1
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Perdigão PR, Cunha-Santos C, Barbas CF, Santa-Marta M, Goncalves J. Protein Delivery of Cell-Penetrating Zinc-Finger Activators Stimulates Latent HIV-1-Infected Cells. Mol Ther Methods Clin Dev 2020; 18:145-158. [PMID: 32637446 PMCID: PMC7317221 DOI: 10.1016/j.omtm.2020.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/19/2020] [Indexed: 01/06/2023]
Abstract
Despite efforts to develop effective treatments for eradicating HIV-1, a cure has not yet been achieved. Whereas antiretroviral drugs target an actively replicating virus, latent, nonreplicative forms persist during treatment. Pharmacological strategies that reactivate latent HIV-1 and expose cellular reservoirs to antiretroviral therapy and the host immune system have, so far, been unsuccessful, often triggering severe side effects, mainly due to systemic immune activation. Here, we present an alternative approach for stimulating latent HIV-1 expression via direct protein delivery of cell-penetrating zinc-finger activators (ZFAs). Cys2-His2 zinc-fingers, fused to a transcription activation domain, were engineered to recognize the HIV-1 promoter and induce targeted viral transcription. Following conjugation with multiple positively charged nuclear localization signal (NLS) repeats, protein delivery of a single ZFA (3NLS-PBS1-VP64) efficiently internalized HIV-1 latently infected T-lymphocytes and specifically stimulated viral expression. We show that short-term treatment with this ZFA protein induces higher levels of viral reactivation in cell line models of HIV-1 latency than those observed with gene delivery. Our work establishes protein delivery of ZFA as a novel and safe approach toward eradication of HIV-1 reservoirs.
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Affiliation(s)
- Pedro R.L. Perdigão
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catarina Cunha-Santos
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos F. Barbas
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mariana Santa-Marta
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Joao Goncalves
- Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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2
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Nagano M, Carrillo N, Otsubo N, Hakamata W, Ban H, Fuller RP, Bashiruddin NK, Barbas CF. In vivo programming of endogenous antibodies via oral administration of adaptor ligands. Bioorg Med Chem 2017; 25:5952-5961. [DOI: 10.1016/j.bmc.2017.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 01/03/2023]
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3
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Patterson JT, Wilson HD, Asano S, Nilchan N, Fuller RP, Roush WR, Rader C, Barbas CF. Human Serum Albumin Domain I Fusion Protein for Antibody Conjugation. Bioconjug Chem 2016; 27:2271-2275. [PMID: 27666414 DOI: 10.1021/acs.bioconjchem.6b00432] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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
Bioorthogonal labeling of antibodies enables the conjugation of compounds, such as small molecules or peptides, which expand targeting capacity or enhance cytotoxicity. Taking advantage of a cyclohexene sulfonamide compound that site-selectively labels Lys64 in human serum albumin (HSA), we demonstrate that domain I of HSA can be used as a fusion protein for the preparation of antibody conjugates. Trastuzumab fusions were expressed at the N-terminus of the light chain or the C-terminus of the heavy chain enabling conjugation to small molecules. Moreover, these conjugates retained HER2 binding and proved to be highly stable in human plasma. Antibody conjugation via HSA domain I fusion should therefore have broad utility for making serum-stable antibody conjugates, particularly for antibody-drug conjugates.
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Affiliation(s)
- James T Patterson
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Henry D Wilson
- Department of Cancer Biology, Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida , Jupiter, Florida 33458, United States
| | - Shigehiro Asano
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Napon Nilchan
- Department of Chemistry, The Scripps Research Institute, Scripps Florida , Jupiter, Florida 33458, United States
| | - Roberta P Fuller
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Scripps Florida , Jupiter, Florida 33458, United States
| | - Christoph Rader
- Department of Cancer Biology, Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida , Jupiter, Florida 33458, United States
| | - Carlos F Barbas
- Department of Chemistry, Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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4
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Perdigão P, Gaj T, Santa-Marta M, Barbas CF, Goncalves J. Reactivation of Latent HIV-1 Expression by Engineered TALE Transcription Factors. PLoS One 2016; 11:e0150037. [PMID: 26933881 PMCID: PMC4774903 DOI: 10.1371/journal.pone.0150037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
The presence of replication-competent HIV-1 -which resides mainly in resting CD4+ T cells--is a major hurdle to its eradication. While pharmacological approaches have been useful for inducing the expression of this latent population of virus, they have been unable to purge HIV-1 from all its reservoirs. Additionally, many of these strategies have been associated with adverse effects, underscoring the need for alternative approaches capable of reactivating viral expression. Here we show that engineered transcriptional modulators based on customizable transcription activator-like effector (TALE) proteins can induce gene expression from the HIV-1 long terminal repeat promoter, and that combinations of TALE transcription factors can synergistically reactivate latent viral expression in cell line models of HIV-1 latency. We further show that complementing TALE transcription factors with Vorinostat, a histone deacetylase inhibitor, enhances HIV-1 expression in latency models. Collectively, these findings demonstrate that TALE transcription factors are a potentially effective alternative to current pharmacological routes for reactivating latent virus and that combining synthetic transcriptional activators with histone deacetylase inhibitors could lead to the development of improved therapies for latent HIV-1 infection.
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Affiliation(s)
- Pedro Perdigão
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Mariana Santa-Marta
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joao Goncalves
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
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5
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Liu J, Gaj T, Yang Y, Wang N, Shui S, Kim S, Kanchiswamy CN, Kim JS, Barbas CF. Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nat Protoc 2015; 10:1842-59. [DOI: 10.1038/nprot.2015.117] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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6
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Inokuma T, Fuller RP, Barbas CF. N-Sulfonyl-β-lactam hapten as an effective labeling reagent for aldolase mAb. Bioorg Med Chem Lett 2015; 25:1684-1687. [PMID: 25791455 DOI: 10.1016/j.bmcl.2015.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 01/07/2015] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
Abstract
Utilization of chemically programmed antibodies (cpAbs) is regarded to be one of the most efficient methods for the development of therapeutic systems. cpAbs can extend the half-life of programming reagents, activate immune systems via the Fc region of antibodies and achieve universal vaccination by attaching varieties of small, programmed molecules. In the current study, we aimed to develop a novel labeling reagent for the preparation of cpAbs and found that N-sulfonyl-β-lactams (NSBLs) were optimal. NSBL can be synthesized from readily available 4-(bromomethyl)benzenesulfonyl chloride via few simple manipulations and can label the aldolase monoclonal antibody (mAb) 84G3, which could not be labeled effectively by the conventional labeling reagent, N-acyl-β-lactam (NABL). We also demonstrated that the conjugate, which consists of mAb 84G3 and an NSBL bearing a biotin moiety, maintained strong binding activity to streptavidin. In addition, the stability assay of NSBL revealed that NSBLs can tolerate aqueous media without significant decomposition over 24h.
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Affiliation(s)
- Tsubasa Inokuma
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
| | - Roberta P Fuller
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Carlos F Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
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7
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Abstract
The construction of increasingly sophisticated synthetic biological circuits is dependent on the development of extensible tools capable of providing specific control of gene expression in eukaryotic cells. Here, we describe a new class of synthetic transcription factors that activate gene expression in response to extracellular chemical stimuli. These inducible activators consist of customizable transcription activator-like effector (TALE) proteins combined with steroid hormone receptor ligand-binding domains. We demonstrate that these ligand-responsive TALE transcription factors allow for tunable and conditional control of gene activation and can be used to regulate the expression of endogenous genes in human cells. Since TALEs can be designed to recognize any contiguous DNA sequence, the conditional gene regulatory system described herein will enable the design of advanced synthetic gene networks.
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Affiliation(s)
- Andrew C. Mercer
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Thomas Gaj
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shannon J. Sirk
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brian M. Lamb
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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8
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Asano S, Patterson JT, Gaj T, Barbas CF. Site-selective labeling of a lysine residue in human serum albumin. Angew Chem Int Ed Engl 2014; 53:11783-6. [PMID: 25196737 DOI: 10.1002/anie.201405924] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [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: 06/04/2014] [Indexed: 11/11/2022]
Abstract
Conjugation to human serum albumin (HSA) has emerged as a powerful approach for extending the in vivo half-life of many small molecule and peptide/protein drugs. Current HSA conjugation strategies, however, can often yield heterogeneous mixtures with inadequate pharmacokinetics, low efficacies, and variable safety profiles. Here, we designed and synthesized analogues of TAK-242, a small molecule inhibitor of Toll-like receptor 4, that primarily reacted with a single lysine residue of HSA. These TAK-242-based cyclohexene compounds demonstrated robust reactivity, and Lys64 was identified as the primary conjugation site. A bivalent HSA conjugate was also prepared in a site-specific manner. Additionally, HSA-cyclohexene conjugates maintained higher levels of stability both in human plasma and in mice than the corresponding maleimide conjugates. This new conjugation strategy promises to broadly enhance the performance of HSA conjugates for numerous applications.
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Affiliation(s)
- Shigehiro Asano
- The Skaggs Institute for Chemical Biology, Department of Chemistry, and Department of Molecular and Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
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9
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10
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Abstract
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The understanding
of gene regulation and the structure and function
of the human genome increased dramatically at the end of the 20th
century. Yet the technologies for manipulating the genome have been
slower to develop. For instance, the field of gene therapy has been
focused on correcting genetic diseases and augmenting tissue repair
for more than 40 years. However, with the exception of a few very
low efficiency approaches, conventional genetic engineering methods
have only been able to add auxiliary genes to cells. This has been
a substantial obstacle to the clinical success of gene therapies and
has also led to severe unintended consequences in several cases. Therefore,
technologies that facilitate the precise modification of cellular
genomes have diverse and significant implications in many facets of
research and are essential for translating the products of the Genomic
Revolution into tangible benefits for medicine and biotechnology.
To address this need, in the 1990s, we embarked on a mission to develop
technologies for engineering protein–DNA interactions with
the aim of creating custom tools capable of targeting any DNA sequence.
Our goal has been to allow researchers to reach into genomes to specifically
regulate, knock out, or replace any gene. To realize these goals,
we initially focused on understanding and manipulating zinc finger
proteins. In particular, we sought to create a simple and straightforward
method that enables unspecialized laboratories to engineer custom
DNA-modifying proteins using only defined modular components, a web-based
utility, and standard recombinant DNA technology. Two significant
challenges we faced were (i) the development of zinc finger domains
that target sequences not recognized by naturally occurring zinc finger
proteins and (ii) determining how individual zinc finger domains could
be tethered together as polydactyl proteins to recognize unique locations
within complex genomes. We and others have since used this modular
assembly method to engineer artificial proteins and enzymes that activate,
repress, or create defined changes to user-specified genes in human
cells, plants, and other organisms. We have also engineered novel
methods for externally controlling protein activity and delivery,
as well as developed new strategies for the directed evolution of
protein and enzyme function. This Account summarizes our work in these
areas and highlights independent studies that have successfully used
the modular assembly approach to create proteins with novel function.
We also discuss emerging alternative methods for genomic targeting,
including transcription activator-like effectors (TALEs) and CRISPR/Cas
systems, and how they complement the synthetic zinc finger protein
technology.
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Affiliation(s)
- Charles A. Gersbach
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Thomas Gaj
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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11
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Abstract
The development of new methods for delivering proteins into cells is a central challenge for advancing both basic research and therapeutic applications. We previously reported that zinc-finger nuclease proteins are intrinsically cell-permeable due to the cell-penetrating activity of the Cys2-His2 zinc-finger domain. Here, we demonstrate that genetically fused zinc-finger motifs can transport proteins and enzymes into a wide range of primary and transformed mammalian cell types. We show that zinc-finger domains mediate protein uptake at efficiencies that exceed conventional protein transduction systems and do so without compromising enzyme activity. In addition, we demonstrate that zinc-finger proteins enter cells primarily through macropinocytosis and facilitate high levels of cytosolic delivery. These findings establish zinc-finger proteins as not only useful tools for targeted genome engineering but also effective reagents for protein delivery.
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Affiliation(s)
- Thomas Gaj
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jia Liu
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kimberly E. Anderson
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shannon J. Sirk
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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12
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Abstract
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Current routes for synthesizing antibody–drug
conjugates
commonly rely on maleimide linkers to react with cysteine thiols.
However, thioether exchange with metabolites and serum proteins can
compromise conjugate stability and diminish in vivo efficacy. We report the application of a phenyloxadiazole sulfone
linker for the preparation of trastuzumab conjugates. This sulfone
linker site-specifically labeled engineered cysteine residues in THIOMABs
and improved antibody conjugate stability in human plasma at sites
previously shown to be labile for maleimide conjugates. Similarly,
sulfone conjugation with selenocysteine in an anti-ROR1 scFv-Fc improved
human plasma stability relative to maleimide conjugation. Kinetically
controlled labeling of a THIOMAB containing two cysteine substitutions
was also achieved, offering a strategy for producing antibody conjugates
with expanded valency.
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Affiliation(s)
- James T Patterson
- The Skaggs Institute for Chemical Biology, Department of Chemistry, and Department of Cell and Molecular Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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13
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Abstract
The isolation of therapeutic and functional protease inhibitors in vitro via combinatorial chemistry and phage display technology has been described previously. Here we report the construction of a combinatorial mouse-human chimeric antibody fragment (Fab) antibody library targeted against the protease of the tropical pathogen, Burkholderia pseudomallei. The resulting library was biopanned against the protease, and selected clones were analyzed for their ability to function as protease inhibitors. Three families of Fabs were identified by restriction fingerprinting, all of which demonstrated high specificity towards the protease of B. pseudomallei. Purified Fabs also demonstrated the capacity to inhibit B. pseudomallei protease activity in vitro, and this inhibitory property was exclusive to the pathogenic protease. Thus these recombinant antibodies are candidates for immunotherapy and tools to aid in further elucidation of the mechanism of action of the B. pseudomallei protease.
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Affiliation(s)
- Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selanger
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14
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Gaj T, Sirk SJ, Tingle RD, Mercer AC, Wallen MC, Barbas CF. Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign. J Am Chem Soc 2014; 136:5047-56. [PMID: 24611715 PMCID: PMC3985937 DOI: 10.1021/ja4130059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Despite
recent advances in genome engineering made possible by
the emergence of site-specific endonucleases, there remains a need
for tools capable of specifically delivering genetic payloads into
the human genome. Hybrid recombinases based on activated catalytic
domains derived from the resolvase/invertase family of serine recombinases
fused to Cys2-His2 zinc-finger or TAL effector
DNA-binding domains are a class of reagents capable of achieving this.
The utility of these enzymes, however, has been constrained by their
low overall targeting specificity, largely due to the formation of
side-product homodimers capable of inducing off-target modifications.
Here, we combine rational design and directed evolution to re-engineer
the serine recombinase dimerization interface and generate a recombinase
architecture that reduces formation of these undesirable homodimers
by >500-fold. We show that these enhanced recombinases demonstrate
substantially improved targeting specificity in mammalian cells and
achieve rates of site-specific integration similar to those previously
reported for site-specific nucleases. Additionally, we show that enhanced
recombinases exhibit low toxicity and promote the delivery of the
human coagulation factor IX and α-galactosidase genes into endogenous
genomic loci with high specificity. These results provide a general
means for improving hybrid recombinase specificity by protein engineering
and illustrate the potential of these enzymes for basic research and
therapeutic applications.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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15
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16
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Asano S, Gavrilyuk J, Burton DR, Barbas CF. Preparation and activities of macromolecule conjugates of the CCR5 antagonist Maraviroc. ACS Med Chem Lett 2014; 5:133-137. [PMID: 24563723 DOI: 10.1021/ml400370w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
CCR5 antagonists are among the most advanced approaches in HIV therapy and may also be relevant to treatment of graft-versus-host disease and Staphylococcus aureus infection. To expand the potential of the only approved CCR5 antagonist, Maraviroc, we studied derivatives that would enable functional linkage of Maraviroc to long-lived carriers. Through targeted synthesis, we discovered an effective linkage site on Maraviroc and demonstrate the potential of these derivatives to prepare potent chemically programmed antibodies and PEGylated derivatives. The resulting compounds effectively neutralized a variety of HIV-1 isolates. Both chemically programmed antibody and PEGylation approaches extend the neutralization activity of serum circulating Maraviroc. Derivation of a successful conjugation strategy for Maraviroc should further enable its use in chemically programmed vaccines, novel bispecific antibodies, and topical microbicides.
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Affiliation(s)
- Shigehiro Asano
- Departments
of Chemistry and Cell and Molecular Biology, The Skaggs Institute
for Chemical Biology, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Julia Gavrilyuk
- Departments
of Chemistry and Cell and Molecular Biology, The Skaggs Institute
for Chemical Biology, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis R. Burton
- Department
of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- Departments
of Chemistry and Cell and Molecular Biology, The Skaggs Institute
for Chemical Biology, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
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17
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Cheng D, Ishihara Y, Tan B, Barbas CF. Organocatalytic Asymmetric Assembly Reactions: Synthesis of Spirooxindoles via Organocascade Strategies. ACS Catal 2014. [DOI: 10.1021/cs401172r] [Citation(s) in RCA: 673] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Daojuan Cheng
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People’s Republic of China
| | - Yoshihiro Ishihara
- The
Skaggs Institute for Chemical Biology and Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, 10550
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bin Tan
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen, 518055, People’s Republic of China
- The
Skaggs Institute for Chemical Biology and Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, 10550
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The
Skaggs Institute for Chemical Biology and Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, 10550
North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Sirk SJ, Gaj T, Jonsson A, Mercer AC, Barbas CF. Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants. Nucleic Acids Res 2014; 42:4755-66. [PMID: 24452803 PMCID: PMC3985619 DOI: 10.1093/nar/gkt1389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The serine recombinases are a diverse family of modular enzymes that promote high-fidelity DNA rearrangements between specific target sites. Replacement of their native DNA-binding domains with custom-designed Cys2–His2 zinc-finger proteins results in the creation of engineered zinc-finger recombinases (ZFRs) capable of achieving targeted genetic modifications. The flexibility afforded by zinc-finger domains enables the design of hybrid recombinases that recognize a wide variety of potential target sites; however, this technology remains constrained by the strict recognition specificities imposed by the ZFR catalytic domains. In particular, the ability to fully reprogram serine recombinase catalytic specificity has been impeded by conserved base requirements within each recombinase target site and an incomplete understanding of the factors governing DNA recognition. Here we describe an approach to complement the targeting capacity of ZFRs. Using directed evolution, we isolated mutants of the β and Sin recombinases that specifically recognize target sites previously outside the scope of ZFRs. Additionally, we developed a genetic screen to determine the specific base requirements for site-specific recombination and showed that specificity profiling enables the discovery of unique genomic ZFR substrates. Finally, we conducted an extensive and family-wide mutational analysis of the serine recombinase DNA-binding arm region and uncovered a diverse network of residues that confer target specificity. These results demonstrate that the ZFR repertoire is extensible and highlights the potential of ZFRs as a class of flexible tools for targeted genome engineering.
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Affiliation(s)
- Shannon J Sirk
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA and Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Liu J, Gaj T, Patterson JT, Sirk SJ, Barbas CF. Cell-penetrating peptide-mediated delivery of TALEN proteins via bioconjugation for genome engineering. PLoS One 2014; 9:e85755. [PMID: 24465685 PMCID: PMC3896395 DOI: 10.1371/journal.pone.0085755] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 12/02/2013] [Indexed: 12/21/2022] Open
Abstract
Transcription activator-like (TAL) effector nucleases (TALENs) have enabled the introduction of targeted genetic alterations into a broad range of cell lines and organisms. These customizable nucleases are comprised of programmable sequence-specific DNA-binding modules derived from TAL effector proteins fused to the non-specific FokI cleavage domain. Delivery of these nucleases into cells has proven challenging as the large size and highly repetitive nature of the TAL effector DNA-binding domain precludes their incorporation into many types of viral vectors. Furthermore, viral and non-viral gene delivery methods carry the risk of insertional mutagenesis and have been shown to increase the off-target activity of site-specific nucleases. We previously demonstrated that direct delivery of zinc-finger nuclease proteins enables highly efficient gene knockout in a variety of mammalian cell types with reduced off-target effects. Here we show that conjugation of cell-penetrating poly-Arg peptides to a surface-exposed Cys residue present on each TAL effector repeat imparted cell-penetrating activity to purified TALEN proteins. These modifications are reversible under reducing conditions and enabled TALEN-mediated gene knockout of the human CCR5 and BMPR1A genes at rates comparable to those achieved with transient transfection of TALEN expression vectors. These findings demonstrate that direct protein delivery, facilitated by conjugation of chemical functionalities onto the TALEN protein surface, is a promising alternative to current non-viral and viral-based methods for TALEN delivery into mammalian cells.
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Affiliation(s)
- Jia Liu
- The Departments of Chemistry and Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Gaj
- The Departments of Chemistry and Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - James T Patterson
- The Departments of Chemistry and Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Shannon J Sirk
- The Departments of Chemistry and Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Carlos F Barbas
- The Departments of Chemistry and Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
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LaFleur DW, Abramyan D, Kanakaraj P, Smith RG, Shah RR, Wang G, Yao XT, Kankanala S, Boyd E, Zaritskaya L, Nam V, Puffer BA, Buasen P, Kaithamana S, Burnette AF, Krishnamurthy R, Patel D, Roschke VV, Kiener PA, Hilbert DM, Barbas CF. Monoclonal antibody therapeutics with up to five specificities: functional enhancement through fusion of target-specific peptides. MAbs 2013; 5:208-18. [PMID: 23575268 PMCID: PMC3893231 DOI: 10.4161/mabs.23043] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The recognition that few human diseases are thoroughly addressed by mono-specific, monoclonal antibodies (mAbs) continues to drive the development of antibody therapeutics with additional specificities and enhanced activity. Historically, efforts to engineer additional antigen recognition into molecules have relied predominantly on the reformatting of immunoglobulin domains. In this report we describe a series of fully functional mAbs to which additional specificities have been imparted through the recombinant fusion of relatively short polypeptides sequences. The sequences are selected for binding to a particular target from combinatorial libraries that express linear, disulfide-constrained, or domain-based structures. The potential for fusion of peptides to the N- and C- termini of both the heavy and light chains affords the bivalent expression of up to four different peptides. The resulting molecules, called zybodies, can gain up to four additional specificities, while retaining the original functionality and specificity of the scaffold antibody. We explore the use of two clinically significant oncology antibodies, trastuzumab and cetuximab, as zybody scaffolds and demonstrate functional enhancements in each case. The affect of fusion position on both peptide and scaffold function is explored, and penta-specific zybodies are demonstrated to simultaneously engage five targets (ErbB2, EGFR, IGF-1R, Ang2 and integrin αvβ3). Bispecific, trastuzumab-based zybodies targeting ErbB2 and Ang2 are shown to exhibit superior efficacy to trastuzumab in an angiogenesis-dependent xenograft tumor model. A cetuximab-based bispecific zybody that targeting EGFR and ErbB3 simultaneously disrupted multiple intracellular signaling pathways; inhibited tumor cell proliferation; and showed efficacy superior to that of cetuximab in a xenograft tumor model.
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Toda N, Asano S, Barbas CF. Rapid, stable, chemoselective labeling of thiols with Julia-Kocieński-like reagents: a serum-stable alternative to maleimide-based protein conjugation. Angew Chem Int Ed Engl 2013; 52:12592-6. [PMID: 24123851 PMCID: PMC3865870 DOI: 10.1002/anie.201306241] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [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: 07/18/2013] [Indexed: 01/12/2023]
Abstract
Cysteine-maleimide chemistry is widely used for peptide and protein modification. However, the formed succinimide linkage is readily hydrolyzed and is susceptible to an exchange reaction in vivo. We demonstrate that methylsulfonyl phenyloxadiazole compounds react specifically with cysteine under various buffer conditions and found that the resulting protein conjugates had superior stability to cysteine-maleimide conjugates in human plasma. This Thiol-Click chemistry promises a new approach to stable protein conjugates and pegylated proteins.
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Affiliation(s)
| | | | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular and Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
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Toda N, Asano S, Barbas CF. Rapid, Stable, Chemoselective Labeling of Thiols with Julia-Kocieński-like Reagents: A Serum-Stable Alternative to Maleimide-Based Protein Conjugation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306241] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Gaj T, Sirk SJ, Barbas CF. Expanding the scope of site-specific recombinases for genetic and metabolic engineering. Biotechnol Bioeng 2013; 111:1-15. [PMID: 23982993 DOI: 10.1002/bit.25096] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [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: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 12/20/2022]
Abstract
Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, 92037
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25
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Abstract
Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.
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Affiliation(s)
- Brian M Lamb
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037 USA, Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA and Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
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Jiang X, Tan B, Barbas CF. Core-structure-motivated design of iminium-enolate organocascade reactions: enantioselective syntheses of 5,6-dihydroindolizines. Angew Chem Int Ed Engl 2013; 52:9261-5. [PMID: 23843168 DOI: 10.1002/anie.201303300] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/18/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Xianxing Jiang
- The Skaggs Institute for Chemical Biology and the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Jiang X, Tan B, Barbas CF. Core‐Structure‐Motivated Design of Iminium–Enolate Organocascade Reactions: Enantioselective Syntheses of 5,6‐Dihydroindolizines. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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)
- Xianxing Jiang
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Bin Tan
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
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Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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29
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78495111110.1016/j.tibtech.2013.04.004" />
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Albertshofer K, Tan B, Barbas CF. Asymmetric Construction of Spirocyclopentenebenzofuranone Core Structures via Highly Selective Phosphine-Catalyzed [3 + 2] Cycloaddition Reactions. Org Lett 2013; 15:2958-61. [DOI: 10.1021/ol401087a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Klaus Albertshofer
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bin Tan
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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31
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Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013; 31:397-405. [PMID: 23664777 DOI: 10.1016/j.tibtech.2013.04.004] [Citation(s) in RCA: 2321] [Impact Index Per Article: 211.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/13/2013] [Accepted: 04/13/2013] [Indexed: 12/11/2022]
Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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32
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Abstract
Herein we describe the design and application of two small-molecule anti-HIV compounds for the creation of chemically programmed antibodies. N-acyl-β-lactam derivatives of two previously described molecules BMS-378806 and BMS-488043 that inhibit the interaction between HIV-1 gp120 and T-cells were synthesized and used to program the binding activity of aldolase antibody 38C2. Discovery of a successful linkage site to BMS-488043 allowed for the synthesis of chemically programmed antibodies with affinity for HIV-1 gp120 and potent HIV-1 neutralization activity. Derivation of a successful conjugation strategy for this family of HIV-1 entry inhibitors enables its application in chemically programmed antibodies and vaccines and may facilitate the development of novel bispecific antibodies and topical microbicides.
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Affiliation(s)
- Shinichi Sato
- Department
of Molecular Biology and Chemistry and the
Skaggs Institute for Chemical Biology and Department of Immunology
and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Tsubasa Inokuma
- Department
of Molecular Biology and Chemistry and the
Skaggs Institute for Chemical Biology and Department of Immunology
and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Nobumasa Otsubo
- Department
of Molecular Biology and Chemistry and the
Skaggs Institute for Chemical Biology and Department of Immunology
and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Dennis R. Burton
- Department
of Molecular Biology and Chemistry and the
Skaggs Institute for Chemical Biology and Department of Immunology
and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Carlos F. Barbas
- Department
of Molecular Biology and Chemistry and the
Skaggs Institute for Chemical Biology and Department of Immunology
and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
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Ban H, Nagano M, Gavrilyuk J, Hakamata W, Inokuma T, Barbas CF. Facile and stabile linkages through tyrosine: bioconjugation strategies with the tyrosine-click reaction. Bioconjug Chem 2013; 24:520-32. [PMID: 23534985 DOI: 10.1021/bc300665t] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The scope, chemoselectivity, and utility of the click-like tyrosine labeling reaction with 4-phenyl-3H-1,2,4-triazoline-3,5(4H)-diones (PTADs) is reported. To study the utility and chemoselectivity of PTAD derivatives in peptide and protein chemistry, we synthesized PTAD derivatives possessing azide, alkyne, and ketone groups and studied their reactions with amino acid derivatives and peptides of increasing complexity. With proteins we studied the compatibility of the tyrosine click reaction with cysteine and lysine-targeted labeling approaches and demonstrate that chemoselective trifunctionalization of proteins is readily achieved. In particular cases, we noted that PTAD decomposition resulted in formation of a putative isocyanate byproduct that was promiscuous in labeling. This side reaction product, however, was readily scavenged by the addition of a small amount of 2-amino-2-hydroxymethyl-propane-1,3-diol (Tris) to the reaction medium. To study the potential of the tyrosine click reaction to introduce poly(ethylene glycol) chains onto proteins (PEGylation), we demonstrate that this novel reagent provides for the selective PEGylation of chymotrypsinogen, whereas traditional succinimide-based PEGylation targeting lysine residues provided a more diverse range of PEGylated products. Finally, we applied the tyrosine click reaction to create a novel antibody-drug conjugate. For this purpose, we synthesized a PTAD derivative linked to the HIV entry inhibitor aplaviroc. Labeling of the antibody trastuzumab with this reagent provided a labeled antibody conjugate that demonstrated potent HIV-1 neutralization activity demonstrating the potential of this reaction in creating protein conjugates with small molecules. The tyrosine click linkage demonstrated stability to extremes of pH, temperature, and exposure to human blood plasma indicating that this linkage is significantly more robust than maleimide-type linkages that are commonly employed in bioconjugations. These studies support the broad utility of this reaction in the chemoselective modification of small molecules, peptides, and proteins under mild aqueous conditions over a broad pH range using a wide variety of biologically acceptable buffers such as phosphate buffered saline (PBS) and 2-amino-2-hydroxymethyl-propane-1,3-diol (Tris) buffers as well as others and mixed buffered compositions.
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Affiliation(s)
- Hitoshi Ban
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Gaj T, Mercer AC, Sirk SJ, Smith HL, Barbas CF. A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells. Nucleic Acids Res 2013; 41:3937-46. [PMID: 23393187 PMCID: PMC3616721 DOI: 10.1093/nar/gkt071] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Zinc-finger recombinases (ZFRs) represent a potentially powerful class of tools for targeted genetic engineering. These chimeric enzymes are composed of an activated catalytic domain derived from the resolvase/invertase family of serine recombinases and a custom-designed zinc-finger DNA-binding domain. The use of ZFRs, however, has been restricted by sequence requirements imposed by the recombinase catalytic domain. Here, we combine substrate specificity analysis and directed evolution to develop a diverse collection of Gin recombinase catalytic domains capable of recognizing an estimated 3.77 × 107 unique DNA sequences. We show that ZFRs assembled from these engineered catalytic domains recombine user-defined DNA targets with high specificity, and that designed ZFRs integrate DNA into targeted endogenous loci in human cells. This study demonstrates the feasibility of generating customized ZFRs and the potential of ZFR technology for a diverse range of applications, including genome engineering, synthetic biology and gene therapy.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Gavrilyuk J, Ban H, Nagano M, Hakamata W, Barbas CF. Formylbenzene diazonium hexafluorophosphate reagent for tyrosine-selective modification of proteins and the introduction of a bioorthogonal aldehyde. Bioconjug Chem 2012. [PMID: 23181702 DOI: 10.1021/bc300410p] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
4-Formylbenzene diazonium hexafluorophosphate (FBDP) is a novel bench-stable crystalline diazonium salt that reacts selectively with tyrosine to install a bioorthogonal aldehyde functionality. Model studies with N-acyl-tyrosine methylamide allowed us to identify conditions optimal for tyrosine ligation reactions with small peptides and proteins. FBDP-based conjugation was used for the facile introduction of small molecule tags, poly(ethylene glycol) chains (PEGylation), and functional small molecules onto model proteins and to label the surface of living cells.
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Affiliation(s)
- Julia Gavrilyuk
- Departments of Chemistry and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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Albertshofer K, Anderson KE, Barbas CF. Assembly of Spirooxindole Derivatives via Organocatalytic Iminium-Enamine Cascade Reactions. Org Lett 2012; 14:5968-71. [DOI: 10.1021/ol302876c] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Klaus Albertshofer
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kimberly E. Anderson
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Tan B, Toda N, Barbas CF. Organocatalytic amidation and esterification of aldehydes with activating reagents by a cross-coupling strategy. Angew Chem Int Ed Engl 2012; 51:12538-41. [PMID: 23135813 DOI: 10.1002/anie.201205921] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/21/2012] [Indexed: 01/29/2023]
Abstract
Formation on demand: An organocatalytic cross-coupling reaction of aldehydes with N-hydroxyimides, hexafluoroisopropyl alcohol, and sulfonimides has been developed. The resulting active intermediates can be directly converted into amides or esters in one pot. This simple method makes use of readily available starting materials, and the newly discovered activating reagents should find broad application in the synthesis of amides and esters.
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Affiliation(s)
- Bin Tan
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Tan B, Toda N, Barbas CF. Organocatalytic Amidation and Esterification of Aldehydes with Activating Reagents by a Cross-Coupling Strategy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205921] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Hayakawa M, Toda N, Carrillo N, Thornburg NJ, Crowe JE, Barbas CF. A chemically programmed antibody is a long-lasting and potent inhibitor of influenza neuraminidase. Chembiochem 2012; 13:2191-5. [PMID: 22965667 PMCID: PMC3517015 DOI: 10.1002/cbic.201200439] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Indexed: 11/10/2022]
Abstract
Programming an anti-flu strategy: A new and potent neuraminidase inhibitor that maintains long-term systemic exposure of an antibody and the therapeutic activity of the neuraminadase inhibitor zanamivir has been created. This strategy could provide a promising new class of influenza A drugs for therapy and prophylaxis, and validates enzyme inhibitors as programming agents in synthetic immunology.
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Affiliation(s)
- Masahiko Hayakawa
- Departments of Chemistry, Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North, Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Narihiro Toda
- Departments of Chemistry, Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North, Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Nancy Carrillo
- Departments of Chemistry, Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North, Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Natalie J. Thornburg
- Departments of Pediatrics, Pathology, Microbiology and Immunology, and Vanderbilt Vaccine Center, Vanderbilt University Medical Center, 11475 Medical Research Building IV - 2213 Garland Ave. Nashville, TN 37232-0417
| | - James E. Crowe
- Departments of Pediatrics, Pathology, Microbiology and Immunology, and Vanderbilt Vaccine Center, Vanderbilt University Medical Center, 11475 Medical Research Building IV - 2213 Garland Ave. Nashville, TN 37232-0417
| | - Carlos F. Barbas
- Departments of Chemistry, Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North, Torrey Pines Road, La Jolla, CA 92037 (USA)
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40
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Abstract
Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.
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Affiliation(s)
- Andrew C Mercer
- The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Sakkhachornphop S, Barbas CF, Keawvichit R, Wongworapat K, Tayapiwatana C. Zinc finger protein designed to target 2-long terminal repeat junctions interferes with human immunodeficiency virus integration. Hum Gene Ther 2012; 23:932-42. [PMID: 22429108 PMCID: PMC3440019 DOI: 10.1089/hum.2011.124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [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] [Received: 07/13/2011] [Accepted: 03/13/2012] [Indexed: 12/22/2022] Open
Abstract
Integration of the human immunodeficiency virus type 1 (HIV-1) genome into the host chromosome is a vital step in the HIV life cycle. The highly conserved cytosine-adenine (CA) dinucleotide sequence immediately upstream of the cleavage site is crucial for integrase (IN) activity. As this viral enzyme has an important role early in the HIV-1 replication cycle, interference with the IN substrate has become an attractive strategy for therapeutic intervention. We demonstrated that a designed zinc finger protein (ZFP) fused to green fluorescent protein (GFP) targets the 2-long terminal repeat (2-LTR) circle junctions of HIV-1 DNA with nanomolar affinity. We report now that 2LTRZFP-GFP stably transduced into 293T cells interfered with the expression of vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped lentiviral red fluorescent protein (RFP), as shown by the suppression of RFP expression. We also used a third-generation lentiviral vector and pCEP4 expression vector to deliver the 2LTRZFP-GFP transgene into human T-lymphocytic cells, and a stable cell line for long-term expression studies was selected for HIV-1 challenge. HIV-1 integration and replication were inhibited as measured by Alu-gag real-time PCR and p24 antigen assay. In addition, the molecular activity of 2LTRZFP-GFP was evaluated in peripheral blood mononuclear cells. The results were confirmed by Alu-gag real-time PCR for integration interference. We suggest that the expression of 2LTRZFP-GFP limited viral integration on intracellular immunization, and that it has potential for use in HIV gene therapy in the future.
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Affiliation(s)
- Supachai Sakkhachornphop
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Carlos F. Barbas
- Skaggs Institute for Chemical Biology, and Departments of Molecular Biology and Chemistry, Scripps Research Institute, La Jolla, CA 92037
| | - Rassamee Keawvichit
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanlaya Wongworapat
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Biomedical Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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42
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Kanakaraj P, Puffer BA, Yao XT, Kankanala S, Boyd E, Shah RR, Wang G, Patel D, Krishnamurthy R, Kaithamana S, Smith RG, LaFleur DW, Barbas CF, Hilbert DM, Kiener PA, Roschke VV. Simultaneous targeting of TNF and Ang2 with a novel bispecific antibody enhances efficacy in an in vivo model of arthritis. MAbs 2012; 4:600-13. [PMID: 22864384 PMCID: PMC3499301 DOI: 10.4161/mabs.21227] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite the clinical success of anti-tumor necrosis factor (TNF) therapies in the treatment of inflammatory conditions such as rheumatoid arthritis, Crohn disease and psoriasis, full control of the diseases only occurs in a subset of patients and there is a need for new therapeutics with improved efficacy against broader patient populations. One possible approach is to combine biological therapeutics, but both the cost of the therapeutics and the potential for additional toxicities needs to be considered. In addition to the various mediators of immune and inflammatory pathways, angiogenesis is reported to contribute substantially to the overall pathogenesis of inflammatory diseases. The combination of an anti-angiogenic agent with anti-TNF into one molecule could be more efficacious without the risk of severe immunosuppression. To evaluate this approach with our Zybody technology, we generated bispecific antibodies that contain an Ang2 targeting peptide genetically fused to the anti-TNF antibody adalimumab (Humira®). The bispecific molecules retain the binding and functional characteristics of the anti-TNF antibody, but with additional activity that neutralizes Ang2. In a TNF transgenic mouse model of arthritis, the bispecific anti-TNF-Ang2 molecules showed a dose-dependent reduction in both clinical symptoms and histological scores that were significantly better than that achieved by adalimumab alone.
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Abstract
Zinc-finger nucleases (ZFNs) are versatile reagents that have redefined genome engineering. Realizing the full potential of this technology requires the development of safe and effective methods for delivering ZFNs into cells. We demonstrate the intrinsic cell-penetrating capabilities of the standard ZFN architecture and show that direct delivery of ZFNs as proteins leads to efficient endogenous gene disruption in various mammalian cell types with minimal off-target effects.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
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Tan B, Zeng X, Leong WWY, Shi Z, Barbas CF, Zhong G. Corrigendum: Core Structure-Based Design of Organocatalytic [3+2]-Cycloaddition Reactions: Highly Efficient and Stereocontrolled Syntheses of 3,3′-Pyrrolidonyl Spirooxindoles. Chemistry 2012. [DOI: 10.1002/chem.201201323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Tan B, Hernández-Torres G, Barbas CF. Rationally Designed Amide Donors for Organocatalytic Asymmetric Michael Reactions. Angew Chem Int Ed Engl 2012; 51:5381-5. [DOI: 10.1002/anie.201200996] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Indexed: 11/09/2022]
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Tan B, Hernández-Torres G, Barbas CF. Rationally Designed Amide Donors for Organocatalytic Asymmetric Michael Reactions. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200996] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hernández-Torres G, Tan B, Barbas CF. Organocatalysis as a Safe Practical Method for the Stereospecific Dibromination of Unsaturated Compounds. Org Lett 2012; 14:1858-61. [DOI: 10.1021/ol300456x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gloria Hernández-Torres
- The Skaggs Institute for Chemical Biology and Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 Torrey Pines Road, La Jolla, California 92037, United States, and Departamento de Química Orgánica, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Bin Tan
- The Skaggs Institute for Chemical Biology and Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 Torrey Pines Road, La Jolla, California 92037, United States, and Departamento de Química Orgánica, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 Torrey Pines Road, La Jolla, California 92037, United States, and Departamento de Química Orgánica, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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48
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Albertshofer K, Tan B, Barbas CF. Assembly of Spirooxindole Derivatives Containing Four Consecutive Stereocenters via Organocatalytic Michael–Henry Cascade Reactions. Org Lett 2012; 14:1834-7. [DOI: 10.1021/ol300441z] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Klaus Albertshofer
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bin Tan
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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49
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Tan B, Zeng X, Leong WWY, Shi Z, Barbas CF, Zhong G. Core Structure-Based Design of Organocatalytic [3+2]-Cycloaddition Reactions: Highly Efficient and Stereocontrolled Syntheses of 3,3′-Pyrrolidonyl Spirooxindoles. Chemistry 2011; 18:63-7. [DOI: 10.1002/chem.201103449] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Indexed: 01/15/2023]
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50
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Gersbach CA, Gaj T, Gordley RM, Mercer AC, Barbas CF. Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase. Nucleic Acids Res 2011; 39:7868-78. [PMID: 21653554 PMCID: PMC3177191 DOI: 10.1093/nar/gkr421] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 05/06/2011] [Accepted: 05/09/2011] [Indexed: 11/13/2022] Open
Abstract
The development of new methods for gene addition to mammalian genomes is necessary to overcome the limitations of conventional genetic engineering strategies. Although a variety of DNA-modifying enzymes have been used to directly catalyze the integration of plasmid DNA into mammalian genomes, there is still an unmet need for enzymes that target a single specific chromosomal site. We recently engineered zinc-finger recombinase (ZFR) fusion proteins that integrate plasmid DNA into a synthetic target site in the human genome with exceptional specificity. In this study, we present a two-step method for utilizing these enzymes in any cell type at randomly-distributed target site locations. The piggyBac transposase was used to insert recombinase target sites throughout the genomes of human and mouse cell lines. The ZFR efficiently and specifically integrated a transfected plasmid into these genomic target sites and into multiple transposons within a single cell. Plasmid integration was dependent on recombinase activity and the presence of recombinase target sites. This work demonstrates the potential for broad applicability of the ZFR technology in genome engineering, synthetic biology and gene therapy.
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Affiliation(s)
- Charles A. Gersbach
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas Gaj
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Russell M. Gordley
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew C. Mercer
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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