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Giancola JB, Grimm JB, Jun JV, Petri YD, Lavis LD, Raines RT. Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye. ACS Chem Biol 2024; 19:908-915. [PMID: 38525961 DOI: 10.1021/acschembio.3c00713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/26/2024]
Abstract
The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.
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Affiliation(s)
- JoLynn B Giancola
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Joomyung V Jun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Wralstad EC, Raines RT. Sensitive detection of SARS-CoV-2 main protease 3CL pro with an engineered ribonuclease zymogen. Protein Sci 2024; 33:e4916. [PMID: 38501598 PMCID: PMC10949392 DOI: 10.1002/pro.4916] [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: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 03/20/2024]
Abstract
Alongside vaccines and antiviral therapeutics, diagnostic tools are a crucial aid in combating the COVID-19 pandemic caused by the etiological agent SARS-CoV-2. All common assays for infection rely on the detection of viral sub-components, including structural proteins of the virion or fragments of the viral genome. Selective pressure imposed by human intervention of COVID-19 can, however, induce viral mutations that decrease the sensitivity of diagnostic assays based on biomolecular structure, leading to an increase in false-negative results. In comparison, mutations are unlikely to alter the function of viral proteins, and viral machinery is under less selective pressure from vaccines and therapeutics. Accordingly, diagnostic assays that rely on biomolecular function can be more robust than ones that rely on biopolymer structure. Toward this end, we used a split intein to create a circular ribonuclease zymogen that is activated by the SARS-CoV-2 main protease, 3CLpro . Zymogen activation by 3CLpro leads to a >300-fold increase in ribonucleolytic activity, which can be detected with a highly sensitive fluorogenic substrate. This coupled assay can detect low nanomolar concentrations of 3CLpro within a timeframe comparable to that of common antigen-detection protocols. More generally, the concept of detecting a protease by activating a ribonuclease could be the basis of diagnostic tools for other indications.
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Affiliation(s)
- Evans C. Wralstad
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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3
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Araiza-Olivera D, Prudnikova TY, Uribe-Alvarez C, Cai KQ, Franco-Barraza J, Dones JM, Raines RT, Chernoff J. Identifying and targeting key driver genes for collagen production within the 11q13/14 breast cancer amplicon. bioRxiv 2024:2024.03.27.587019. [PMID: 38586042 PMCID: PMC10996585 DOI: 10.1101/2024.03.27.587019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Genetic studies indicate that breast cancer can be divided into several basic molecular groups. One of these groups, termed IntClust-2, is characterized by amplification of a small portion of chromosome 11 and has a median survival of only five years. Several cancer-relevant genes occupy this portion of chromosome 11, and it is thought that overexpression of a combination of driver genes in this region is responsible for the poor outcome of women in this group. In this study we used a gene editing method to knock out, one by one, each of 198 genes that are located within the amplified region of chromosome 11 and determined how much each of these genes contributed to the survival of breast cancer cells. In addition to well-known drivers such as CCND1 and PAK1 , we identified two different genes ( SERPINH1 and P4HA3 ), that encode proteins involved in collagen synthesis and organization. Using both in vitro and in vivo functional analyses, we determined that P4HA3 and/or SERPINH1 provide a critical driver function on IntClust-2 basic processes, such as viability, proliferation, and migration. Inhibiting these enzymes via genetic or pharmacologic means reduced collagen synthesis and impeded oncogenic signaling transduction in cell culture models, and a small-molecule inhibitor of P4HA3 was effective in treating 11q13 tumor growth in an animal model. As collagen has a well-known association with tissue stiffness and aggressive forms of breast cancer, we believe that the two genes we identified provide an opportunity for a new therapeutic strategy in IntClust-2 breast cancers.
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Levandowski BJ, Graham BJ, Houk KN, Raines RT. Click Organocatalysis: Acceleration of Azide-Alkyne Cycloadditions with Mutually Orthogonal Click Reactions. J Org Chem 2024; 89:2232-2237. [PMID: 38275285 PMCID: PMC10922906 DOI: 10.1021/acs.joc.3c02182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
"Click organocatalysis" uses mutually orthogonal click reactions to organocatalyze a click reaction. We report the development of an isobenzofuran organocatalyst that increases the rate and regioselectivity of an azide-alkyne cycloaddition. The organocatalytic cycle consists of (1) a Diels-Alder reaction of an alkyne with a diarylisobenzofuran to form a benzooxanorbornadiene, (2) a 1,3-dipolar cycloaddition with an azide to form a 4,5-dihydro-1,2,3-triazole, and (3) a retro-Diels-Alder reaction that releases the triazole product and regenerates the diarylisobenzofuran organocatalyst. The diarylisobenzofuran organocatalyst was computationally designed to catalyze the reaction of perfluorophenyl azide and methyl propiolate to selectively form a 1,4-triazole product. Experimental validation of the designed organocatalyst was obtained with methyl 4-azido-2,3,5,6-tetrafluorobenzoate and methyl propiolate.
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Affiliation(s)
- Brian J. Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - Brian J. Graham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United States
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Abstract
Organoboron acids are stable, organic-soluble Lewis acids with potential application as catalysts for a wide variety of chemical reactions. In this review, we summarize the utility of boronic and borinic acids, as well as boric acid, as catalysts for organic transformations. Typically, the catalytic processes exploit the Lewis acidity of trivalent boron, enabling the reversible formation of a covalent bond with oxygen. Our focus is on recent developments in the catalysis of dehydration, carbonyl condensation, acylation, alkylation, and cycloaddition reactions. We conclude that organoboron acids have a highly favorable prospectus as the source of new catalysts.
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Affiliation(s)
- Brian J Graham
- Department of Chemistry, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Tanrikulu IC, Dang L, Nelavelli L, Ellison AJ, Olsen BD, Jin S, Raines RT. Synthetic Collagen Hydrogels through Symmetric Self-Assembly of Small Peptides. Adv Sci (Weinh) 2024; 11:e2303228. [PMID: 37997193 PMCID: PMC10797479 DOI: 10.1002/advs.202303228] [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] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/10/2023] [Indexed: 11/25/2023]
Abstract
Animal-sourced hydrogels, such as collagen, are widely used as extracellular-matrix (ECM) mimics in tissue engineering but are plagued with problems of reproducibility, immunogenicity, and contamination. Synthetic, chemically defined hydrogels can avoid such issues. Despite the abundance of collagen in the ECM, synthetic collagen hydrogels are extremely rare due to design challenges brought on by the triple-helical structure of collagen. Sticky-ended symmetric self-assembly (SESSA) overcomes these challenges by maximizing interactions between the strands of the triple helix, allowing the assembly of collagen-mimetic peptides (CMPs) into robust synthetic collagen nanofibers. This optimization, however, also minimizes interfiber contacts. In this work, symmetric association states for the SESSA of short CMPs to probe their increased propensity for interfiber association are modelled. It is found that 33-residue CMPs not only self-assemble through sticky ends, but also form hydrogels. These self-assemblies behave with remarkable consistency across multiple scales and present a clear link between their triple-helical architecture and the properties of their hydrogels. The results show that SESSA is an effective and robust design methodology that enables the rational design of synthetic collagen hydrogels.
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Affiliation(s)
- I. Caglar Tanrikulu
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Lianna Dang
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Lekha Nelavelli
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Aubrey J. Ellison
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Bradley D. Olsen
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMA02139USA
| | - Song Jin
- Department of ChemistryUniversity of Wisconsin–MadisonMadisonWI53706USA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMA02139USA
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7
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Borgula IM, Shuvaev S, Abston E, Rotile NJ, Weigand-Whittier J, Zhou IY, Caravan P, Raines RT. Detection of Pulmonary Fibrosis with a Collagen-Mimetic Peptide. ACS Sens 2023; 8:4008-4013. [PMID: 37930825 PMCID: PMC10842190 DOI: 10.1021/acssensors.3c00717] [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] [Indexed: 11/08/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a disease of unknown etiology that is characterized by excessive deposition and abnormal remodeling of collagen. IPF has a mean survival time of only 2-5 years from diagnosis, creating a need to detect IPF at an earlier stage when treatments might be more effective. We sought to develop a minimally invasive probe that could detect molecular changes in IPF-associated collagen. Here, we describe the design, synthesis, and performance of [68Ga]Ga·DOTA-CMP, which comprises a positron-emitting radioisotope linked to a collagen-mimetic peptide (CMP). This peptide mimics the natural structure of collagen and detects irregular collagen matrices by annealing to damaged collagen triple helices. We assessed the ability of the peptide to detect aberrant lung collagen selectively in a bleomycin-induced mouse model of pulmonary fibrosis using positron emission tomography (PET). [68Ga]Ga·DOTA-CMP PET demonstrated higher and selective uptake in a fibrotic mouse lung compared to controls, minimal background signal in adjacent organs, and rapid clearance via the renal system. These studies suggest that [68Ga]Ga·DOTA-CMP identifies fibrotic lungs and could be useful in the early diagnosis of IPF.
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Affiliation(s)
- Isabella M. Borgula
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sergey Shuvaev
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Eric Abston
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
- Department of Thoracic Surgery, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
| | - Nicholas J. Rotile
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Jonah Weigand-Whittier
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Iris Y. Zhou
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Peter Caravan
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02124, United States
- Athinoula A. Martinos Center for Biomedical Imaging, The Institute for Innovation in Imaging, Massachusetts General Hospital and Harvard Medical School, 149 Thirteenth Street, Charlestown, Massachusetts 02129, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Levandowski BJ, Abularrage NS, Graham BJ, Raines RT. Computational study of an oxetane 4 H-pyrazole as a Diels-Alder diene. Tetrahedron Lett 2023; 130:154768. [PMID: 37860707 PMCID: PMC10584014 DOI: 10.1016/j.tetlet.2023.154768] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
We combine the effects of spirocyclization and hyperconjugation to increase the Diels-Alder reactivity of the 4H-pyrazole scaffold. A density functional theory (DFT) investigation predicts that 4H-pyrazoles containing an oxetane functionality at the saturated center are extremely reactive despite having a relatively high-lying lowest unoccupied molecular orbital (LUMO) energy.
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Affiliation(s)
- Brian J. Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Nile S. Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Brian J. Graham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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9
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Wralstad EC, Sayers J, Raines RT. Bayesian Inference Elucidates the Catalytic Competency of the SARS-CoV-2 Main Protease 3CL pro. Anal Chem 2023; 95:14981-14989. [PMID: 37750823 PMCID: PMC10662973 DOI: 10.1021/acs.analchem.3c02459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/27/2023]
Abstract
The main protease of SARS-CoV-2, 3CLpro, is a dimeric enzyme that is indispensable to viral replication and presents an attractive opportunity for therapeutic intervention. Previous reports regarding the key properties of 3CLpro and its highly similar SARS-CoV homologue conflict dramatically. Values of the dimeric Kd and enzymic kcat/KM differ by 106- and 103-fold, respectively. Establishing a confident benchmark of the intrinsic capabilities of this enzyme is essential for combating the current pandemic as well as potential future outbreaks. Here, we use enzymatic methods to characterize the dimerization and catalytic efficiency of the authentic protease from SARS-CoV-2. Specifically, we use the rigor of Bayesian inference in a Markov Chain Monte Carlo analysis of progress curves to circumvent the limitations of traditional Michaelis-Menten initial rate analysis. We report that SARS-CoV-2 3CLpro forms a dimer at pH 7.5 that has Kd = 16 ± 4 nM and is capable of catalysis with kcat = 9.9 ± 1.5 s-1, KM = 0.23 ± 0.01 mM, and kcat/KM = (4.3 ± 0.7) × 104 M-1 s-1. We also find that enzymatic activity decreases substantially in solutions of high ionic strength, largely as a consequence of impaired dimerization. We conclude that 3CLpro is a more capable catalyst than appreciated previously, which has important implications for the design of antiviral therapeutic agents that target 3CLpro.
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Affiliation(s)
- Evans C Wralstad
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jessica Sayers
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Calabretta LO, Petri YD, Raines RT. Fluorescent Guanidinium-Azacarbazole for Oxoanion Binding in Water. J Org Chem 2023; 88:11694-11701. [PMID: 37530571 PMCID: PMC10530381 DOI: 10.1021/acs.joc.3c00982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2023]
Abstract
Oxoanions such as carboxylates, phosphates, and sulfates play important roles in both chemistry and biology and are abundant on the cell surface. We report on the synthesis and properties of a rationally designed guanidinium-containing oxoanion binder, 1-guanidino-8-amino-2,7-diazacarbazole (GADAC). GADAC binds to a carboxylate, phosphate, and sulfate in pure water with affinities of 3.6 × 104, 1.1 × 103, and 4.2 × 103 M-1, respectively. Like 2-azacarbazole, which is a natural product that enables scorpions to fluoresce, GADAC is fluorescent in water (λabs = 356 nm, λem = 403 nm, ε = 13,400 M-1 cm-1). The quantum yield of GADAC is pH-sensitive, increasing from Φ = 0.12 at pH 7.4 to Φ = 0.53 at pH 4.0 as a result of the protonation of the aminopyridine moiety. The uptake of GADAC into live human melanoma cells is detectable in the DAPI channel at low micromolar concentrations. Its properties make GADAC a promising candidate for applications in oxoanion binding and fluorescence labeling in biological (e.g., the delivery of cargo into cells) and other contexts.
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Affiliation(s)
- Lindsey O. Calabretta
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Lee TH, Checco JW, Malcolm T, Eller CH, Raines RT, Gellman SH, Lee EF, Fairlie WD, Aguilar MI. Differential membrane binding of α/β-peptide foldamers: implications for cellular delivery and mitochondrial targeting. Aust J Chem 2023; 76:482-492. [PMID: 37780415 PMCID: PMC10540276 DOI: 10.1071/ch23063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The intrinsic pathway of apoptosis is regulated by the Bcl-2 family of proteins. Inhibition of the anti-apoptotic members represents a strategy to induce apoptotic cell death in cancer cells. We have measured the membrane binding properties of a series of peptides, including modified α/β-peptides, designed to exhibit enhanced membrane permeability to allow cell entry and improved access for engagement of Bcl-2 family members. The peptide cargo is based on the pro-apoptotic protein Bim, which interacts with all anti-apoptotic proteins to initiate apoptosis. The α/β-peptides contained cyclic β-amino acid residues designed to increase their stability and membrane-permeability. Dual polarisation interferometry was used to study the binding of each peptide to two different model membrane systems designed to mimic either the plasma membrane or the outer mitochondrial membrane. The impact of each peptide on the model membrane structure was also investigated, and the results demonstrated that the modified peptides had increased affinity for the mitochondrial membrane and significantly altered the structure of the bilayer. The results also showed that the presence of an RRR motif significantly enhanced the ability of the peptides to bind to and insert into the mitochondrial membrane mimic, and provide insights into the role of selective membrane targeting of peptides.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry & Molecular Biology, Monash University, Clayton Vic, 3800, Australia
| | - James W Checco
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Current address: Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- Current address: The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tess Malcolm
- Department of Biochemistry & Molecular Biology, Monash University, Clayton Vic, 3800, Australia
- Current address: School of Chemistry, University of Melbourne, Parkville, Vic 3052, Australia
| | - Chelcie H Eller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ronald T Raines
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Erinna F Lee
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria 3086, Australia
| | - W Douglas Fairlie
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry & Molecular Biology, Monash University, Clayton Vic, 3800, Australia
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Abularrage NS, Levandowski BJ, Giancola JB, Graham BJ, Raines RT. Bioorthogonal 4 H-pyrazole "click" reagents. Chem Commun (Camb) 2023; 59:4451-4454. [PMID: 36987784 PMCID: PMC10088812 DOI: 10.1039/d3cc00112a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
4H-Pyrazoles are emerging as useful click reagents. Fluorinating the saturated center enables 4H-pyrazoles to react rapidly as Diels-Alder dienes without a catalyst but compromises the stability of these dienes under physiological conditions. To identify more stable 4H-pyrazoles for bioorthogonal chemistry applications, we investigated the Diels-Alder reactivity and biological stability of three 4-oxo-substituted 4H-pyrazoles. We found that these dienes undergo rapid Diels-Alder reactions with endo-bicyclo[6.1.0]non-4-yne (BCN) while being much more stable to biological nucleophiles than their fluorinated counterparts. We attribute the rapid Diels-Alder reactivity of the optimal oxygen-substituted pyrazole to a combination of antiaromaticity, predistortion, and spirocyclization. Their reactivity and stability suggest that 4-oxo-4H-pyrazoles can be useful bioorthogonal reagents.
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Affiliation(s)
- Nile S Abularrage
- Department of Chemistry, Massachusetts institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Brian J Levandowski
- Department of Chemistry, Massachusetts institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - JoLynn B Giancola
- Department of Chemistry, Massachusetts institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Brian J Graham
- Department of Chemistry, Massachusetts institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Ronald T Raines
- Department of Chemistry, Massachusetts institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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13
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Levandowski BJ, Abularrage NS, Raines RT. Cover Image. J PHYS ORG CHEM 2023. [DOI: 10.1002/poc.4367] [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: 03/12/2023]
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14
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Petri YD, Gutierrez CS, Raines RT. Chemoselective Caging of Carboxyl Groups for On‐Demand Protein Activation with Small Molecules. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202215614] [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: 03/29/2023]
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15
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Petri YD, Gutierrez CS, Raines RT. Chemoselective Caging of Carboxyl Groups for On-Demand Protein Activation with Small Molecules. Angew Chem Int Ed Engl 2023; 62:e202215614. [PMID: 36964973 DOI: 10.1002/anie.202215614] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Tools for on-demand protein activation enable impactful gain-of-function studies in biological settings. Thus far, however, proteins have been chemically caged at primarily Lys, Tyr, and Sec, typically through the genetic encoding of unnatural amino acids. Here, we report that the preferential reactivity of diazo compounds with protonated acids can be used to expand this toolbox to solvent-accessible carboxyl groups with an elevated pKa. As a model protein, we employed lysozyme (Lyz), which has an active-site Glu35 with a pKa of 6.2. A diazo compound with a bioorthogonal self-immolative handle esterified Glu35 selectively, inactivating Lyz. The hydrolytic activity of the caged Lyz on bacterial cell walls was restored with two small-molecule triggers. The decaging was more efficient by small molecules than by esterases. This simple chemical strategy was also applied to a hemeprotein and an aspartyl protease, setting the stage for broad applicability.
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Affiliation(s)
- Yana D Petri
- Massachusetts Institute of Technology, Department of Chemistry, UNITED STATES
| | - Clair S Gutierrez
- Massachusetts Institute of Technology, Department of Chemistry, UNITED STATES
| | - Ronald T Raines
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, 18-498, 02139-4307, Cambridge, UNITED STATES
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Jun JV, Petri YD, Erickson LW, Raines RT. Modular Diazo Compound for the Bioreversible Late-Stage Modification of Proteins. J Am Chem Soc 2023; 145:6615-6621. [PMID: 36920197 PMCID: PMC10175043 DOI: 10.1021/jacs.2c11325] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
We introduce a versatile strategy for the bioreversible modification of proteins. Our strategy is based on a tricomponent molecule, synthesized in three steps, that incorporates a diazo moiety for chemoselective esterification of carboxyl groups, a pyridyl disulfide group for late-stage functionalization with thiolated ligands, and a self-immolative carbonate group for esterase-mediated cleavage. Using cytochrome c (Cyt c) and the green fluorescent protein (GFP) as models, we generated protein conjugates modified with diverse domains for cellular delivery that include a small molecule, targeting and cell-penetrating peptides (CPPs), and a large polysaccharide. As a proof of concept, we used our strategy to effect the delivery of proteins into the cytosol of live mammalian cells in the presence of serum. The cellular delivery of functional Cyt c, which induces apoptosis, highlighted the advantage of bioreversible conjugation on a carboxyl group versus irreversible conjugation on an amino group. The ease and utility of this traceless modification provide new opportunities for chemical biologists.
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17
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Graham B, Windsor IW, Raines RT. Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability. ACS Med Chem Lett 2023; 14:171-175. [PMID: 36793428 PMCID: PMC9923841 DOI: 10.1021/acsmedchemlett.2c00464] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
HIV-1 protease is an important target for pharmaceutical intervention in HIV infection. Extensive structure-based drug design led to darunavir becoming a key chemotherapeutic agent. We replaced the aniline group of darunavir with a benzoxaborolone to form BOL-darunavir. This analogue has the same potency as darunavir as an inhibitor of catalysis by wild-type HIV-1 protease and, unlike darunavir, does not lose potency as an inhibitor of the common D30N variant. Moreover, BOL-darunavir is much more stable to oxidation than is a simple phenylboronic acid analogue of darunavir. X-ray crystallography revealed an extensive network of hydrogen bonds between the enzyme and benzoxaborolone moiety, including a novel direct hydrogen bond from a main-chain nitrogen to the carbonyl oxygen of the benzoxaborolone moiety that displaces a water molecule. These data highlight the utility of benzoxaborolone as a pharmacophore.
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Affiliation(s)
- Brian
J. Graham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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18
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Levandowski BJ, Abularrage NS, Raines RT. Spirocyclization enhances the Diels–Alder reactivities of geminally substituted cyclopentadienes and 4
H
‐pyrazoles. J PHYS ORG CHEM 2022; 36. [PMID: 36968255 PMCID: PMC10038129 DOI: 10.1002/poc.4478] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Diels-Alder reactivity of 5-membered dienes is tunable through spirocyclization at the saturated center. As the size of the spirocycle decreases, the Diels-Alder reactivity increases with the cyclobutane spirocycle, spiro[3.4]octa-5,7-diene, being the most reactive. Density functional theory calculations suggest that spiro[3.4]octa-5,7-diene dimerizes 220,000-fold faster than 5,5-dimethylcyclopentadiene and undergoes a Diels-Alder reaction with ethylene 1,200-fold faster than 5,5-dimethylcyclopentadiene. These findings show that spirocyclization is an effective way to enhance the Diels-Alder reactivity of geminally substituted 5-membered dienes.
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Affiliation(s)
- Brian J. Levandowski
- Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts United States
| | - Nile S. Abularrage
- Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts United States
| | - Ronald T. Raines
- Department of Chemistry Massachusetts Institute of Technology Cambridge Massachusetts United States
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19
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Calabretta LO, Yang J, Raines RT. N α -Methylation of arginine: Implications for cell-penetrating peptides. J Pept Sci 2022; 29:e3468. [PMID: 36494904 PMCID: PMC10073267 DOI: 10.1002/psc.3468] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The field of cell-penetrating peptides is dominated by the use of oligomers of arginine residues. Octanol-water partitioning in the presence of an anionic lipid is a validated proxy for cell-penetrative efficacy. Here, we add one, two, or three N-methyl groups to Ac-Arg-NH2 and examine the effects on octanol-water partitioning. In the absence of an anionic lipid, none of these arginine derivatives can be detected in the octanol layer. In the presence of sodium dodecanoate, however, increasing N-methylation correlates with increasing partitioning into octanol, which is predictive of higher cell-penetrative ability. We then evaluated fully Nα -methylated oligoarginine peptides and observed an increase in their cellular penetration compared with canonical oligoarginine peptides in some contexts. These findings indicate that a simple modification, Nα -methylation, can enhance the performance of cell-penetrating peptides.
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Affiliation(s)
- Lindsey O Calabretta
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jinyi Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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20
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Cheah KM, Jun JV, Wittrup KD, Raines RT. Host-Guest Complexation by β-Cyclodextrin Enhances the Solubility of an Esterified Protein. Mol Pharm 2022; 19:3869-3876. [PMID: 36036888 DOI: 10.1021/acs.molpharmaceut.2c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The carboxyl groups of a protein can be esterified by reaction with a diazo compound, 2-diazo-2-(p-methylphenyl)-N,N-dimethylacetamide. This esterification enables the entry of the protein into the cytosol of a mammalian cell, where the nascent ester groups are hydrolyzed by endogenous esterases. The low aqueous solubility of the ensuing esterified protein is, however, a major practical challenge. Solubility screening revealed that β-cyclodextrin (β-CD) is an optimal solubilizing agent for esterified green fluorescent protein (est-GFP). Its addition can increase the recovery of est-GFP by 10-fold. α-CD, γ-CD, and cucurbit-7-uril are less effective excipients. 1H NMR titration experiments revealed that β-CD encapsulates the hydrophobic tolyl group of ester conjugates with Ka = 321 M-1. Combining l-arginine and sucrose with β-CD enables the nearly quantitative recovery of est-GFP. Thus, the insolubility of esterified proteins can be overcome with excipients.
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21
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Backman LRF, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Structurally investigating a niche pathway for chemical reversal of proline hydroxylation in the pathogen
Clostridioides difficile. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2341] [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: 11/11/2022]
Affiliation(s)
| | | | | | | | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMA
| | - Emily P. Balskus
- Harvard UniversityCambridgeMA
- Howard Hughes Medical InstituteCambridgeMA
| | - Catherine L. Drennan
- Massachusetts Institute of TechnologyCambridgeMA
- Howard Hughes Medical InstituteCambridgeMA
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22
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Abstract
The S‐alkylation of Cys residues with a maleimide and the Nϵ‐acylation of Lys residues with an N‐hydroxysuccinimide (NHS) ester are common methods for bioconjugation. Using Cys and Lys derivatives as proxies, we assessed differences in reactivity depending on the position of Cys or Lys in a protein sequence. We find that Cys position is exploitable to improve site‐selectivity in maleimide‐based modifications. Reactivity decreases substantially in the order N‐terminal>in‐chain>C‐terminal Cys due to modulation of sulfhydryl pKa by the α‐ammonium and carboxylate groups at the termini. A lower pKa value yields a larger fraction thiolate, which promotes selectivity while somewhat decreasing thiolate nucleophilicity in accord with βnuc
=0.41. Lowering pH and salt concentration enhances selectivity still further. In contrast, differences in the reactivity of Lys towards an NHS ester were modest due to an appreciable decrease in amino group nucleophilicity with a lower pKa of its conjugate acid. Hence, site‐selective Lys modification protocols will require electrophiles other than NHS esters.
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Affiliation(s)
- Linus B. Boll
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Avenue 02139 Cambridge UNITED STATES
| | - Ronald T. Raines
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Avenue, 18-498 02139-4307 Cambridge UNITED STATES
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23
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Chattopadhyay S, Teixeira LBC, Kiessling LL, McAnulty JF, Raines RT. Bifunctional Peptide that Anneals to Damaged Collagen and Clusters TGF-β Receptors Enhances Wound Healing. ACS Chem Biol 2022; 17:314-321. [PMID: 35084170 DOI: 10.1021/acschembio.1c00745] [Citation(s) in RCA: 3] [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] [Indexed: 11/29/2022]
Abstract
Transforming growth factor-β (TGF-β) plays important roles in wound healing. The activity of TGF-β is initiated upon the binding of the growth factor to the extracellular domains of its receptors. We sought to facilitate the activation by clustering these extracellular domains. To do so, we used a known peptide that binds to TGF-β receptors without diminishing their affinity for TGF-β. We conjugated this peptide to a collagen-mimetic peptide that can anneal to the damaged collagen in a wound bed. We find that the conjugate enhances collagen deposition and wound closure in mice in a manner consistent with the clustering of TGF-β receptors. This strategy provides a means to upregulate the TGF-β signaling pathway without adding exogenous TGF-β and could inspire means to treat severe wounds.
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Affiliation(s)
- Sayani Chattopadhyay
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Leandro B. C. Teixeira
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan F. McAnulty
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Hetrick KJ, Raines RT. Assessing and utilizing esterase specificity in antimicrobial prodrug development. Methods Enzymol 2022; 664:199-220. [DOI: 10.1016/bs.mie.2021.11.008] [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: 11/25/2022]
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25
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Abstract
Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here, we review the functions of two ptRNases: RNase 1 and angiogenin. RNase 1, which is an abundant ptRNase with high catalytic activity, has newly discovered roles in inflammation and blood coagulation. Angiogenin, which promotes neovascularization, is now known to play roles in the progression of cancer and amyotrophic lateral sclerosis, as well as in the cellular stress response. Ongoing work is illuminating the biology of these and other ptRNases.
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Affiliation(s)
- Emily R Garnett
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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26
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Abstract
BACKGROUND Targeting RNA is a promising yet underdeveloped modality for the selective killing of cells infected with HIV-1. The secretory ribonucleases (RNases) found in vertebrates have cytotoxic ribonucleolytic activity that is kept in check by a cytosolic ribonuclease inhibitor protein, RI. METHODS We engineered amino acid substitutions that enable human RNase 1 to evade RI upon its cyclization into a zymogen that is activated by the HIV-1 protease. In effect, the zymogen has an HIV-1 protease cleavage site between the termini of the wild-type enzyme, thereby positioning a cleavable linker over the active site that blocks access to a substrate. RESULTS The amino acid substitutions in RNase 1 diminish its affinity for RI by 106-fold and confer high toxicity for T-cell leukemia cells. Pretreating these cells with the zymogen leads to a substantial drop in their viability upon HIV-1 infection, indicating specific toxicity toward infected cells. CONCLUSIONS These data demonstrate the utility of ribonuclease zymogens as biologic prodrugs.
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Affiliation(s)
- Ian W Windsor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
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27
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Levandowski BJ, Abularrage NS, Raines RT. Geminal Repulsion Disrupts Diels-Alder Reactions of Geminally Substituted Cyclopentadienes and 4 H-Pyrazoles. Tetrahedron 2021; 91. [PMID: 34290459 DOI: 10.1016/j.tet.2021.132160] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have experimentally and computationally explored the sluggish Diels-Alder reactivities of the geminally substituted 5,5-dimethylcyclopentadiene and 5,5-dimethyl-2,3-diazacyclopentadiene (4,4-dimethyl-4H-pyrazole) scaffolds. We found that geminal dimethylation of 1,2,3,4-tetramethylcyclopentadiene to 1,2,3,4,5,5-hexamethylcyclopentadiene decreases the Diels-Alder reactivity towards maleimide by 954-fold. Quantum mechanical calculations revealed that the decreased Diels-Alder reactivities of gem-dimethyl substituted cyclopentadienes and 2,3-diazacyclopentadienes are not a consequence of unfavorable steric interactions between the diene and dienophile as reported previously, but a consequence of the increased repulsion within the gem-dimethyl group in the transition state. The findings have implications for the use of cyclopentadienes in "click" chemistry.
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Affiliation(s)
- Brian J Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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28
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Dones JM, Abularrage NS, Khanal N, Gold B, Raines RT. Acceleration of 1,3-Dipolar Cycloadditions by Integration of Strain and Electronic Tuning. J Am Chem Soc 2021; 143:9489-9497. [PMID: 34151576 DOI: 10.1021/jacs.1c03133] [Citation(s) in RCA: 6] [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: 01/17/2023]
Abstract
The 1,3-dipolar cycloaddition between azides and alkynes provides new means to probe and control biological processes. A major challenge is to achieve high reaction rates with stable reagents. The optimization of alkynyl reagents has relied on two strategies: increasing strain and tuning electronics. We report on the integration of these strategies. A computational analysis suggested that a CH → N aryl substitution in dibenzocyclooctyne (DIBO) could be beneficial. In transition states, the nitrogen of 2-azabenzo-benzocyclooctyne (ABC) engages in an n→π* interaction with the C=O of α-azidoacetamides and forms a hydrogen bond with the N-H of α-diazoacetamides. These dipole-specific interactions act cooperatively with electronic activation of the strained π-bond to increase reactivity. We found that ABC does indeed react more quickly with α-azidoacetamides and α-diazoacetamides than its constitutional isomer, dibenzoazacyclooctyne (DIBAC). ABC and DIBAC have comparable chemical stability in a biomimetic solution. Both ABC and DIBO are accessible in three steps by the alkylidene carbene-mediated ring expansion of commercial cycloheptanones. Our findings enhance the accessibility and utility of 1,3-dipolar cycloadditions and encourage further innovation.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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29
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Abstract
Cyclopentadiene is one of the most reactive dienes in normal electron-demand Diels-Alder reactions. The high reactivities and yields of cyclopentadiene cycloadditions make them ideal as click reactions. In this review, we discuss the history of the cyclopentadiene cycloaddition as well as applications of cyclopentadiene click reactions. Our emphasis is on experimental and theoretical studies on the reactivity and stability of cyclopentadiene and cyclopentadiene derivatives.
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Affiliation(s)
- Brian J. Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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30
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Abstract
In light of the continued threat of antimicrobial-resistant bacteria, new strategies to expand the repertoire of antimicrobial compounds are necessary. Prodrugs are an underexploited strategy in this effort. Here, we report on the enhanced antimicrobial activity of a prodrug toward bacteria having an enzyme capable of its activation. A screen led us to the sulfurol ester of the antibiotic trans-3-(4-chlorobenzoyl)acrylic acid. An endogenous esterase makes Mycolycibacterium smegmatis sensitive to this prodrug. Candidate esterases were identified, and their heterologous production made Escherichia coli sensitive to the ester prodrug. Taken together, these data suggest a new approach to the development of antimicrobial compounds that takes advantage of endogenous enzymatic activities to target specific bacteria.
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Affiliation(s)
- Kenton J. Hetrick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Miguel A. Aguilar Ramos
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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31
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Abstract
α-Aryl-α-diazoamides were synthesized in two steps under mild conditions. This expeditious route employs Pd-catalyzed C-H arylation of N-succinimidyl 2-diazoacetate to obtain N-succinimidyl 2-aryl-2-diazoacetates, followed by aminolysis. The ensuing diazo compounds can esterify carboxyl groups in aqueous solution, and the ester products are substrates for an esterase. The broad scope of the synthetic route enables the continued development of diazo compounds in chemical biology.
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Affiliation(s)
- Joomyung V Jun
- Department of Chemistry and Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry and Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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32
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Dhanjee HH, Buslov I, Windsor IW, Raines RT, Pentelute BL, Buchwald SL. Palladium-Protein Oxidative Addition Complexes by Amine-Selective Acylation. J Am Chem Soc 2020; 142:21237-21242. [PMID: 33319995 DOI: 10.1021/jacs.0c09180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Palladium oxidative addition complexes (OACs) are traditionally accessed by treating an aryl halide-containing substrate with a palladium(0) source. Here, a new strategy to selectively prepare stable OACs from amino groups on native proteins is presented. The approach relies on an amine-selective acylation reaction that occurs without modification of a preformed palladium(II)-aryl group. Once transferred onto a protein substrate, the palladium(II)-aryl group facilitates conjugation by undergoing reaction with a second, cysteine-containing protein. This operationally simple method is applicable to native, nonengineered enzymes as well as antibodies and is carried out in an aqueous setting and open to air. The resulting Pd-protein OACs are stable, storable reagents that retain biological activity and can be used to achieve protein-protein cross-coupling at nanomolar concentrations within hours.
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Affiliation(s)
- Heemal H Dhanjee
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ivan Buslov
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ian W Windsor
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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33
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Sayers J, Wralstad EC, Raines RT. Semisynthesis of Human Ribonuclease-S. Bioconjug Chem 2020; 32:82-87. [PMID: 33296182 DOI: 10.1021/acs.bioconjchem.0c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its conception, the ribonuclease S complex (RNase S) has led to historic discoveries in protein chemistry, enzymology, and related fields. Derived by the proteolytic cleavage of a single peptide bond in bovine pancreatic ribonuclease (RNase A), RNase S serves as a convenient and reliable model system for incorporating unlimited functionality into an enzyme. Applications of the RNase S system in biomedicine and biotechnology have, however, been hindered by two shortcomings: (1) the bovine-derived enzyme could elicit an immune response in humans, and (2) the complex is susceptible to dissociation. Here, we have addressed both limitations in the first semisynthesis of an RNase S conjugate derived from human pancreatic ribonuclease and stabilized by a covalent interfragment cross-link. We anticipate that this strategy will enable unprecedented applications of the "RNase-S" system.
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Affiliation(s)
- Jessica Sayers
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Evans C Wralstad
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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34
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Abstract
LL-37 is a secretory peptide that has antimicrobial activity. Ribonuclease 1 (RNase 1) is a secretory enzyme that is not cytotoxic. We find that human LL-37 and human RNase 1 can act synergistically to kill Gram-negative bacterial cells. In the presence of nontoxic concentrations of LL-37, RNase 1 is toxic to Escherichia coli cells at picomolar levels. Using wild-type RNase 1 and an inactive variant labeled with a fluorophore, we observe the adherence of RNase 1 to E. coli cells and its cellular entry in the presence of LL-37. These data suggest a natural means of modulating the human microbiome via the cooperation of an endogenous peptide (37 residues) and small enzyme (128 residues).
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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35
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Hu Y, Roberts JM, Kilgore HR, Lani ASM, Raines RT, Schomaker JM. Triple, Mutually Orthogonal Bioorthogonal Pairs through the Design of Electronically Activated Sulfamate-Containing Cycloalkynes. J Am Chem Soc 2020; 142:18826-18835. [PMID: 33085477 PMCID: PMC7891878 DOI: 10.1021/jacs.0c06725] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 12/14/2022]
Abstract
Interest in mutually exclusive pairs of bioorthogonal labeling reagents continues to drive the design of new compounds that are capable of fast and predictable reactions. The ability to easily modify S-, N-, and O-containing cyclooctynes (SNO-OCTs) enables electronic tuning of various SNO-OCTs to influence their cycloaddition rates with Type I-III dipoles. As opposed to optimizations based on just one specific dipole class, the electrophilicity of the alkynes in SNO-OCTs can be manipulated to achieve divergent reactivities and furnish mutually orthogonal dual ligation systems. Significant reaction rate enhancements of a difluorinated SNO-OCT derivative, as compared to the parent scaffold, were noted, with the second-order rate constant in cycloadditions with diazoacetamides exceeding 5.13 M-1 s-1. Computational and experimental studies were employed to inform the design of triple ligation systems that encompass three orthogonal reactivities. Finally, polar SNO-OCTs are rapidly internalized by mammalian cells and remain functional in the cytosol for live-cell labeling, highlighting their potential for diverse in vitro and in vivo applications.
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Affiliation(s)
- Yun Hu
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jessica M. Roberts
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Henry R. Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Amirah S. Mat Lani
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jennifer M. Schomaker
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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Arora PS, Raines RT. Daniel S. Kemp (1936-2020): A Pioneer of Bioorganic Chemistry. ACS Chem Biol 2020; 15:2620-2622. [PMID: 33059455 DOI: 10.1021/acschembio.0c00589] [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: 11/29/2022]
Affiliation(s)
- Paramjit S Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Kilgore HR, Olsson CR, D'Angelo KA, Movassaghi M, Raines RT. n→π* Interactions Modulate the Disulfide Reduction Potential of Epidithiodiketopiperazines. J Am Chem Soc 2020; 142:15107-15115. [PMID: 32701272 DOI: 10.1021/jacs.0c06477] [Citation(s) in RCA: 7] [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] [Indexed: 12/18/2022]
Abstract
Epithiodiketopiperazines (ETPs) are a structurally complex class of fungal natural products with potent anticancer activity. In ETPs, the diketopiperazine ring is spanned by a disulfide bond that is constrained in a high-energy eclipsed conformation. We employed computational, synthetic, and spectroscopic methods to investigate the physicochemical attributes of this atypical disulfide bond. We find that the disulfide bond is stabilized by two n→π* interactions, each with large energies (3-5 kcal/mol). The n→π* interactions in ETPs make disulfide reduction much more difficult, endowing stability in physiological environments in a manner that could impact their biological activity. These data reveal a previously unappreciated means to stabilize a disulfide bond and highlight the utility of the n→π* interaction in molecular design.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chase R Olsson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kyan A D'Angelo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Schroeder AB, Karim A, Ocotl E, Dones JM, Chacko JV, Liu A, Raines RT, Gibson ALF, Eliceiri KW. Optical imaging of collagen fiber damage to assess thermally injured human skin. Wound Repair Regen 2020; 28:848-855. [PMID: 32715561 DOI: 10.1111/wrr.12849] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 05/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Surgery is the definitive treatment for burn patients who sustain full-thickness burn injuries. Visual assessment of burn depth is made by the clinician early after injury but is accurate only up to 70% of the time among experienced surgeons. Collagen undergoes denaturation as a result of thermal injury; however, the association of collagen denaturation and cellular death in response to thermal injury is unknown. While gene expression assays and histologic staining allow for ex vivo identification of collagen changes, these methods do not provide spatial or integrity information in vivo. Thermal effects on collagen and the role of collagen in wound repair have been understudied in human burn models due to a lack of methods to visualize both intact and denatured collagen. Hence, there is a critical need for a clinically applicable method to discriminate between damaged and intact collagen fibers in tissues. We present two complementary candidate methods for visualization of collagen structure in three dimensions. Second harmonic generation imaging offers a label-free, high-resolution method to identify intact collagen. Simultaneously, a fluorophore-tagged collagen-mimetic peptide can detect damaged collagen. Together, these methods enable the characterization of collagen damage in human skin biopsies from burn patients, as well as ex vivo thermally injured human skin samples. These combined methods could enhance the understanding of the role of collagen in human wound healing after thermal injury and potentially assist in clinical decision-making.
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Affiliation(s)
- Alexandra B Schroeder
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Medical Engineering, Morgridge Institute for Research, Madison, Wisconsin, USA.,Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aos Karim
- Department of Surgery, University of Wisconsin-Madison Hospitals and Clinics, Madison, Wisconsin, USA
| | - Edgar Ocotl
- Department of Surgery, University of Wisconsin-Madison Hospitals and Clinics, Madison, Wisconsin, USA
| | - Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jenu V Chacko
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aiping Liu
- Department of Surgery, University of Wisconsin-Madison Hospitals and Clinics, Madison, Wisconsin, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin-Madison Hospitals and Clinics, Madison, Wisconsin, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Medical Engineering, Morgridge Institute for Research, Madison, Wisconsin, USA.,Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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39
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Levandowski BJ, Abularrage NS, Raines RT. Front Cover: Differential Effects of Nitrogen Substitution in 5‐ and 6‐Membered Aromatic Motifs (Chem. Eur. J. 41/2020). Chemistry 2020. [DOI: 10.1002/chem.202001541] [Citation(s) in RCA: 1] [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: 11/06/2022]
Affiliation(s)
- Brian J. Levandowski
- Department of ChemistryMassachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Nile S. Abularrage
- Department of ChemistryMassachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Ronald T. Raines
- Department of ChemistryMassachusetts Institute of Technology Cambridge Massachusetts 02139 USA
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40
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Abstract
Group A Streptococcus (GAS) displays cell-surface proteins that resemble human collagen. We find that a fluorophore-labeled collagen mimetic peptide (CMP) labels GAS cells but not Escherichia coli or Bacillus subtilis cells, which lack such proteins. The CMP likely engages in a heterotrimeric helix with endogenous collagen, as the nonnatural d enantiomer of the CMP does not label GAS cells. To identify a molecular target, we used reverse genetics to "knock-in" the GAS genes that encode two proteins with collagen-like domains, Scl1 and Scl2, into B. subtilis. The fluorescent CMP labels the cells of these B. subtilis strains. Moreover, these strains bind tightly to a surface of mammalian collagen. These data are consistent with streptococcal collagen forming triple helices with damaged collagen in a wound bed and thus have implications for microbial virulence.
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Affiliation(s)
| | - Felix Dempwolff
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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41
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Abstract
Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine residues 34, 76, and 88. We have produced the three individual glycoforms that display the core heptasaccharide, Man5GlcNAc2, and analyzed the structure of each glycoform by using small-angle X-ray scattering along with molecular dynamics simulations. The glycan on Asn34 is relatively compact and rigid, donates hydrogen bonds that "cap" the carbonyl groups at the C-terminus of an α-helix, and enhances protein thermostability. In contrast, the glycan on Asn88 is flexible and can even enter the enzymic active site, hindering catalysis. The N-glycosylation of Asn76 has less pronounced consequences. These data highlight the diverse behaviors of Man5GlcNAc2 pendants and provide a structural underpinning to the functional consequences of protein glycosylation.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Valerie T Ressler
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Levandowski BJ, Abularrage NS, Raines RT. Differential Effects of Nitrogen Substitution in 5- and 6-Membered Aromatic Motifs. Chemistry 2020; 26:8862-8866. [PMID: 32166866 DOI: 10.1002/chem.202000825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/10/2020] [Indexed: 12/30/2022]
Abstract
The replacement of carbon with nitrogen can affect the aromaticity of organic rings. Nucleus-independent chemical shift (NICS) calculations at the center of the aromatic π-systems reveal that incorporating nitrogen into 5-membered heteroaromatic dienes has only a small influence on aromaticity. In contrast, each nitrogen incorporated into benzene results in a sequential and substantial loss of aromaticity. The contrasting effects of nitrogen substitution in 5-membered dienes and benzene are reflected in their Diels-Alder reactivities as dienes. 1,2-Diazine experiences a 1011 -fold increase in reactivity upon nitrogen substitution at the 4- and 5-positions, whereas a 5-membered heteroaromatic diene, furan, experiences a comparatively incidental 102 -fold increase in reactivity upon nitrogen substitution at the 3- and 4-positions.
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Affiliation(s)
- Brian J Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
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Levandowski BJ, Abularrage NS, Raines RT. Differential Effects of Nitrogen Substitution in 5- and 6-Membered Aromatic Motifs. Chemistry 2020; 26:8833. [PMID: 32530082 DOI: 10.1002/chem.202001542] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Invited for the cover of this issue is the group of Ronald T. Raines at the Massachusetts Institute of Technology. The image depicts the consequence of replacing carbon with nitrogen in aromatic systems, represented by Kekulé's allegorical snake. Read the full text of the article at 10.1002/chem.202000825.
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Affiliation(s)
- Brian J Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
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Abularrage NS, Levandowski BJ, Raines RT. Synthesis and Diels-Alder Reactivity of 4-Fluoro-4-Methyl-4 H-Pyrazoles. Int J Mol Sci 2020; 21:ijms21113964. [PMID: 32486503 PMCID: PMC7312747 DOI: 10.3390/ijms21113964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 02/01/2023] Open
Abstract
4H-Pyrazoles are emerging scaffolds for “click” chemistry. Late-stage fluorination with Selectfluor® is found to provide a reliable route to 4-fluoro-4-methyl-4H-pyrazoles. 4-Fluoro-4-methyl-3,5-diphenyl-4H-pyrazole (MFP) manifested 7-fold lower Diels–Alder reactivity than did 4,4-difluoro-3,5-diphenyl-4H-pyrazole (DFP), but higher stability in the presence of biological nucleophiles. Calculations indicate that a large decrease in the hyperconjugative antiaromaticity in MFP relative to DFP does not lead to a large loss in Diels–Alder reactivity because the ground-state structure of MFP avoids hyperconjugative antiaromaticity by distorting into an envelope-like conformation like that in the Diels–Alder transition state. This predistortion enhances the reactivity of MFP and offsets the decrease in reactivity from the diminished hyperconjugative antiaromaticity.
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Abstract
Bonds between sulfur atoms are prevalent in natural products, peptides, and proteins. Disulfide bonds have a distinct chromophore. The wavelength of their maximal absorbance varies widely, from 250 to 500 nm. Here, we demonstrate that this wavelength derives from stereoelectronic effects and is predictable using quantum chemistry. We also provide a sinusoidal equation, analogous to the Karplus equation, that relates the absorbance maximum and the C-S-S-C dihedral angle. These insights provide a facile means to characterize important attributes of disulfide bonds and to design disulfides with specified photophysical properties.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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46
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Abstract
Collagen is the most abundant protein in humans and the major component of human skin. Collagen mimetic peptides (CMPs) can anneal to damaged collagen in vitro and in vivo. A duplex of CMPs was envisioned as a macromolecular mimic for damaged collagen. The duplex was synthesized on a solid support from the amino groups of a lysine residue and by using olefin metathesis to link the N termini. The resulting cyclic peptide, which is a monomer in solution, binds to CMPs to form a triple helix. Among these, CMPs that are engineered to avoid the formation of homotrimers but preorganized to adopt the conformation of a collagen strand exhibit enhanced association. Thus, this cyclic peptide enables the assessment of CMPs for utility in annealing to damaged collagen. Such CMPs have potential use in the diagnosis and treatment of fibrotic diseases and wounds.
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Affiliation(s)
| | - I Caglar Tanrikulu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Backman LRF, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL. Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. eLife 2020; 9:e51420. [PMID: 32180548 PMCID: PMC7077986 DOI: 10.7554/elife.51420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/19/2020] [Indexed: 02/04/2023] Open
Abstract
The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.
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Affiliation(s)
- Lindsey RF Backman
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yolanda Y Huang
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Mary C Andorfer
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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48
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Abstract
Recognition of distinct glycans is central to biology, and lectins mediate this function. Lectin glycan preferences are usually centered on specific monosaccharides. In contrast, human intelectin-1 (hItln-1, also known as Omentin-1) is a soluble lectin that binds a range of microbial sugars, including β-d-galactofuranose (β-Galf), d-glycerol 1-phosphate, d-glycero-d-talo-oct-2-ulosonic acid (KO), and 3-deoxy-d-manno-oct-2-ulosonic acid (KDO). Though these saccharides differ dramatically in structure, they share a common feature-an exocyclic vicinal diol. How and whether such a small fragment is sufficient for recognition was unclear. We tested several glycans with this epitope and found that l-glycero-α-d-manno-heptose and d-glycero-α-d-manno-heptose possess the critical diol motif yet bind weakly. To better understand hItln-1 recognition, we determined the structure of the hItln-1·KO complex using X-ray crystallography, and our 1.59 Å resolution structure enabled unambiguous assignment of the bound KO conformation. This carbohydrate conformation was present in >97% of the KDO/KO structures in the Protein Data Bank. Bioinformatic analysis revealed that KO and KDO adopt a common conformation, while heptoses prefer different conformers. The preferred conformers of KO and KDO favor hItln-1 engagement, but those of the heptoses do not. Natural bond orbital (NBO) calculations suggest these observed conformations, including the side chain orientations, are stabilized by not only steric but also stereoelectronic effects. Thus, our data highlight a role for stereoelectronic effects in dictating the specificity of glycan recognition by proteins. Finally, our finding that hItln-1 avoids binding prevalent glycans with a terminal 1,2-diol (e.g., N-acetyl-neuraminic acid and l-glycero-α-d-manno-heptose) suggests the lectin has evolved to recognize distinct bacterial species.
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Affiliation(s)
- Caitlin M McMahon
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Christine R Isabella
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ian W Windsor
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Paul Kosma
- Department of Chemistry , University of Natural Resources and Life Sciences , A-1190 Vienna , Austria
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Laura L Kiessling
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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49
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Abstract
The self-assembly of collagen-mimetic peptides (CMPs) that form sticky-ended triple helices has allowed the production of surprisingly stable artificial collagen fibers and hydrogels. Assembly through sticky ends requires the recognition of a single strand by a templated strand dimer. Although CMPs and their triple helices have been studied extensively, the structure of a strand dimer is unknown. Here, we evaluate the physical characteristics of such dimers, using disulfide-templated (PPG)10 dimers as a model. Such "linked-dimers" retain their collagen-like structure even in the absence of a third strand, but only when their strands are capable of adopting a triple-helical fold. The intrinsic collagen-like structure of templated CMP pairs helps to explain the success of sticky-ended CMP association and changes the conception of new synthetic collagen designs.
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Affiliation(s)
- I. Caglar Tanrikulu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - William M. Westler
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- NMRFAM, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Aubrey J. Ellison
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - John L. Markley
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- NMRFAM, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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50
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Dones JM, Tanrikulu IC, Chacko JV, Schroeder AB, Hoang TT, Gibson ALF, Eliceiri KW, Raines RT. Optimization of interstrand interactions enables burn detection with a collagen-mimetic peptide. Org Biomol Chem 2019; 17:9906-9912. [PMID: 31720665 DOI: 10.1039/c9ob01839e] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Collagen is an abundant component of the extracellular matrix and connective tissues. Some collagen-mimetic peptides (CMPs) that do not form homotrimers can anneal to damaged tissue. Here, through a computational screen, we identify (flpHypGly)7 as an optimal monomeric CMP for heterotrimer formation. We find that (flpHypGly)7 forms stable triple helices with (ProProGly)7 but not with itself. The nonnatural amino acid HflpOH, which is (2S,4S)-4-fluoroproline, is not toxic to human fibroblasts or keratinocytes. Conjugation of (flpHypGly)7 to a fluorescent dye enables the facile detection of burned collagenous tissue with high specificity. The ubiquity of collagen and the prevalence of injuries and diseases that disrupt endogenous collagen suggests widespread utility for this approach.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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