1
|
Ferraresso L, de Arruda E, de Moraes T, Fazzi R, Da Costa Ferreira A, Abbehausen C. Copper(II) and zinc(II) dinuclear enzymes model compounds: The nature of the metal ion in the biological function. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
2
|
Odoux A, Jindal D, Tamas TC, Lim BWH, Pollard D, Xu W. Experimental and molecular dynamics studies showed that CBP KIX mutation affects the stability of CBP:c-Myb complex. Comput Biol Chem 2016; 62:47-59. [PMID: 27082784 DOI: 10.1016/j.compbiolchem.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/06/2016] [Accepted: 03/21/2016] [Indexed: 11/29/2022]
Abstract
The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright's group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen bonds of the E665:R294 pair exhibited a fast decreasing trend over time during MD simulations. In addition, our data showed that the KIX mutations attenuate CBP's hydrophobic interaction with Leu302 of c-Myb. Furthermore, our 500-ns MD simulations showed that CBP KIX with the mutations has a slightly lower potential energy than wild-type CBP. The CBP KIX structures with or without its interacting protein c-Myb are different for both wild-type and mutant CBP KIX, and this is likewise the case for c-Myb with or without CBP, suggesting that the presence of an interacting protein influences the structure of a protein. Taken together, these analyses will improve our understanding of the exact functions of CBP and its interaction with c-Myb.
Collapse
Affiliation(s)
- Anne Odoux
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Darren Jindal
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Tamara C Tamas
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Benjamin W H Lim
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Drake Pollard
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
| |
Collapse
|
3
|
Grassmann F, Schoenberger PGA, Brandl C, Schick T, Hasler D, Meister G, Fleckenstein M, Lindner M, Helbig H, Fauser S, Weber BHF. A circulating microrna profile is associated with late-stage neovascular age-related macular degeneration. PLoS One 2014; 9:e107461. [PMID: 25203061 PMCID: PMC4159338 DOI: 10.1371/journal.pone.0107461] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/11/2014] [Indexed: 01/10/2023] Open
Abstract
Age-related macular degeneration (AMD) is the leading cause of severe vision impairment in Western populations over 55 years. A growing number of gene variants have been identified which are strongly associated with an altered risk to develop AMD. Nevertheless, gene-based biomarkers which could be dysregulated at defined stages of AMD may point toward key processes in disease mechanism and thus may support efforts to design novel treatment regimens for this blinding disorder. Circulating microRNAs (cmiRNAs) which are carried by nanosized exosomes or microvesicles in blood plasma or serum, have been recognized as valuable indicators for various age-related diseases. We therefore aimed to elucidate the role of cmiRNAs in AMD by genome-wide miRNA expression profiling and replication analyses in 147 controls and 129 neovascular AMD patients. We identified three microRNAs differentially secreted in neovascular (NV) AMD (hsa-mir-301-3p, pcorrected = 5.6*10−5, hsa-mir-361-5p, pcorrected = 8.0*10−4 and hsa-mir-424-5p, pcorrected = 9.6*10−3). A combined profile of the three miRNAs revealed an area under the curve (AUC) value of 0.727 and was highly associated with NV AMD (p = 1.2*10−8). To evaluate subtype-specificity, an additional 59 AMD cases with pure unilateral or bilateral geographic atrophy (GA) were analyzed for microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p. While we found no significant differences between GA AMD and controls neither individually nor for a combined microRNAs profile, hsa-mir-424-5p levels remained significantly higher in GA AMD when compared to NV (pcorrected<0.005). Pathway enrichment analysis on genes predicted to be regulated by microRNAs hsa-mir-301-3p, hsa-mir-361-5p, and hsa-mir-424-5p, suggests canonical TGFβ, mTOR and related pathways to be involved in NV AMD. In addition, knockdown of hsa-mir-361-5p resulted in increased neovascularization in an invitro angiogenesis assay.
Collapse
Affiliation(s)
- Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | | | - Caroline Brandl
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
| | - Tina Schick
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | | | - Moritz Lindner
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Horst Helbig
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Bernhard H. F. Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- * E-mail:
| |
Collapse
|
4
|
Targeting RNA polymerase I to treat MYC-driven cancer. Oncogene 2014; 34:403-12. [PMID: 24608428 DOI: 10.1038/onc.2014.13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/08/2014] [Accepted: 01/08/2014] [Indexed: 02/06/2023]
Abstract
The MYC oncoprotein and transcription factor is dysregulated in a majority of human cancers and is considered a major driver of the malignant phenotype. As such, developing drugs for effective inhibition of MYC in a manner selective to malignancies is a 'holy grail' of transcription factor-based cancer therapy. Recent advances in elucidating MYC biology in both normal cells and pathological settings were anticipated to bring inhibition of tumorigenic MYC function closer to the clinic. However, while the extensive array of cellular pathways that MYC impacts present numerous fulcrum points on which to leverage MYC's therapeutic potential, identifying the critical target(s) for MYC-specific cancer therapy has been difficult to achieve. Somewhat unexpectedly, MYC's fundamental role in regulating the 'housekeeping' process of ribosome biogenesis, one of the most ubiquitously required and conserved cell functions, may provide the Achilles' heel for therapeutically targeting MYC-driven tumors.
Collapse
|
5
|
Bywater MJ, Pearson RB, McArthur GA, Hannan RD. Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat Rev Cancer 2013; 13:299-314. [PMID: 23612459 DOI: 10.1038/nrc3496] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations that directly affect transcription by RNA polymerases rank among the most central mediators of malignant transformation, but the frequency of new anticancer drugs that selectively target defective transcription apparatus entering the clinic has been limited. This is because targeting the large protein-protein and protein-DNA interfaces that control both generic and selective aspects of RNA polymerase transcription has proved extremely difficult. However, recent technological advances have led to a 'quantum leap' in our comprehension of the structure and function of the core RNA polymerase components, how they are dysregulated in a broad range of cancers and how they may be targeted for 'transcription therapy'.
Collapse
Affiliation(s)
- Megan J Bywater
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne 8006, Victoria, Australia
| | | | | | | |
Collapse
|
6
|
Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
7
|
Rettig M, Germann MW, Ismail MA, Batista-Parra A, Munde M, Boykin DW, Wilson WD. Microscopic rearrangement of bound minor groove binders detected by NMR. J Phys Chem B 2012; 116:5620-7. [PMID: 22530735 DOI: 10.1021/jp301143e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thermodynamic and structural studies are commonly utilized to optimize small molecules for specific DNA interactions, and, thus, a significant amount of binding data is available. However, the dynamic processes that are involved in minor groove complex formation and maintenance are not fully understood. To help define the processes involved, we have conducted 1D and 2D NMR in conjunction with biosensor-SPR experiments with a variety of compounds and symmetric, as well as asymmetric, AT tract DNA sequences. Surprisingly, the NMR data clearly show exchange between equivalent binding sites for strongly binding compounds like netropsin and DB921 (Ka > 10(8) M(-1)) that does not involve dissociation off the DNA. A quantitative analysis of the data revealed that these bound exchange rates are indeed much faster than the macroscopic dissociation rates which were independently determined by biosensor-SPR. Additionally, we could show the existence of at least two 1:1 compound DNA complexes at the same site for the interaction of these compounds with an asymmetric DNA sequence. To explain this behavior we introduced a model in which the ligand is rapidly flipping between two orientations while in close association with the DNA. The ligand reorientation will contribute favorably to the binding entropy. As the potential of minor groove binders to form more than a single complex with asymmetric, as well as symmetric, duplexes is widely unknown, the consequences for binding thermodynamics and compound design are discussed.
Collapse
Affiliation(s)
- Michael Rettig
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30303, United States
| | | | | | | | | | | | | |
Collapse
|
8
|
Sánchez MI, Vázquez O, Martínez-Costas J, Vázquez ME, Mascareñas JL. Straightforward access to bisbenzamidine DNA binders and their use as versatile adaptors for DNA-promoted processes. Chem Sci 2012. [DOI: 10.1039/c2sc00027j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
9
|
Wetzler DE, Comin MJ, Krajewski K, Gallo M. New human papilloma virus E2 transcription factor mimics: a tripyrrole-peptide conjugate with tight and specific DNA-recognition. PLoS One 2011; 6:e22409. [PMID: 21799846 PMCID: PMC3143144 DOI: 10.1371/journal.pone.0022409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 06/21/2011] [Indexed: 12/02/2022] Open
Abstract
Background Human papillomavirus (HPV) is the main causative agent of cervical cancer, particularly high risk strains such us HPV-16, -18 and -31. The viral encoded E2 protein acts as a transcriptional modulator and exerts a key role in viral DNA replication. Thus, E2 constitutes an attractive target for developing antiviral agents. E2 is a homodimeric protein that interacts with the DNA target through an α-helix of each monomer. However, a peptide corresponding to the DNA recognition helix of HPV-16 E2 binds DNA with lower affinity than its full-length DNA binding domain. Therefore, in an attempt to promote the DNA binding of the isolated peptide, we have designed a conjugate compound of the E2 α-helix peptide and a derivative of the antibiotic distamycin, which involves simultaneous minor- and major-groove interactions. Methodology/Principal Findings An E2 α-helix peptide-distamycin conjugate was designed and synthesized. It was characterized by NMR and CD spectroscopy, and its DNA binding properties were investigated by CD, DNA melting and gel shift experiments. The coupling of E2 peptide with distamycin does not affect its structural properties. The conjugate improves significantly the affinity of the peptide for specific DNA. In addition, stoichiometric amounts of specific DNA increase meaningfully the helical population of the peptide. The conjugate enhances the DNA binding constant 50-fold, maintaining its specificity. Conclusions/Significance These results demonstrate that peptide-distamycin conjugates are a promising tool to obtain compounds that bind the E2 target DNA-sequences with remarkable affinity and suggest that a bipartite major/minor groove binding scaffold can be a useful approach for therapeutic treatment of HPV infection.
Collapse
Affiliation(s)
- Diana E. Wetzler
- Department of Biological Chemistry, FCEN, University of Buenos Aires, Buenos Aires, Argentina
| | - Maria J. Comin
- Center for Research and Development in Chemistry, INTI, Buenos Aires, Argentina
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Mariana Gallo
- Fundación Instituto Leloir, Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
10
|
Lo ATS, Salam NK, Hibbs DE, Rutledge PJ, Todd MH. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal. PLoS One 2011; 6:e17446. [PMID: 21573061 PMCID: PMC3090394 DOI: 10.1371/journal.pone.0017446] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.
Collapse
Affiliation(s)
- Anthony T. S. Lo
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Noeris K. Salam
- Schrödinger, Inc., New York, New York, United States of
America
| | - David E. Hibbs
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales,
Australia
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| |
Collapse
|
11
|
Bates CA, Pomerantz WC, Mapp AK. Transcriptional tools: Small molecules for modulating CBP KIX-dependent transcriptional activators. Biopolymers 2011; 95:17-23. [PMID: 20882601 PMCID: PMC3535496 DOI: 10.1002/bip.21548] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Previously it was demonstrated that amphipathic isoxazolidines are able to functionally replace the transcriptional activation domains of endogenous transcriptional activators. In addition, in vitro binding studies suggested that a key binding partner of these molecules is the CREB Binding Protein (CBP), more specifically the KIX domain within this protein. Here we show that CBP plays an essential role in the ability of isoxazolidine transcriptional activation domains to activate transcription in cells. Consistent with this model, isoxazolidines are able to function as competitive inhibitors of the activators MLL and Jun, both of which utilize a binding interaction with KIX to up-regulate transcription. Further, modification of the N2 side chain produced three analogs with enhanced potency against Jun-mediated transcription, although increased cytotoxicity was also observed. Collectively these small KIX-binding molecules will be useful tools for dissecting the role of the KIX domain in a variety of pathological processes.
Collapse
Affiliation(s)
- Caleb A. Bates
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Anna K. Mapp
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
12
|
Li C, Du C, Tian H, Jiang C, Du M, Liu Y, Qiao RZ, Jia YX, Zhao YF. Artificial Transcription Factors which Mediate Double-Strand DNA Cleavage. Chemistry 2010; 16:12935-40. [DOI: 10.1002/chem.201000552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
13
|
Morisaki T, Imanishi M, Futaki S, Sugiura Y. [Artificial transcription factors based on multi-zinc finger motifs]. YAKUGAKU ZASSHI 2010; 130:45-8. [PMID: 20046064 DOI: 10.1248/yakushi.130.45] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial transcription factors targeting any desired genes are very attractive from the standpoint of regulating biological functions for life science studies and clinical applications. In order to generate such transcription factors, specific DNA binding domains are required to address a single site for each gene promoter. C(2)H(2) type zinc finger motif is one of the best frameworks to create new artificial DNA binding proteins for the following features: the zinc finger motif can recognize three bases DNA, be tandemly repeated by covalent linkage, and work as a monomer. Taking advantage of these features, manifold zinc finger proteins targeting various DNA sequences have been created so far. For application to a target in sequences as complex as the human genome, the significantly strict specificity in DNA binding must be required. Conjugating multiple fingers (multi-zinc fingers) enables to recognize longer sequences which are sufficient for addressing a single site in the human genome, whereas it has become known that as the number of finger motifs increases, the equilibrium time with the target sequence is significantly longer by in vitro experiments. Our recent study showed that the multi-zinc finger type artificial transcription factor could activate the reporter gene promptly. There is much interest in creating gene regulators, and the artificial transcription factors based on multi-zinc finger motifs could be a superior scaffold.
Collapse
Affiliation(s)
- Tatsuya Morisaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
| | | | | | | |
Collapse
|
14
|
Liu Y, Wilson WD. Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection. Methods Mol Biol 2010; 613:1-23. [PMID: 19997874 DOI: 10.1007/978-1-60327-418-0_1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.
Collapse
Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | | |
Collapse
|
15
|
Liu B, Kodadek T. Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides. J Med Chem 2009; 52:4604-12. [PMID: 19610652 DOI: 10.1021/jm9002999] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are a group of chemicals that are able to bind specifically to DNA sequences in vitro and in mammalian cells. Using a cell based reporter assay, we investigated the size and linker affects on the cellular permeability of polyamides. We found that the conventional beta-alanine-3,3'-diamino-N-methyldipropylamine (betaDa) linker strongly limited the cellular permeability. We discovered that a short ethylene diamine (Et) linker displayed high cellular permeability. With the improved Et linker, we found that the cellular permeability of polyamides was size-dependent.
Collapse
Affiliation(s)
- Bo Liu
- Department of Internal Medicine, Division of Translational Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | | |
Collapse
|
16
|
Bishop AC, Chen VL. Brought to life: targeted activation of enzyme function with small molecules. J Chem Biol 2008; 2:1-9. [PMID: 19568788 DOI: 10.1007/s12154-008-0012-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 09/04/2008] [Indexed: 11/30/2022] Open
Abstract
Cell-permeable small molecules that are capable of activating particular enzymes would be invaluable tools for studying protein function in complex cell-signaling cascades. But, is it feasible to identify compounds that allow chemical-biology researchers to activate specific enzymes in a cellular context? In this review, we describe some recent advances in achieving targeted enzyme activation with small molecules. In addition to surveying progress in the identification and targeting of enzymes that contain natural allosteric-activation sites, we focus on recently developed protein-engineering strategies that allow researchers to render an enzyme of interest "activatable" by a pre-chosen compound. Three distinct strategies for targeting an engineered enzyme are discussed: direct chemical "rescue" of an intentionally inactivated enzyme, activation of an enzyme by targeting a de novo small-molecule-binding site, and the generation of activatable enzymes via fusion of target enzymes to previously characterized small-molecule-binding domains.
Collapse
Affiliation(s)
- Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, MA, 01002, USA,
| | | |
Collapse
|
17
|
Morisaki T, Imanishi M, Futaki S, Sugiura Y. Rapid Transcriptional Activity in Vivo and Slow DNA Binding in Vitro by an Artificial Multi-Zinc Finger Protein. Biochemistry 2008; 47:10171-7. [DOI: 10.1021/bi801124b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatsuya Morisaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan, PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan, and Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Kyotanabe, Kyoto 610-0395, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan, PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan, and Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Kyotanabe, Kyoto 610-0395, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan, PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan, and Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Kyotanabe, Kyoto 610-0395, Japan
| | - Yukio Sugiura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan, PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan, and Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Kyotanabe, Kyoto 610-0395, Japan
| |
Collapse
|