- and α3β1-dependent manner. We conclude that, following the initial metastatic cell attachment to endothelial cells mediated by TF-Ag/Gal-3 interactions, endothelial integrin α3β1 stabilizes tumor/endothelial cell adhesion and induces the formation of macromolecular signaling complex activating several major signaling pathways in endothelial cells.
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Affiliation(s)
- Olga V Glinskii
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO
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15
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Barchi JJ. Mucin-Type Glycopeptide Structure in Solution: Past, Present, and Future. Biopolymers 2013; 99:713-23. [DOI: 10.1002/bip.22313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 06/05/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Joseph J. Barchi
- Chemical Biology Laboratory; Center for Cancer Research, National Cancer Institute at Frederick; Frederick; MD; 21702
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16
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Luo M, Velikovsky CA, Yang X, Siddiqui MA, Hong X, Barchi JJ, Gildersleeve JC, Pancer Z, Mariuzza RA. Recognition of the Thomsen-Friedenreich pancarcinoma carbohydrate antigen by a lamprey variable lymphocyte receptor. J Biol Chem 2013; 288:23597-606. [PMID: 23782692 DOI: 10.1074/jbc.m113.480467] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs were recently shown to recognize glycans, such as the tumor-associated Thomsen-Friedenreich antigen (TFα; Galβ1-3GalNAcα), with a selectivity rivaling or exceeding that of lectins and antibodies. To understand the basis for TFα recognition by one such VLR (VLRB.aGPA.23), we measured thermodynamic parameters for the binding interaction and determined the structure of the VLRB.aGPA.23-TFα complex to 2.2 Å resolution. In the structure, four tryptophan residues form a tight hydrophobic cage encasing the TFα disaccharide that completely excludes buried water molecules. This cage together with hydrogen bonding of sugar hydroxyls to polar side chains explains the exquisite selectivity of VLRB.aGPA.23. The topology of the glycan-binding site of VLRB.aGPA.23 differs markedly from those of lectins or antibodies, which typically consist of long, convex grooves for accommodating the oligosaccharide. Instead, the TFα disaccharide is sandwiched between a variable loop and the concave surface of the VLR formed by the β-strands of the leucine-rich repeat modules. Longer oligosaccharides are predicted to extend perpendicularly across the β-strands, requiring them to bend to match the concavity of the VLR solenoid.
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Affiliation(s)
- Ming Luo
- University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, USA
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17
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Mallajosyula SS, Adams KM, Barchi JJ, MacKerell AD. Conformational determinants of the activity of antiproliferative factor glycopeptide. J Chem Inf Model 2013; 53:1127-37. [PMID: 23627670 DOI: 10.1021/ci400147s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic APF provided a platform to study amino acid modifications and their effect on APF activity, based on which a structure-activity relationship (SAR) for APF activity was previously proposed. However, this SAR model could not explain the change in activity associated with minor alterations in the peptide sequence. Presented is computational analysis of 14 APF derivatives to identify structural trends from which a more detailed SAR is obtained. The APF activity is found to be dictated by the close interplay between carbohydrate-peptide and peptide-peptide interactions. The former involves hydrogen bond and hydrophobic interactions, and the latter is dominated by hydrophobic interactions. The highly flexible hydrophobic peptide adopts collapsed conformations separated by low energy barriers. APF activity correlates with hydrophobic clustering associated with amino acids 4A, 6V, and 8V. Peptide conformations are highly sensitive to single point mutations, which explain the experimental trends. The presented SAR will act as a guide for lead optimization of more potent APF analogues of potential therapeutic utility.
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Affiliation(s)
- Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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18
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Hong X, Ma MZ, Gildersleeve JC, Chowdhury S, Barchi JJ, Mariuzza RA, Murphy MB, Mao L, Pancer Z. Sugar-binding proteins from fish: selection of high affinity "lambodies" that recognize biomedically relevant glycans. ACS Chem Biol 2013; 8:152-60. [PMID: 23030719 PMCID: PMC3756686 DOI: 10.1021/cb300399s] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Glycan-binding proteins are important for a wide variety of basic research and clinical applications, but proteins with high affinity and selectivity for carbohydrates are difficult to obtain. Here we describe a facile and cost-effective strategy to generate monoclonal lamprey antibodies, called lambodies, that target glycan determinants. We screened a library of yeast surface-displayed (YSD) lamprey variable lymphocyte receptors (VLR) for clones that can selectively bind various biomedically important glycotopes. These glycoconjugates included tumor-associated carbohydrate antigens (Tn and TFα), Lewis antigens (LeA and LeX), N-glycolylneuraminic acid, targets of broadly neutralizing HIV antibodies (poly-Man9 and the HIV gp120), and the glycoproteins asialo-ovine submaxillary mucin (aOSM) and asialo-human glycophorin A (aGPA). We isolated clones that bind each of these targets in a glycan-dependent manner and with very strong binding constants, for example, 6.2 nM for Man9 and 44.7 nM for gp120, determined by surface plasmon resonance (SPR). One particular lambody, VLRB.aGPA.23, was shown by glycan array analysis to be selective for the blood group H type 3 trisaccharide (BG-H3, Fucα1-2Galβ1-3GalNAcα), aGPA, and TFα (Galβ1-3GalNAcα), with affinity constants of 0.2, 1, and 8 nM, respectively. In human tissue microarrays this lambody selectively detected cancer-associated carbohydrate antigens in 14 different types of cancers. It stained 27% of non-small cell lung cancer (NSCLC) samples in a pattern that correlated with poor patient survival. Lambodies with exquisite affinity and selectivity for glycans may find myriad uses in glycobiology and biomedical research.
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Affiliation(s)
- Xia Hong
- Institute of Marine and Environmental Technology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Columbus Center Suite 236, 701 East Pratt St., Baltimore, Maryland 21202, United States
| | - Mark Z. Ma
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 West Baltimore St., Baltimore, Maryland 21201, United States
| | - Jeffrey C. Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Sudipa Chowdhury
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joseph J. Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Roy A. Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr., Rockville, Maryland 20850, United States
| | - Michael B. Murphy
- GE Healthcare Life Sciences, 800 Centennial Ave., Piscataway, New Jersey 08854, United States
| | - Li Mao
- Department of Oncology and Diagnostic Sciences, University of Maryland Dental School, 650 West Baltimore St., Baltimore, Maryland 21201, United States
| | - Zeev Pancer
- Institute of Marine and Environmental Technology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Columbus Center Suite 236, 701 East Pratt St., Baltimore, Maryland 21202, United States
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19
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Jayasekara PS, Phan K, Tosh DK, Kumar TS, Moss SM, Zhang G, Barchi JJ, Gao ZG, Jacobson KA. Modulation of G protein-coupled adenosine receptors by strategically functionalized agonists and antagonists immobilized on gold nanoparticles. Purinergic Signal 2012. [PMID: 23179047 DOI: 10.1007/s11302-012-9338-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gold nanoparticles (AuNPs) allow the tuning of pharmacokinetic and pharmacodynamic properties by active or passive targeting of drugs for cancer and other diseases. We have functionalized gold nanoparticles by tethering specific ligands, agonists and antagonists, of adenosine receptors (ARs) to the gold surface as models for cell surface interactions with G protein-coupled receptors (GPCRs). The AuNP conjugates with chain-extended AR ligands alone (PEGylated nucleosides and nonnucleosides, anchored to the Au via thioctic acid) were found to be insoluble in water due to hydrophobic entities in the ligand. Therefore, we added a second, biologically inactive pendant moiety to increase the water solubility, consisting of a PEGylated chain terminating in a carboxylic or phosphate group. The purity and stability of the immobilized biologically active ligand were examined by ultrafiltration and HPLC. Pharmacological receptor binding studies on these GPCR ligand-derivatized AuNPs (2-5 nm in diameter), performed using membranes of mammalian cells stably expressing human A1, A2A, and A3ARs, showed that the desired selectivity was retained with K(i) values (nanomolar) of A3AR agonist 21b and A2AAR antagonists 24 and 26a of 14 (A3), 34 (A2A), and 69 (A2A), respectively. The corresponding monomers displayed K i values of 37, 61, and 1,420 nM, respectively. In conclusion, we have synthesized stable, water-soluble AuNP derivatives of tethered A3 and A2AAR ligands that retain the biological properties of their monomeric ligands and are intended for therapeutic and imaging applications. This is the first prototypical application to gold carriers of small molecule (nonpeptide) GPCR ligands, which are under investigation for treatment of cancer and inflammatory diseases.
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Affiliation(s)
- P Suresh Jayasekara
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0810, USA
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20
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Acchione M, Lee YC, DeSantis ME, Lipschultz CA, Wlodawer A, Li M, Shanmuganathan A, Walter RL, Smith-Gill S, Barchi JJ. Specific fluorine labeling of the HyHEL10 antibody affects antigen binding and dynamics. Biochemistry 2012; 51:6017-27. [PMID: 22769726 PMCID: PMC3508667 DOI: 10.1021/bi300455t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To more fully understand the molecular mechanisms responsible for variations in binding affinity with antibody maturation, we explored the use of site specific fluorine labeling and (19)F nuclear magnetic resonance (NMR). Several single-chain (scFv) antibodies, derived from an affinity-matured series of anti-hen egg white lysozyme (HEL) mouse IgG1, were constructed with either complete or individual replacement of tryptophan residues with 5-fluorotryptophan ((5F)W). An array of biophysical techniques was used to gain insight into the impact of fluorine substitution on the overall protein structure and antigen binding. SPR measurements indicated that (5F)W incorporation lowered binding affinity for the HEL antigen. The degree of analogue impact was residue-dependent, and the greatest decrease in affinity was observed when (5F)W was substituted for residues near the binding interface. In contrast, corresponding crystal structures in complex with HEL were essentially indistinguishable from the unsubstituted antibody. (19)F NMR analysis showed severe overlap of signals in the free fluorinated protein that was resolved upon binding to antigen, suggesting very distinct chemical environments for each (5F)W in the complex. Preliminary relaxation analysis suggested the presence of chemical exchange in the antibody-antigen complex that could not be observed by X-ray crystallography. These data demonstrate that fluorine NMR can be an extremely useful tool for discerning structural changes in scFv antibody-antigen complexes with altered function that may not be discernible by other biophysical techniques.
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Affiliation(s)
- Mauro Acchione
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Yi-Chien Lee
- Chemical Biology Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Morgan E. DeSantis
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Claudia A. Lipschultz
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Mi Li
- Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Basic Research Program, SAIC-Frederick, Frederick, Maryland 21702, United States
| | - Aranganathan Shanmuganathan
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Richard L. Walter
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Sandra Smith-Gill
- Structural Biophysics Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joseph J. Barchi
- Chemical Biology Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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21
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Brinãs RP, Sundgren A, Sahoo P, Morey S, Rittenhouse-Olson K, Wilding GE, Deng W, Barchi JJ. Design and synthesis of multifunctional gold nanoparticles bearing tumor-associated glycopeptide antigens as potential cancer vaccines. Bioconjug Chem 2012; 23:1513-23. [PMID: 22812418 DOI: 10.1021/bc200606s] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of vaccines against specific types of cancers will offer new modalities for therapeutic intervention. Here, we describe the synthesis of a novel vaccine construction prepared from spherical gold nanoparticles of 3-5 nm core diameters. The particles were coated with both the tumor-associated glycopeptides antigens containing the cell-surface mucin MUC4 with Thomsen Friedenreich (TF) antigen attached at different sites and a 28-residue peptide from the complement derived protein C3d to act as a B-cell activating "molecular adjuvant". The synthesis entailed solid-phase glycopeptide synthesis, design of appropriate linkers, and attachment chemistry of the various molecules to the particles. Attachment to the gold surface was mediated by a novel thiol-containing 33 atom linker which was further modified to be included as a third "spacer" component in the synthesis of several three-component vaccine platforms. Groups of mice were vaccinated either with one of the nanoplatform constructs or with control particles without antigen coating. Evaluation of sera from the immunized animals in enzyme immunoassays (EIA) against each glycopeptide antigen showed a small but statistically significant immune response with production of both IgM and IgG isotypes. Vaccines with one carbohydrate antigen (B, C, and E) gave more robust responses than the one with two contiguous disaccharides (D), and vaccine E with a TF antigen attached to threonine at the 10th position of the peptide was selected for IgG over IgM suggesting isotype switching. The data suggested that this platform may be a viable delivery system for tumor-associated glycopeptide antigens.
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Affiliation(s)
- Raymond P Brinãs
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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22
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Zhang Y, Muthana SM, Barchi JJ, Gildersleeve JC. Divergent behavior of glycosylated threonine and serine derivatives in solid phase peptide synthesis. Org Lett 2012; 14:3958-61. [PMID: 22817697 DOI: 10.1021/ol301723e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid phase peptide coupling of glycosylated threonine derivatives was systematically evaluated. In contrast to glycosylated serine derivatives which are highly prone to epimerization, glycosylated threonine derivatives produce only negligible amounts of epimerization. Under forcing conditions, glycosylated threonine analogs undergo β-elimination, rather than epimerization. Mechanistic studies and molecular modeling were used to understand the origin of the differences in reactivity.
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Affiliation(s)
- Yalong Zhang
- Chemical Biology Laboratory, National Cancer Institute, 376 Boyles Street, Building 376, Frederick, Maryland 21702, USA
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23
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Briñas RP, Maetani M, Barchi JJ. A survey of place-exchange reaction for the preparation of water-soluble gold nanoparticles. J Colloid Interface Sci 2012; 392:415-421. [PMID: 23149107 DOI: 10.1016/j.jcis.2012.06.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 06/14/2012] [Accepted: 06/17/2012] [Indexed: 12/19/2022]
Abstract
Water-soluble gold nanoparticles (AuNPs) have gained considerable attention because they offer a myriad of potential applications, especially in the fields of biology and medicine. One method to prepare such gold nanoparticles is through the well-known Murray place-exchange reaction. In this method, precursor gold nanoparticles, bearing labile ligands and with very good size distribution, are synthesized first, and then reacted with a large excess of the desired ligand. We report a comparison of the reactivity of several known precursor gold nanoparticles (citrate-stabilized, pentanethiol-stabilized, tetraoctylammonium bromide-stabilized, and 4-dimethylaminopyridine-stabilized) to several biologically relevant ligands, including amino acids, peptides, and carbohydrates. We found that citrate-stabilized and 4-dimethylaminopyridine-stabilized gold nanoparticles have broader reactivities than the other precursors studied. Citrate-stabilized gold nanoparticles are more versatile precursors because they can be prepared in a wide range of sizes and are very stable. The hydrophobic pentane-stabilized gold nanoparticles made them "inert" toward highly water-soluble ligands. Tetraoctylammonium bromide-stabilized gold nanoparticles exhibited selective reactivity, especially for small, unhindered and amphiphilic ligands. Depending on the desired ligand and size of AuNPs, a judicious selection of the available precursors can be made for use in place-exchange reactions. In preparing water-soluble AuNPs with biologically relevant ligands, the nature of the incoming ligand and the size of the AuNP should be taken into account in order to choose the most suitable place-exchange procedure.
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Affiliation(s)
- Raymond P Briñas
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Micah Maetani
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States
| | - Joseph J Barchi
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, United States.
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24
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Zhang Y, Muthana SM, Farnsworth D, Ludek O, Adams K, Barchi JJ, Gildersleeve JC. Enhanced epimerization of glycosylated amino acids during solid-phase peptide synthesis. J Am Chem Soc 2012; 134:6316-25. [PMID: 22390544 DOI: 10.1021/ja212188r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycopeptides are extremely useful for basic research and clinical applications, but access to structurally defined glycopeptides is limited by the difficulties in synthesizing this class of compounds. In this study, we demonstrate that many common peptide coupling conditions used to prepare O-linked glycopeptides result in substantial amounts of epimerization at the α position. In fact, epimerization resulted in up to 80% of the non-natural epimer, indicating that it can be the major product in some reactions. Through a series of mechanistic studies, we demonstrate that the enhanced epimerization relative to nonglycosylated amino acids is due to a combination of factors, including a faster rate of epimerization, an energetic preference for the unnatural epimer over the natural epimer, and a slower overall rate of peptide coupling. In addition, we demonstrate that use of 2,4,6-trimethylpyridine (TMP) as the base in peptide couplings produces glycopeptides with high efficiency and low epimerization. The information and improved reaction conditions will facilitate the preparation of glycopeptides as therapeutic compounds and vaccine antigens.
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Affiliation(s)
- Yalong Zhang
- Chemical Biology Laboratory, National Cancer Institute, 376 Boyles Street, Building 376, Frederick, Maryland 21702, USA
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25
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Keay S, Kaczmarek P, Zhang CO, Koch K, Szekely Z, Barchi JJ, Michejda C. Normalization of proliferation and tight junction formation in bladder epithelial cells from patients with interstitial cystitis/painful bladder syndrome by d-proline and d-pipecolic acid derivatives of antiproliferative factor. Chem Biol Drug Des 2011; 77:421-30. [PMID: 21352500 DOI: 10.1111/j.1747-0285.2011.01108.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interstitial cystitis/painful bladder syndrome is a chronic bladder disorder with epithelial thinning or ulceration, pain, urinary frequency and urgency, for which there is no reliably effective therapy. We previously reported that interstitial cystitis/painful bladder syndrome bladder epithelial cells make a glycopeptide antiproliferative factor or 'APF' (Neu5Acα2-3Galβ1-3GalNAcα-O-TVPAAVVVA) that induces abnormalities in normal cells similar to those in interstitial cystitis/painful bladder syndrome cells in vitro, including decreased proliferation, decreased tight junction formation, and increased paracellular permeability. We screened inactive APF derivatives for their ability to block antiproliferative activity of asialylated-APF ('as-APF') in normal bladder cells and determined the ability of as-APF-blocking derivatives to normalize tight junction protein expression, paracellular permeability, and/or proliferation of interstitial cystitis/painful bladder syndrome cells. Only two of these derivatives [Galβ1-3GalNAcα-O-TV-(d-pipecolic acid)-AAVVVA and Galβ1-3GalNAcα-O-TV-(d-proline)-AAVVVA] blocked as-APF antiproliferative activity in normal cells (p < 0.001 for both). Both of these antagonists also 1) significantly increased mRNA expression of ZO-1, occludin, and claudins 1, 4, 8, and 12 in interstitial cystitis/painful bladder syndrome cells by qRT-PCR; 2) normalized interstitial cystitis/painful bladder syndrome epithelial cell tight junction protein expression and tight junction formation by confocal immunofluorescence microscopy; and 3) decreased paracellular permeability of (14) C-mannitol and (3) H-inulin between confluent interstitial cystitis/painful bladder syndrome epithelial cells on Transwell plates, suggesting that these potent APF antagonists may be useful for the development as interstitial cystitis/painful bladder syndrome therapies.
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Affiliation(s)
- Susan Keay
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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26
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Johannessen L, Remsberg J, Gaponenko V, Adams KM, Barchi JJ, Tarasov SG, Jiang S, Tarasova NI. Peptide structure stabilization by membrane anchoring and its general applicability to the development of potent cell-permeable inhibitors. Chembiochem 2011; 12:914-21. [PMID: 21365731 DOI: 10.1002/cbic.201000563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Indexed: 11/08/2022]
Abstract
Isolated protein motifs that are involved in interactions with their binding partners can be used to inhibit these interactions. However, peptides corresponding to protein fragments tend to have no defined secondary or tertiary structure in the absence of scaffolding by the rest of protein molecule. This results in low inhibitor potency. NMR and CD spectroscopy studies of lipopeptide inhibitors of the Hedgehog pathway revealed that membrane anchoring allows the cell membrane to function as a scaffold and facilitate the folding of short peptides. In addition, lipidation enhances cell permeability and increases the concentration of the compounds near the membrane, thus facilitating potent inhibition. The general applicability of this rational approach was further confirmed by the generation of selective antagonists of the insulin-like growth factor 1 receptor with GI(50) values in the nanomolar range. Lipopeptides corresponding to protein fragments were found to serve as potent and selective inhibitors of a number of nondruggable molecular targets.
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Affiliation(s)
- Liv Johannessen
- Cancer and Inflammation Program, Center for Cancer Research NCI-Frederick, Frederick, MD, 21702, USA
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27
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Kim T, Barchi JJ, Marquez VE, Shapiro BA. Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign. J Mol Graph Model 2011; 29:624-34. [PMID: 21159533 PMCID: PMC3040123 DOI: 10.1016/j.jmgm.2010.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/05/2010] [Accepted: 11/10/2010] [Indexed: 11/28/2022]
Abstract
Relatively new types of the modified nucleotides, namely carbocyclic sugars that are constrained to north or south (C2' or C3' exo) conformations, can be used for RNA nanoparticle design to control their structures and stability by rigidifying nucleotides and altering the helical properties of RNA duplexes. Two RNA structures, an RNA dodecamer and an HIV kissing loop complex where several nucleotides were replaced with north or south constrained sugars, were studied by molecular dynamics (MD) simulations. The substituted south constrained nucleotides in the dodecamer widened the major groove and narrowed and deepened the minor groove thus inducing local conformational changes that resemble a B-form DNA helix. In the HIV kissing loop complex, north and south constrained nucleotides were substituted into flanking bases and stems. The modified HIV kissing loop complex showed a lower RMSD value than the normal kissing loop complex. The overall twist angle was also changed and its standard deviation was reduced. In addition, the modified RNA dodecamer and HIV kissing loop complex were characterized by principal component analysis (PCA) and steered molecular dynamics (SMD). PCA results showed that the constrained sugars stabilized the overall motions. The results of the SMD simulations indicated that as the backbone δ angles were increased by elongation, more force was applied to the modified RNA due to the constrained sugar analogues.
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Affiliation(s)
- Taejin Kim
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
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Kaczmarek P, Tocci GM, Keay SK, Adams KM, Zhang CO, Koch KR, Grkovic D, Guo L, Michejda CJ, Barchi JJ. Structure-Activity Studies on Antiproliferative Factor (APF) Glycooctapeptide Derivatives. ACS Med Chem Lett 2010; 1:390-4. [PMID: 24900223 DOI: 10.1021/ml100087a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/09/2010] [Indexed: 11/29/2022] Open
Abstract
Antiproliferative factor (APF), a sialylated glycopeptide secreted by explanted bladder epithelial cells from interstitial cystitis/painful bladder syndrome (IC/PBS) patients, and its unsialylated analogue (as-APF) significantly decrease proliferation of bladder epithelial cells and/or certain carcinoma cell lines in vitro. We recently reported a structure-activity relationship profile for the peptide portion of as-APF and revealed that truncation of the C-terminal alanine did not significantly affect antiproliferative activity. To better understand the structural basis for the maintenance of activity of this truncated eight amino acid as-APF (as-APF8), we synthesized several amino acid-substituted derivatives and studied their ability to inhibit bladder epithelial cell proliferation in vitro as well as their solution conformations by CD and NMR spectroscopy. While single amino acid changes to as-APF8 often strongly reduced activity, full potency was retained when the trivaline tail was replaced with three alanines. The Ala(6-8) derivative 9 is the simplest, fully potent APF analogue synthesized to date.
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Affiliation(s)
| | - Gillian M. Tocci
- Molecular Aspects of Drug Design Section, Structural Biophysics Laboratory
| | - Susan K. Keay
- Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
- Research Service, Veterans Administration Maryland Health Care System, Baltimore, Maryland 21201
| | | | - Chen-Ou Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Kristopher R. Koch
- Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - David Grkovic
- Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Li Guo
- Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201
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Moon HR, Siddiqui MA, Sun G, Filippov IV, Landsman NA, Lee YC, Adams KM, Barchi JJ, Deschamps JR, Nicklaus MC, Kelley JA, Marquez VE. Using conformationally locked nucleosides to calibrate the anomeric effect: Implications for glycosyl bond stability. Tetrahedron 2010; 66:6707-6717. [PMID: 21052524 PMCID: PMC2967253 DOI: 10.1016/j.tet.2010.06.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Steric and electronic parameters such as the anomeric effect (AE) and gauche effect play significant roles in steering the North ⇆ South equilibrium of nucleosides in solution. Two isomeric oxa-bicyclo[3.1.0]hexane nucleosides that are conformationally locked in either the North or the South conformation of the pseudorotational cycle were designed to study the consequences of having the AE operational or not, independent of other parameters. The rigidity of the system allowed the orientation of the orbitals involved to be set in "fixed" relationships, either antiperiplanar where the AE is permanently "on", or gauche where the AE is impaired. The consequences of these two alternatives were subject to high-level calculations and measured experimentally by x-ray crystallography, hydrolytic stability of the glycosyl bond, and pKa values.
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Affiliation(s)
- Hyung Ryong Moon
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, NIH
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Abstract
Glycopeptides are a class of molecules that comprise two distinct families of biologically important scaffolds, peptides and oligosaccharides, each playing important roles in cellular communication and signaling. Rarely are small, endogenous secreted glycopeptides found that have significant impact on the progression of a specific disease state, but such is the case for the antiproliferative factor (APF) found in the urine and tissue of patients with the poorly understood bladder diseases collectively referred to as interstitial cystitis (IC). APF is a 9-mer peptide containing a sialylated O-linked trisaccharide glycan attached to the N-terminal threonine. APF dramatically inhibits normal bladder cell proliferation and is thought to cause some of the characteristic pathological changes in the bladder of IC patients. Importantly, APF also potently inhibits the growth of certain tumor cells. The details of the cellular receptors to which APF interacts, and the structural features that are critical for its potency are now beginning to unfold. This interesting molecule is a powerful model for the design of new treatments and diagnostic tests for IC, as well as an unprecedented lead agent for novel anticancer drug design.
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Affiliation(s)
- Joseph J Barchi
- National Cancer Institute at Frederick, 376 Boyles Street, PO Box B, Frederick, MD 21702, USA
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31
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Saavedra JE, Davies KM, Barchi JJ, Keefer LK. Unexpected Incorporation of Bromine at a Non-anomeric Position during the Synthesis of an O-Glycosylated Diazeniumdiolate. ORG PREP PROCED INT 2009; 41:143-147. [PMID: 20354584 DOI: 10.1080/00304940902801968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Joseph E Saavedra
- Basic Research Program, SAIC-Frederick, National Cancer Institute at Frederick, Frederick, Maryland, USA
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Kaczmarek P, Keay SK, Tocci GM, Koch KR, Zhang CO, Barchi JJ, Grkovic D, Guo L, Michejda CJ. Structure-activity relationship studies for the peptide portion of the bladder epithelial cell antiproliferative factor from interstitial cystitis patients. J Med Chem 2008; 51:5974-83. [PMID: 18788730 DOI: 10.1021/jm8002763] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We performed comprehensive structure-activity relationship (SAR) studies on the peptide portion of antiproliferative factor (APF), a sialylated frizzled-8 related glycopeptide that inhibits normal bladder epithelial and urothelial carcinoma cell proliferation. Glycopeptide derivatives were synthesized by solid-phase methods using standard Fmoc chemistry and purified by RP-HPLC; all intermediate and final products were verified by HPLC-MS and NMR analyses. Antiproliferative activity of each derivative was determined by inhibition of (3)H-thymidine incorporation in primary normal human bladder epithelial cells. Structural components of the peptide segment of APF that proved to be important for biological activity included the presence of at least eight of the nine N-terminal amino acids, a negative charge in the C-terminal amino acid, a free amino group at the N-terminus, maintenance of a specific amino acid sequence in the C-terminal tail, and trans conformation for the peptide bonds. These data provide critical guidelines for optimization of structure in design of APF analogues as potential therapeutic agents.
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Affiliation(s)
- Piotr Kaczmarek
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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Valdez CA, Saavedra JE, Showalter BM, Davies KM, Wilde TC, Citro ML, Barchi JJ, Deschamps JR, Parrish D, El-Gayar S, Schleicher U, Bogdan C, Keefer LK. Hydrolytic reactivity trends among potential prodrugs of the O2-glycosylated diazeniumdiolate family. Targeting nitric oxide to macrophages for antileishmanial activity. J Med Chem 2008; 51:3961-70. [PMID: 18533711 PMCID: PMC2574667 DOI: 10.1021/jm8000482] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Indexed: 11/30/2022]
Abstract
Glycosylated diazeniumdiolates of structure R 2NN(O)NO-R' (R' = a saccharide residue) are potential prodrugs of the nitric oxide (NO)-releasing but acid-sensitive R 2NN(O)NO (-) ion. Moreover, cleaving the acid-stable glycosides under alkaline conditions provides a convenient protecting group strategy for diazeniumdiolate ions. Here, we report comparative hydrolysis rate data for five representative glycosylated diazeniumdiolates at pH 14, 7.4, and 3.8-4.6 as background for further developing both the protecting group application and the ability to target NO pharmacologically to macrophages harboring intracellular pathogens. Confirming the potential in the latter application, adding R 2NN(O)NO-GlcNAc (where R 2N = diethylamino or pyrrolidin-l-yl and GlcNAc = N-acetylglucosamin-l-yl) to cultures of infected mouse macrophages that were deficient in inducible NO synthase caused rapid death of the intracellular protozoan parasite Leishmania major with no host cell toxicity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Larry K. Keefer
- To whom correspondence should be addressed. Phone: 301-846-1467. Fax: 301-846-5946. E-mail:
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Barchi JJ, Karki RG, Nicklaus MC, Siddiqui MA, George C, Mikhailopulo IA, Marquez VE. Comprehensive structural studies of 2',3'-difluorinated nucleosides: comparison of theory, solution, and solid state. J Am Chem Soc 2008; 130:9048-57. [PMID: 18558684 DOI: 10.1021/ja800964g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations.
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Affiliation(s)
- Joseph J Barchi
- Laboratory of Medicinal Chemistry, National Cancer Institute, Frederick, National Institutes of Health, 376 Boyles Street, P.O. Box B, Frederick, Maryland 21702, USA.
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35
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Garg H, Francella N, Tony KA, Augustine LA, Barchi JJ, Fantini J, Puri A, Mootoo DR, Blumenthal R. Glycoside analogs of beta-galactosylceramide, a novel class of small molecule antiviral agents that inhibit HIV-1 entry. Antiviral Res 2008; 80:54-61. [PMID: 18538869 DOI: 10.1016/j.antiviral.2008.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 04/02/2008] [Accepted: 04/09/2008] [Indexed: 10/22/2022]
Abstract
The interaction between HIV gp120 and galactose-containing cell surface glycolipids such as GalCer or Gb3 is known to facilitate HIV binding to both CD4+ as well as CD4- cells. In an effort to develop small molecule HIV-1 entry inhibitors with improved solubility and efficacy, we have synthesized a series of C-glycoside analogs of GalCer and tested their anti HIV-1 activity. The analogs were tested for gp120 binding using a HIV-1 (IIIB) V3-loop specific peptide. Two of the six analogs that interfered with gp120 binding also inhibited HIV Env-mediated cell-to-cell fusion and viral entry in the absence of any significant cytotoxicity. Analogs with two side chains did not show inhibition of fusion and/or infection under identical conditions. The inhibition of virus infection seen by these compounds was not coreceptor dependent, as they inhibited CXCR4, CCR5 as well as dual tropic viruses. These compounds showed inhibition of HIV entry at early steps in viral infection since the compounds were inactive if added post viral entry. Temperature-arrested state experiments showed that the compounds act at the level of virus attachment to the cells likely at a pre-CD4 engagement step. These compounds also showed inhibition of VSV glycoprotein-pseudotyped virus. The results presented here show that the glycoside derivatives of GalCer with simple side chains may serve as a novel class of small molecule HIV-1 entry inhibitors that would be active against a number of HIV isolates as well as other enveloped viruses.
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Affiliation(s)
- Himanshu Garg
- Membrane Structure and Function Section, Nanobiology Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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36
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Sundgren A, Barchi JJ. Varied presentation of the Thomsen-Friedenreich disaccharide tumor-associated carbohydrate antigen on gold nanoparticles. Carbohydr Res 2008; 343:1594-604. [PMID: 18502409 DOI: 10.1016/j.carres.2008.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 04/23/2008] [Accepted: 05/04/2008] [Indexed: 10/22/2022]
Abstract
Three-dimensional self-assembled monolayers of gold coated with the Thomsen-Friedenreich antigen (TF(ag)) disaccharide (beta-Galp-(1-->3)-GalpNAc) in a variety of presentations have been prepared and characterized. Anomalies in the size distribution of our originally synthesized TF(ag)-bearing nanoparticles as shown in dynamic light scattering experiments prompted us to explore the effect of antigen density on the uniformity of the particles. Gold nanoparticles containing a range of densities 'diluted' with copies of the PEG-thiol spacer unit showed that lower antigen density affords more uniform particles. We also wanted to study the constitution of the actual antigen by synthesizing nanoparticles not only with the linker-extended disaccharide, but also within the context of the surrounding peptide sequence where it may be presented in vivo. The synthesis of TF(ag)-containing glycopeptide thiols based on a mucin peptide repeating unit were prepared, assembled into gold nanoparticles and their physical properties evaluated. These novel multivalent tools should prove extremely useful in exploring the binding properties and immune response to this important carbohydrate antigen.
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Affiliation(s)
- Andreas Sundgren
- Laboratory of Medicinal Chemistry and, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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37
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Marquez VE, Sun G, Siddiqui MA, Lee YC, Barchi JJ, Filippov IV, Landsman NA, Kelley JA. What are the consequences of freezing the anomeric effect in nucleosides? Nucleic Acids Symp Ser (Oxf) 2008; 52:543-544. [PMID: 18776494 PMCID: PMC2700545 DOI: 10.1093/nass/nrn275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The consequences of freezing the orientation of the oxygen's lone pair orbitals--which determines whether the anomeric effect is operative or not--were studied theoretically and experimentally in two oxobicyclo-[3.1.0]hexane nucleosides (1 and 2). The results showed significant differences in the properties of these molecules, which correlated with the magnitude of the n2 --> sigma * delocalization.
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Affiliation(s)
- Victor E Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA.
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Affiliation(s)
- Sergei A. Svarovsky
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, 376 Boyles Street, P.O. Box B, Frederick, MD 21702
- Current address: Glycomimetics, Inc., 101 Orchard Ridge Drive, Suite 1E, Gaithersburg, MD 20878
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, 376 Boyles Street, P.O. Box B, Frederick, MD 21702
- Corresponding author: Fax: 301-846-6033
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Maderia M, Shenoy S, Van QN, Marquez VE, Barchi JJ. Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates. Nucleic Acids Res 2007; 35:1978-91. [PMID: 17341464 PMCID: PMC1895885 DOI: 10.1093/nar/gkm025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Shilpa Shenoy
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Que N. Van
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
- *To whom correspondence should be addressed. +1 301 846 5905+1 301 846 6033
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Furrer J, Luy B, Basrur V, Roberts DD, Barchi JJ. Conformational analysis of an alpha3beta1 integrin-binding peptide from thrombospondin-1: implications for antiangiogenic drug design. J Med Chem 2006; 49:6324-33. [PMID: 17034138 DOI: 10.1021/jm060833l] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The integrin alpha3beta1 plays important roles in development, angiogenesis, and the pathogenesis of cancer, suggesting potential therapeutic uses for antagonists of this receptor. Recently, an alpha3beta1 integrin-binding site was mapped to residues 190-201 (FQGVLQNVRFVF) of the N-terminal domain of the secreted protein thrombospondin-1 (TSP1). This sequence displays diverse biological activities in vitro and inhibits angiogenesis in vivo. Herein we describe the NMR solution conformation of this segment in both water and dodecylphosphocholine micelles. While essentially unstructured in water, a more well-defined conformation is populated in micelles, particularly in the C-terminal half of the peptide and correlated with increased biological activity of the micellar peptide. The data suggested that the residues that are critical for biological activity are contained in a structurally well-defined segment of the peptide. These data support the role of the NVR motif as a required element of full-length TSP1 for specific molecular recognition by the alpha3beta1 integrin.
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Affiliation(s)
- Julien Furrer
- Institut für Organische Chemie and Biochemie II, Technische Universität Muenchen, Garching, Germany
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41
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Marquez VE, Ezzitouni A, Russ P, Siddiqui MA, Ford H, Feldman RJ, Mitsuya H, George C, Barchi JJ. Lessons from the Pseudorotational Cycle: Conformationally Rigid AZT Carbocyclic Nucleosides and Their Interaction with Reverse Transcriptase. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Victor E. Marquez
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
| | - Abdallah Ezzitouni
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
| | - Pamela Russ
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
| | - Maqbool A. Siddiqui
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
| | - Harry Ford
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
| | - Ron J. Feldman
- b Experimental Retrovirology Section , Medicine Branch Division of Clinical Sciences National Cancer Institute, National Institutes of Health , Bethesda , MD , 20892
| | - Hiroaki Mitsuya
- b Experimental Retrovirology Section , Medicine Branch Division of Clinical Sciences National Cancer Institute, National Institutes of Health , Bethesda , MD , 20892
| | - Clifford George
- c Laboratory for the Structure of Matter , Naval Research Laboratory , Washington , DC, 20375
| | - Joseph J. Barchi
- a Laboratory of Medicinal Chemistry, Division of Basic Sciences , Washington , DC , 20375
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Cysyk RL, Parker RJ, Barchi JJ, Steeg PS, Hartman NR, Strong JM. Reaction of geldanamycin and C17-substituted analogues with glutathione: product identifications and pharmacological implications. Chem Res Toxicol 2006; 19:376-81. [PMID: 16544941 DOI: 10.1021/tx050237e] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
17-Dimethylaminoethylamino-17-demethoxygeldanamycin (DMAG) and 17-allylamino-17-demethoxygeldanamycin (17-AAG) are two derivatives of geldanamycin (GA) that are currently undergoing clinical evaluation as anticancer agents. These agents bind to heat shock protein 90 (hsp90), resulting in the destabilization of client proteins and inhibition of tumor growth. In a search for the mechanism of hepatotoxicity, which is a dose-limiting toxicity for these agents, we found that GA and its derivatives, 17-AAG and 17-DMAG, react chemically (i.e., nonenzymatically) with glutathione (GSH). A combination of liquid chromatography/electrospray ionization/mass spectrometry and nuclear magnetic resonance analyses were used to identify the product of this reaction as a GSH adduct in which the thiol group of GSH is substituted in the 19-position of the benzoquinone ring. The reaction proceeds rapidly with GA and 17-DMAG (half-lives of approximately 1.5 and 36 min, respectively) and less rapidly with 17-AAG and its major metabolite, 17-AG (half-lives of approximately 9.8 and 16.7 h). The reaction occurs at pH 7.0, 37 degrees C, and a physiological concentration of GSH, indicating that cellular GSH could play a role in modulating the cellular toxicity of these agents and therefore be a factor in their mechanism of differential toxicity. Moreover, reactions with thiol groups of critical cellular proteins could be important to the mechanism of toxicity with this class of anticancer agents.
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Affiliation(s)
- Richard L Cysyk
- Laboratory of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20993-0002, USA
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Deng J, Kelley JA, Barchi JJ, Sanchez T, Dayam R, Pommier Y, Neamati N. Mining the NCI antiviral compounds for HIV-1 integrase inhibitors. Bioorg Med Chem 2006; 14:3785-92. [PMID: 16460953 DOI: 10.1016/j.bmc.2006.01.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Revised: 01/12/2006] [Accepted: 01/16/2006] [Indexed: 11/18/2022]
Abstract
HIV-1 integrase (IN) is an essential enzyme for effective viral replication and is a validated target for the development of antiretroviral drugs. Currently, there are no approved drugs targeting this enzyme. In this study, we have identified 11 structurally diverse small-molecule inhibitors of IN. These compounds have been selected by mining the moderately active antiviral molecules from a collection of 90,000 compounds screened by the National Cancer Institute (NCI) Antiviral Program. These compounds, which were screened at the NCI during the past 20 years, resulted in approximately 4000 compounds labeled as 'moderately active.' In our study, chalcone 11 shows the most potent activity with an IC(50) of 2+/-1 microM against purified IN in the presence of both Mn(2+) and Mg(2+) as cofactors. Docking simulations using the 11 identified inhibitors as a training set have elucidated two unique binding areas within the active site: the first encompasses the conserved D64-D116-E152 motif, while the other involves the flexible loop region formed by amino acid residues 140-149. The tested inhibitors exhibit favorable interactions with important amino acid residues through van der Waals and H-bonding contacts.
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Affiliation(s)
- Jinxia Deng
- Department of Pharmaceutical Sciences, University of Southern California, School of Pharmacy, 1985 Zonal Avenue, Los Angeles, CA 90089, USA
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Showalter BM, Reynolds MM, Valdez CA, Saavedra JE, Davies KM, Klose JR, Chmurny GN, Citro ML, Barchi JJ, Merz SI, Meyerhoff ME, Keefer LK. Diazeniumdiolate ions as leaving groups in anomeric displacement reactions: a protection-deprotection strategy for ionic diazeniumdiolates. J Am Chem Soc 2006; 127:14188-9. [PMID: 16218605 DOI: 10.1021/ja054510a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diazeniumdiolate ions [R2N-N(O)=N-O-] are of growing interest pharmacologically for their ability to generate up to two molar equivalents of bioactive nitric oxide (NO) spontaneously on protonating the amino nitrogen. Accordingly, their stability increases as the pH is raised. Here we show that the corresponding beta-glucosides [R2N-N(O)=N-O-Glc] decreased in stability with pH; when R2N was diethylamino, the rate equation was kobs = ko + kOH- [OH-], where ko = 7.8 x 10-7 s-1 and kOH- = 5.3 x 10-3 M-1 s-1. The primary products were 1,6-anhydroglucose and the regenerated R2N-N(O)=N-O- ion. The results were qualitatively similar to those of beta-glucosyl fluoride and p-nitrophenoxide, whose hydrolyses have been rationalized as proceeding via a glycal oxide intermediate. This chemistry offers a convenient strategy for protecting heat- and acid-sensitive diazeniumdiolate ions during manipulations that would otherwise destroy them. As an example, a poly(urethane) film that generated NO in physiological buffer at a surface flux comparable to that of the mammalian vascular endothelium was prepared by glucosylating the ionic diazeniumdiolate group attached to the diol monomer before reacting it with the bis-isocyanate, then removing the saccharide with base when the protecting group was no longer needed.
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Affiliation(s)
- Brett M Showalter
- Chemistry Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Maderia M, Wu J, Bax A, Shenoy S, O'Keefe B, Marquez VE, Barchi JJ. Engineering DNA topology with locked nucleosides: a structural study. Nucleosides Nucleotides Nucleic Acids 2005; 24:687-90. [PMID: 16248015 DOI: 10.1081/ncn-200060256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA dodecamers modified with nucleotide building blocks based on a bicyclo[3. 1.0]hexane system that effectively locks the ribose template into an RNA-like or North (N) conformation were analyzed by various biophysical techniques including high field nuclear magnetic resonance (NMR). Replacement of either one or both of the center thymidines in the Dickerson Drew dodecamer (CGCGAAT*T*CGCG) caused a progressive shift in the bending propensity of the double helix as shown by a newly developed rapid technique that compares the residual dipolar coupling (RDC) values of the modified duplexes with those previously determined for the native DNA.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
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Marquez VE, Barchi JJ, Kelley JA, Rao KVR, Agbaria R, Ben-Kasus T, Cheng JC, Yoo CB, Jones PA. Zebularine: a unique molecule for an epigenetically based strategy in cancer chemotherapy. The magic of its chemistry and biology. Nucleosides Nucleotides Nucleic Acids 2005; 24:305-18. [PMID: 16247946 DOI: 10.1081/ncn-200059765] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
1-(beta-D-ribofuranosyl)-1,2-dihydropyrimidin-2-one (zebularine) is structurally 4-deamino cytidine. The increased electrophilic character of this simple aglycon endows the molecule with unique chemical and biological properties, making zebularine a versatile starting material for the synthesis of complex nucleosides and an effective inhibitor of cytidine deaminase and DNA cytosine methyltransferase. Zebularine is a stable, antitumor agent that preferentially targets cancer cells and shows activity both in vitro and in experimental animals, even after oral administration.
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Affiliation(s)
- Victor E Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, NCI at Frederick, NIH, Frederick, MD 21702, USA.
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Oishi S, Karki RG, Shi ZD, Worthy KM, Bindu L, Chertov O, Esposito D, Frank P, Gillette WK, Maderia M, Hartley J, Nicklaus MC, Barchi JJ, Fisher RJ, Burke TR. Evaluation of macrocyclic Grb2 SH2 domain-binding peptide mimetics prepared by ring-closing metathesis of C-terminal allylglycines with an N-terminal beta-vinyl-substituted phosphotyrosyl mimetic. Bioorg Med Chem 2005; 13:2431-8. [PMID: 15755645 DOI: 10.1016/j.bmc.2005.01.052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Accepted: 01/24/2005] [Indexed: 11/28/2022]
Abstract
Preferential binding of ligands to Grb2 SH2 domains in beta-bend conformations has made peptide cyclization a logical means of effecting affinity enhancement. This is based on the concept that constraint of open-chain sequences to bend geometries may reduce entropy penalties of binding. The current study extends this approach by undertaking ring-closing metathesis (RCM) macrocyclization between i and i+3 residues through a process involving allylglycines and beta-vinyl-functionalized residues. Ring closure in this fashion results in minimal macrocyclic tetrapeptide mimetics. The predominant effects of such macrocyclization on Grb2 SH2 domain binding affinity were increases in rates of association (from 7- to 16-fold) relative to an open-chain congener, while decreases in dissociation rates were less pronounced (approximately 2-fold). The significant increases in association rates were consistent with pre-ordering of solution conformations to near those required for binding. Data from NMR experiments and molecular modeling simulations were used to interpret the binding results. An understanding of the conformational consequences of such i to i+3 ring closure may facilitate its application to other systems where bend geometries are desired.
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Affiliation(s)
- Shinya Oishi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, National Institutes of Health, PO Box B, Bldg. 376 Boyles St. Frederick, MD 21702-1201, USA
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Wu Z, Maderia M, Barchi JJ, Marquez VE, Bax A. Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy. Proc Natl Acad Sci U S A 2004; 102:24-8. [PMID: 15618396 PMCID: PMC544063 DOI: 10.1073/pnas.0408498102] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in bending of the DNA helix axis caused by the introduction of conformationally locked nucleotide analogs into the center region of the palindromic Dickerson dodecamer, d(CGCGAATTCGCG)(2), have been studied by NMR measurement of residual one-bond (13)C-(1)H dipolar couplings. Thymidine analogs, in which the deoxyribose was substituted by bicyclo[3.1.0]hexane, were incorporated in the T7, T8, and T7T8 positions. These nucleotide analogs restrict the ring pucker to the C2'-exo or "north" conformation, instead of C2'-endo or "south," which dominates in regular B-form DNA. For all three oligomers, bending toward the major groove is found relative to the native molecule. The effects are additive with bending of 5 +/- 1 degrees per locked nucleotide. Measurement of the change in bending is more accurate than measurement of the bending angle itself and requires far fewer experimental data.
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Affiliation(s)
- Zhengrong Wu
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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Keay SK, Szekely Z, Conrads TP, Veenstra TD, Barchi JJ, Zhang CO, Koch KR, Michejda CJ. An antiproliferative factor from interstitial cystitis patients is a frizzled 8 protein-related sialoglycopeptide. Proc Natl Acad Sci U S A 2004; 101:11803-8. [PMID: 15282374 PMCID: PMC511055 DOI: 10.1073/pnas.0404509101] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Approximately 1 million people in the United States suffer from interstitial cystitis, a chronic painful urinary bladder disorder characterized by thinning or ulceration of the bladder epithelial lining; its etiology is unknown. We have identified a glycosylated frizzled-related peptide inhibitor of cell proliferation that is secreted specifically by bladder epithelial cells from patients with this disorder. This antiproliferative factor (APF) profoundly inhibits bladder cell proliferation by means of regulation of cell adhesion protein and growth factor production. The structure of APF was deduced by using ion trap mass spectrometry (MS), enzymatic digestion, lectin affinity chromatography, and total synthesis, and confirmed by coelution of native and synthetic APF derivatives on microcapillary reversed-phase liquid chromatography (microRPLC)/MS. APF was determined to be an acidic, heat-stable sialoglycopeptide whose peptide chain has 100% homology to the putative sixth transmembrane domain of frizzled 8. Both synthetic and native APF had identical biological activity in normal bladder epithelial cells and T24 bladder cancer cells. Northern blot analysis indicated binding of a probe containing the sequence for the frizzled 8 segment with mRNA extracted from cells of patients with interstitial cystitis but not controls. APF is therefore a frizzled-related peptide growth inhibitor shown to contain exclusively a transmembrane segment of a frizzled protein and is a potential biomarker for interstitial cystitis.
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Affiliation(s)
- Susan K Keay
- Division of Infectious Diseases, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Maier MA, Choi Y, Gaus H, Barchi JJ, Marquez VE, Manoharan M. Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs. Nucleic Acids Res 2004; 32:3642-50. [PMID: 15247346 PMCID: PMC484163 DOI: 10.1093/nar/gkh667] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oligodeoxyribonucleotides containing pseudorotationally locked sites derived from bicyclo[3.1.0]hexane pseudosugars have been synthesized using adenosine, thymidine and abasic versions of North- and South-methanocarba nucleosides. The reaction conditions for coupling and oxidation steps of oligonucleotide synthesis have been investigated and optimized to allow efficient and facile solid-phase synthesis using phosphoramidite chemistry. Our studies demonstrate that the use of iodine for P(III) to P(V) oxidation leads to strand cleavage at the sites where the pseudosugar is North. In contrast, the same cleavage reaction was not observed in the case of South pseudosugars. Iodine oxidation generates a 5'-phosphate oligonucleotide fragment on the resin and releases the North pseudosugar into the solution. This side reaction, which is responsible for the extremely low yields observed for the incorporation of the North pseudosugar analogs, has been studied in detail and can be easily overcome by replacing iodine with t-butylhydroperoxide as oxidant.
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Affiliation(s)
- Martin A Maier
- Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA
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