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Bergey CM, Watkins AM, Arora PS. HippDB: a database of readily targeted helical protein-protein interactions. Bioinformatics 2013; 29:2806-7. [PMID: 23958730 DOI: 10.1093/bioinformatics/btt483] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. AVAILABILITY AND IMPLEMENTATION HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. CONTACT arora@nyu.edu.
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Raj M, Bullock BN, Arora PS. Plucking the high hanging fruit: a systematic approach for targeting protein-protein interactions. Bioorg Med Chem 2013; 21:4051-7. [PMID: 23267671 PMCID: PMC3622812 DOI: 10.1016/j.bmc.2012.11.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/08/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
Abstract
Development of specific ligands for protein targets that help decode the complexities of protein-protein interaction networks is a key goal for the field of chemical biology. Despite the emergence of powerful in silico and experimental high-throughput screening strategies, the discovery of synthetic ligands that selectively modulate protein-protein interactions remains a challenge for bioorganic and medicinal chemists. This Perspective discusses emerging principles for the rational design of PPI inhibitors. Fundamentally, the approach seeks to adapt nature's protein recognition principles for the design of suitable secondary structure mimetics.
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Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PLoS One 2013; 8:e67051. [PMID: 23869206 PMCID: PMC3712014 DOI: 10.1371/journal.pone.0067051] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, -peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones.
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Arora PS. 187 Plucking the high hanging fruit: a systematic approach for targeting protein interfaces. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wang X, Bergenfeld I, Arora PS, Canary JW. Reversible Redox Reconfiguration of Secondary Structures in a Designed Peptide. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wang X, Bergenfeld I, Arora PS, Canary JW. Reversible Redox Reconfiguration of Secondary Structures in a Designed Peptide. Angew Chem Int Ed Engl 2012; 51:12099-101. [DOI: 10.1002/anie.201206009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 01/30/2023]
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Abstract
Oligomers composed of β(3)-amino acid residues and a mixture of α- and β(3)-residues have emerged as proteolytically stable structural mimics of α-helices. An attractive feature of these oligomers is that they adopt defined conformations in short sequences. In this manuscript, we evaluate the impact of β(3)-residues as compared to their α-amino acid analogs in prenucleated helices. Our hydrogen-deuterium exchange results suggest that heterogeneous sequences composed of "αααβ" repeats are conformationally more rigid than the corresponding homogeneous α-peptide helices, with the macrocycle templating the helical conformation having a significant influence.
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Henchey LK, Kushal S, Dubey R, Chapman RN, Olenyuk BZ, Arora PS. Correction to Inhibition of Hypoxia Inducible Factor 1–Transcription Coactivator Interaction by a Hydrogen Bond Surrogate α-Helix. J Am Chem Soc 2012. [DOI: 10.1021/ja302676m] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Grishagin IV, Olenyuk BZ, Bullock B, Arora PS. Abstract 283: OOPs: Novel HIF-1α mimics. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Alpha subunit of the hypoxia-inducible factor 1 (HIF-1α) is an important transcriptional regulator of hypoxia-inducible genes responsible for tumor proliferation and metastasis, and therefore HIF-1α is a valuable therapeutic target. In turn, the interaction between C-terminal activation domain (C-TAD) of HIF-1α and the cysteine-histidine rich domain (CH1) of its coactivator p300 is known to play the key role in the HIF-1 pathway. However, to date very few compounds have been reported to disrupt HIF-1α/p300 complex. We have rationally designed and synthesized non-peptidic mimics of HIF-1α CTAD αA-helix with novel oligooxopiperazine backbone (OOPs). These mimics exhibit relatively low toxicity and substantially downregulate expression levels of selected hypoxia-inducible genes (VEGF, c-MET, LOX, GLUT1, CXCR4) in cellulo in a dose-dependent manner.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 283. doi:1538-7445.AM2012-283
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Mahon AB, Arora PS. End-Capped α-Helices as Modulators of Protein Function. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e1-e70. [PMID: 22712023 DOI: 10.1016/j.ddtec.2011.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Examination of complexes of proteins with other biomolecules reveals that proteins tend to interact with partners via folded sub-domains, in which the backbone possesses secondary structure. α-Helices, the largest class of protein secondary structures, play fundamental roles in a multitude of highly specific protein-protein and protein-nucleic acids interactions. Herein, we describe the potential of a helix nucleation strategy to afford modulators of protein-protein interactions.
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Mahon AB, Arora PS. Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices. Chem Commun (Camb) 2012; 48:1416-8. [PMID: 21952530 PMCID: PMC3412876 DOI: 10.1039/c1cc14730g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Appropriately-placed hydrogen bond surrogates have been demonstrated to efficiently nucleate helical conformations. Herein we describe an efficient method for the synthesis of thioether-based hydrogen bond surrogate (teHBS) helices. A teHBS helix is shown to adopt a stable conformation and target its cognate protein receptor with high affinity.
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Mahon AB, Miller SE, Joy ST, Arora PS. Rational Design Strategies for Developing Synthetic Inhibitors of Helical Protein Interfaces. TOPICS IN MEDICINAL CHEMISTRY 2012. [DOI: 10.1007/978-3-642-28965-1_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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Miller SE, Kallenbach NR, Arora PS. Reversible α-helix formation controlled by a hydrogen bond surrogate. Tetrahedron 2011; 68:4434-4437. [PMID: 23144512 DOI: 10.1016/j.tet.2011.12.068] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Strategically placed covalent linkages have been shown to stabilize helical conformations in short peptide sequences. Here we report the synthesis of a stabilized α-helix that utilizes an internal disulfide linkage. Structural analysis indicates that the dynamic nature of the disulfide bridge allows for the reversible formation of an α-helix through oxidation and reduction reactions.
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Abstract
Structure-based design of synthetic inhibitors of protein-protein interactions (PPIs) requires adept molecular design and synthesis strategies as well as knowledge of targetable complexes. To address the significant gap between the elegant design of helix mimetics and their sporadic use in biology, we analyzed the full set of helical protein interfaces in the Protein Data Bank to obtain a snapshot of how helices that are critical for complex formation interact with the partner proteins. The results of this study are expected to guide the systematic design of synthetic inhibitors of PPIs. We have experimentally evaluated new classes of protein complexes that emerged from this data set, highlighting the significance of the results described herein.
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Guarracino DA, Bullock BN, Arora PS. Mini review: protein-protein interactions in transcription: a fertile ground for helix mimetics. Biopolymers 2011; 95:1-7. [PMID: 20882600 DOI: 10.1002/bip.21546] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Designed ligands that inhibit protein-protein interactions involved in gene expression are valuable as reagents for genomics research and as leads for drug discovery efforts. Selective modulation of protein-protein interactions has proven to be a daunting task for synthetic ligands; however, the last decade has seen significant advances in inhibitor design, especially for helical protein interfaces. This review discusses examples of transcriptional complexes targeted by designer helices.
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Henchey LK, Porter JR, Ghosh I, Arora PS. High specificity in protein recognition by hydrogen-bond-surrogate α-helices: selective inhibition of the p53/MDM2 complex. Chembiochem 2011; 11:2104-7. [PMID: 20821791 DOI: 10.1002/cbic.201000378] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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67
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Porter JR, Helmers MR, Wang P, Furman JL, Joy ST, Arora PS, Ghosh I. Profiling small molecule inhibitors against helix-receptor interactions: the Bcl-2 family inhibitor BH3I-1 potently inhibits p53/hDM2. Chem Commun (Camb) 2010; 46:8020-2. [PMID: 20856941 PMCID: PMC4576826 DOI: 10.1039/c0cc02969f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We validate a practical methodology for the rapid profiling of small molecule inhibitors of protein-protein interactions. We find that a well known BH3 family inhibitor can potently inhibit the p53/hDM2 interaction.
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68
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Patgiri A, Menzenski MZ, Mahon AB, Arora PS. Solid-phase synthesis of short α-helices stabilized by the hydrogen bond surrogate approach. Nat Protoc 2010; 5:1857-65. [PMID: 21030960 DOI: 10.1038/nprot.2010.146] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis behind the design of stabilized helices and helix mimetics is that these medium-sized molecules may pursue their targets with higher specificity because of a larger number of contacts. This protocol describes an optimized synthetic strategy for the preparation of stabilized α-helices that feature a carbon-carbon linkage in place of the characteristic N-terminal main-chain hydrogen bond of canonical helices. Formation of the carbon-carbon bond is enabled by a microwave-assisted ring-closing metathesis reaction between two terminal olefins on the peptide chain. The outlined strategy allows the synthesis and purification of a hydrogen bond surrogate (HBS) α-helix in ∼ 1 week.
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69
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Jochim AL, Arora PS. Systematic analysis of helical protein interfaces reveals targets for synthetic inhibitors. ACS Chem Biol 2010; 5:919-23. [PMID: 20712375 DOI: 10.1021/cb1001747] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic inhibitors of protein-protein interactions are being discovered despite the inherent challenge in targeting large contact surfaces with small molecules. An analysis of available examples identifies common features of complexes that make them tractable for small molecules. We deduced that relative disposition and energetic contributions of "hot spot" residues provide a predictive scale for the potential of protein-protein interactions to be inhibited by small molecules. On the basis of this model, we analyzed the full set of helical protein interfaces in the Protein Data Bank to identify those that are potentially suitable candidates for synthetic ligands.
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70
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Patgiri A, Witten MR, Arora PS. Solid phase synthesis of hydrogen bond surrogate derived alpha-helices: resolving the case of a difficult amide coupling. Org Biomol Chem 2010; 8:1773-6. [PMID: 20449477 DOI: 10.1039/c000905a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Solid phase synthesis of HBS helices involving the Fukuyama-Mitsunobu reaction and triphosgene coupling is described.
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71
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Henchey LK, Kushal S, Dubey R, Chapman RN, Olenyuk BZ, Arora PS. Inhibition of hypoxia inducible factor 1-transcription coactivator interaction by a hydrogen bond surrogate alpha-helix. J Am Chem Soc 2010; 132:941-3. [PMID: 20041650 DOI: 10.1021/ja9082864] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Designed ligands that inhibit hypoxia-inducible gene expression could offer new tools for genomic research and, potentially, drug discovery efforts for the treatment of neovascularization in cancers. We report a stabilized alpha-helix designed to target the binding interface between the C-terminal transactivation domain (C-TAD) of hypoxia-inducible factor 1alpha (HIF-1alpha) and cysteine-histidine rich region (CH1) of transcriptional coactivator CBP/p300. The synthetic helix disrupts the structure and function of this complex, resulting in a rapid downregulation of two hypoxia-inducible genes (VEGF and GLUT1) in cell culture.
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Jochim AL, Miller SE, Angelo NG, Arora PS. Evaluation of triazolamers as active site inhibitors of HIV-1 protease. Bioorg Med Chem Lett 2009; 19:6023-6. [PMID: 19800230 DOI: 10.1016/j.bmcl.2009.09.049] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
Abstract
Proteases typically recognize their peptide substrates in extended conformations. General approaches for designing protease inhibitors often consist of peptidomimetics that feature this conformation. Herein we discuss a combination of computational and experimental studies to evaluate the potential of triazole-linked beta-strand mimetics as inhibitors of HIV-1 protease activity.
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Bao J, Dong XY, Zhang JZH, Arora PS. Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL. J Phys Chem B 2009; 113:3565-71. [PMID: 19231824 DOI: 10.1021/jp809810z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A new peptide modification strategy was recently developed to replace the i to i + 4 hydrogen bond of the main chain of an alpha-helix with a carbon-carbon covalent bond to afford highly stable constrained alpha-helices, termed hydrogen-bond surrogate (HBS) helices. HBS helices that mimic the Bak BH3 domains were experimentally demonstrated to target protein Bcl-x(L) with high affinity. In this study, molecular dynamics (MD) simulation is used to understand how the covalent modification of the natural Bak sequence affects the binding to Bcl-x(L) at molecular levels. The binding mechanism of HBS helix to Bcl-x(L) and the effect of synthesized cyclic structures are analyzed by MD and MM-PBSA calculations for comparison with the native binding of Bak-Bcl-x(L). The present MD result shows that the entropy of the HBS structure is considerably reduced, and the presence of the N-terminal HBS macrocycle impacts residues at the C-terminus of the helix, but the conformation of the corresponding binding structures is not significantly changed. Our analysis shows that substitution of an aspartic acid residue--a helix breaker--with a hydrophobic residue not only enhances the helicity of the peptide but also stabilizes the structure of the binding complex. The present computational result is consistent with the experimental observation and provides explanations for the altered binding properties of the artificial Bak alpha-helix. Our study underscores the importance of the dynamical effect in protein-peptide interaction in which entropic effect plays a major role.
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75
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Jochim AL, Arora PS. Assessment of helical interfaces in protein-protein interactions. MOLECULAR BIOSYSTEMS 2009; 5:924-6. [PMID: 19668855 DOI: 10.1039/b903202a] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we identify and analyze helical protein interfaces as potential targets for synthetic modulators of protein-protein interactions.
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76
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Patgiri A, Jochim AL, Arora PS. A hydrogen bond surrogate approach for stabilization of short peptide sequences in alpha-helical conformation. Acc Chem Res 2008; 41:1289-300. [PMID: 18630933 DOI: 10.1021/ar700264k] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alpha-helices constitute the largest class of protein secondary structures and play a major role in mediating protein-protein interactions. Development of stable mimics of short alpha-helices would be invaluable for inhibition of protein-protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in alpha-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS alpha-helices feature a carbon-carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix-coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short alpha-helices. The HBS method affords preorganized alpha-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an attractive strategy for generation of ligands for protein receptors because placement of the cross-link on the inside of the helix does not block solvent-exposed molecular recognition surfaces of the molecule. Our metathesis-based synthetic strategy utilizes standard Fmoc solid phase peptide synthesis methodology, resins, and reagents and provides HBS helices in sufficient amounts for subsequent biophysical and biological analyses. Extensive conformational analysis of HBS alpha-helices with 2D NMR, circular dichroism spectroscopies and X-ray crystallography confirms the alpha-helical structure in these compounds. The crystal structure indicates that all i and i + 4 C=O and NH hydrogen-bonding partners fall within distances and angles expected for a fully hydrogen-bonded alpha-helix. The backbone conformation of HBS alpha-helix in the crystal structure superimposes with an rms difference of 0.75 A onto the backbone conformation of a model alpha-helix. Significantly, the backbone torsion angles for the HBS helix residues fall within the range expected for a canonical alpha-helix. Thermal and chemical denaturation studies suggest that the HBS approach provides exceptionally stable alpha-helices from a variety of short sequences, which retain their helical conformation in aqueous buffers at exceptionally high temperatures. The high degree of thermal stability observed for HBS helices is consistent with the theoretical predictions for a nucleated helix. The HBS approach was devised to afford internally constrained helices so that the molecular recognition surface of the helix and its protein binding properties are not compromised by the constraining moiety. Notably, our preliminary studies illustrate that HBS helices can target their expected protein receptors with high affinity.
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Henchey LK, Jochim AL, Arora PS. Contemporary strategies for the stabilization of peptides in the alpha-helical conformation. Curr Opin Chem Biol 2008; 12:692-7. [PMID: 18793750 DOI: 10.1016/j.cbpa.2008.08.019] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 08/01/2008] [Accepted: 08/07/2008] [Indexed: 11/19/2022]
Abstract
Herein we review contemporary synthetic and protein design strategies to stabilize the alpha-helical motif in short peptides and miniature proteins. Advances in organometallic catalyst design, specifically for the olefin metathesis reaction, enable the use of hydrocarbon bridges to either crosslink side chains of specific residues or mimic intramolecular hydrogen bonds with carbon-carbon bonds. The resulting hydrocarbon-stapled and hydrogen bond surrogate alpha-helices provide unique synthetic ligands for targeting biomolecules. In the protein design realm, several classes of miniature proteins that display stable helical domains have been engineered and manipulated with powerful in vitro selection technologies to yield libraries of sequences that retain their helical folds. Rational re-design of these scaffolds provide distinctive reagents for the modulation of protein-protein interactions.
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Chapman R, Kulp JL, Patgiri A, Kallenbach NR, Bracken C, Arora PS. Trapping a folding intermediate of the alpha-helix: stabilization of the pi-helix. Biochemistry 2008; 47:4189-95. [PMID: 18335996 DOI: 10.1021/bi800136m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the design, synthesis, and characterization of a short peptide trapped in a pi-helix configuration. This high-energy conformation was nucleated by a preorganized pi-turn, which was obtained by replacing an N-terminal intramolecular main chain i and i + 5 hydrogen bond with a carbon-carbon bond. Our studies highlight the nucleation parameter as a key factor contributing to the relative instability of the pi-helix and allow us to estimate fundamental helix-coil transition parameters for this conformation.
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Liu J, Wang D, Zheng Q, Lu M, Arora PS. Atomic Structure of a Short α-Helix Stabilized by a Main Chain Hydrogen-Bond Surrogate. J Am Chem Soc 2008; 130:4334-7. [DOI: 10.1021/ja077704u] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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80
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Angelo NG, Arora PS. Solution- and solid-phase synthesis of triazole oligomers that display protein-like functionality. J Org Chem 2007; 72:7963-7. [PMID: 17880241 DOI: 10.1021/jo701292h] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We recently developed a new class of oligomers that contain alpha-amino acid residues linked by 1,2,3-triazole groups [Angelo, N. G.; Arora, P. S. J. Am. Chem. Soc. 2005, 127, 17134-17135]. Synthesis of these oligomers involves an iterative sequence consisting of diazotransfer and Huisgen 1,3-dipolar cycloaddition steps. In this contribution, we describe an efficient one-pot, two-step sequence for the preparation of triazoles from the corresponding amino acid-derived amines and alkynes in solution. The one-pot sequence affords the desired products in significantly higher yields than our original method. We also outline a highly effective protocol for the synthesis of these triazole-based biomimetic oligomers on the solid phase. We find that amino acid derivatives and iterative formation of triazole rings require nontraditional reaction conditions for high yields.
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81
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Chapman RN, Arora PS. Optimized synthesis of hydrogen-bond surrogate helices: surprising effects of microwave heating on the activity of Grubbs catalysts. Org Lett 2007; 8:5825-8. [PMID: 17134282 PMCID: PMC1828874 DOI: 10.1021/ol062443z] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This manuscript discusses microwave-assisted solid-phase synthesis of hydrogen-bond surrogate based alpha-helices and analogues by ring-closing metathesis (RCM). Microwave-mediated RCM allows access to a greater variety of amino acid residues in the macrocycles in shorter reaction times and higher yields compared to conventional heating. Surprisingly, we discovered that the Grubbs II catalyst is highly active under the influence of microwaves but catalytically dead under oil-bath conditions for the metathesis of these peptide bisolefins. [reaction: see text]
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82
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Wang D, Chen K, Kulp Iii JL, Arora PS. Evaluation of biologically relevant short alpha-helices stabilized by a main-chain hydrogen-bond surrogate. J Am Chem Soc 2007; 128:9248-56. [PMID: 16834399 PMCID: PMC1828873 DOI: 10.1021/ja062710w] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously reported the design and synthesis of a new class of artificial alpha-helices in which an N-terminal main-chain hydrogen bond is replaced by a carbon-carbon bond derived from a ring-closing metathesis reaction [Chapman, R. N.; Dimartino, G.; Arora, P. S. J. Am. Chem. Soc. 2004, 126, 12252-12253]. Our initial study utilized an alanine-rich sequence; in the present manuscript we evaluate the potential of this method for the synthesis of very short (10 residues) alpha-helices representing two different biologically relevant alpha-helical domains. We extensively characterized these two sets of artificial helices by NMR and circular dichroism spectroscopies and find that the hydrogen-bond surrogate approach can afford well-defined short alpha-helical structures from sequences that do not spontaneously form alpha-helical conformations.
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Wang D, Chen K, Dimartino G, Arora PS. Nucleation and stability of hydrogen-bond surrogate-based alpha-helices. Org Biomol Chem 2007; 4:4074-81. [PMID: 17312961 PMCID: PMC1807155 DOI: 10.1039/b612891b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have reported a new class of artificial alpha-helices in which a pre-organized alpha-turn nucleates the helical conformation [R. N. Chapman, G. Dimartino, and P. S. Arora, J Am. Chem. Soc., 2004, 126, 12252 and D. Wang, K. Chen, J. L. Kulp, III, and P. S. Arora, J. Am. Chem. Soc., 2006, 128, 9248]. This manuscript describes the effect of the core nucleation template on the overall helicity of the peptides and demonstrates that the macrocycle which most closely mimics the 13-membered hydrogen-bonded alpha-turn in canonical alpha-helices also affords the most stable artificial alpha-helix. We also investigate the stability of these synthetic helices through classical helix-coil parameters and find that the denaturation behavior of HBS alpha-helices agrees with the theoretical properties of a peptide with a well-defined and stable helix nucleus.
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84
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Angelo NG, Arora PS. Nonpeptidic foldamers from amino acids: synthesis and characterization of 1,3-substituted triazole oligomers. J Am Chem Soc 2006; 127:17134-5. [PMID: 16332031 DOI: 10.1021/ja056406z] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonpeptidic foldamers capable of displaying protein-like functionality were prepared by swapping amide bonds with 1,2,3-triazole rings. The overall conformation of these triazole oligomers is largely dictated by dipole-dipole interactions between adjacent rings. Solution NMR studies suggest that a zigzag conformation, which closely mimics the beta-strand structure, predominates in two different tetramers.
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85
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Wang D, Liao W, Arora PS. Enhanced metabolic stability and protein-binding properties of artificial alpha helices derived from a hydrogen-bond surrogate: application to Bcl-xL. Angew Chem Int Ed Engl 2005; 44:6525-9. [PMID: 16172999 PMCID: PMC1351285 DOI: 10.1002/anie.200501603] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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86
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Wang D, Liao W, Arora PS. Enhanced Metabolic Stability and Protein-Binding Properties of Artificial α Helices Derived from a Hydrogen-Bond Surrogate: Application to Bcl-xL. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501603] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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87
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Abstract
In this issue, Mapp and colleagues describe a significant advance in the design of artificial transcription activators that function in a cell-type-specific manner. [1] The authors show that peptides selected for binding a component of the yeast transcription complex require its presence for effective transcriptional activation.
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Dimartino G, Wang D, Chapman RN, Arora PS. Solid-Phase Synthesis of Hydrogen-Bond Surrogate-Derived α-Helices. Org Lett 2005; 7:2389-92. [PMID: 15932205 DOI: 10.1021/ol0506516] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] This report describes the solid-phase synthesis of hydrogen-bond surrogate-derived artificial alpha-helices by a ring-closing metathesis reaction. From a series of metathesis catalysts evaluated for the synthesis of these helices, the Hoveyda-Grubbs catalyst was found to afford high yields of the macrocycle irrespective of the peptide sequence.
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Chapman RN, Dimartino G, Arora PS. A highly stable short alpha-helix constrained by a main-chain hydrogen-bond surrogate. J Am Chem Soc 2004; 126:12252-3. [PMID: 15453743 DOI: 10.1021/ja0466659] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe a strategy for the preparation of artificial alpha-helices involving replacement of one of the main-chain hydrogen bonds with a covalent linkage. To mimic the C=O...H-N hydrogen bond as closely as possible, we envisioned a covalent bond of the type C=X-Y-N, where X and Y are two carbon atoms connected through an olefin metathesis reaction. Our results demonstrate that the replacement of a hydrogen bond between the i and i + 4 residues at the N-terminus of a short peptide with a carbon-carbon bond results in a highly stable constrained alpha-helix at physiological conditions as indicated by CD and NMR spectroscopies. The advantage of this strategy is that it allows access to short alpha-helices with strict preservation of molecular recognition surfaces required for biomolecular interactions.
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90
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Dickinson LA, Burnett R, Melander C, Edelson BS, Arora PS, Dervan PB, Gottesfeld JM. Arresting Cancer Proliferation by Small-Molecule Gene Regulation. ACTA ACUST UNITED AC 2004; 11:1583-94. [PMID: 15556009 DOI: 10.1016/j.chembiol.2004.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 12/31/2022]
Abstract
A small library of pyrrole-imidazole polyamide-DNA alkylator (chlorambucil) conjugates was screened for effects on morphology and growth characteristics of a human colon carcinoma cell line, and a compound was identified that causes cells to arrest in the G2/M stage of the cell cycle. Microarray analysis indicates that the histone H4c gene is significantly downregulated by this polyamide. RT-PCR and Western blotting experiments confirm this result, and siRNA to H4c mRNA yields the same cellular response. Strikingly, reduction of H4 protein by >50% does not lead to widespread changes in global gene expression. Sequence-specific alkylation within the coding region of the H4c gene in cell culture was confirmed by LM-PCR. The compound is active in a wide range of cancer cell lines, and treated cells do not form tumors in nude mice. The compound is also active in vivo, blocking tumor growth in mice, without obvious animal toxicity.
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92
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Eisenführ A, Arora PS, Sengle G, Takaoka LR, Nowick JS, Famulok M. A ribozyme with michaelase activity: synthesis of the substrate precursors. Bioorg Med Chem 2003; 11:235-49. [PMID: 12470718 DOI: 10.1016/s0968-0896(02)00311-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The ability to generate RNA molecules that can catalyze complex organic transformations not only facilitates the reconstruction and plausibility of possible prebiotic reaction pathways but is also crucial for elucidating the potential of the application of RNA catalysts in organic syntheses. Iterative RNA selection previously identified a ribozyme that catalyzes the Michael addition of a cysteine thiol to an alpha,beta-unsaturated amide. This reaction is chemically similar to the rate limiting step of the thymidylate synthase reaction, which is the corresponding reaction of a cysteine thiol to the double-bond of the uracil nucleobase. Here we provide a detailed description of the synthesis of the ribozyme substrates and the substrate oligonucleotides used for its characterization and the investigation of the background reaction. We also describe the further characterization of the ribozyme with respect to substrate specificity. We show that the thiol group of the cysteine nucleophile is essential for the reaction to proceed. When substituted for a thiomethyl group, no reaction takes place.
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93
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Arora PS, Ansari AZ, Best TP, Ptashne M, Dervan PB. Design of artificial transcriptional activators with rigid poly-L-proline linkers. J Am Chem Soc 2002; 124:13067-71. [PMID: 12405833 DOI: 10.1021/ja0208355] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Typical eukaryotic transcriptional activators are composed of distinct functional domains, including a DNA binding domain and an activating domain. Artificial transcription factors have been designed wherein the DNA binding domain is a minor groove DNA binding hairpin polyamide linked by a flexible tether to short activating peptides, typically 16-20 residues in size. In this study, the linker between the polyamide and the peptide was altered in an incremental fashion using rigid oligoproline "molecular rulers" in the 18-45 A length range. We find that there is an optimal linker length which separates the DNA and the activation region for transcription activation.
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94
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Belitsky JM, Leslie SJ, Arora PS, Beerman TA, Dervan PB. Cellular uptake of N-methylpyrrole/N-methylimidazole polyamide-dye conjugates. Bioorg Med Chem 2002; 10:3313-8. [PMID: 12150878 DOI: 10.1016/s0968-0896(02)00204-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The cellular uptake and localization properties of DNA binding N-methylpyrrole/N-methylimidazole polyamide-dye conjugates in a variety of living cells have been examined by confocal laser scanning microscopy. With the exception of certain T-cell lines, polyamide-dye conjugates localize mainly in the cytoplasm and not in the nucleus. Reagents such as methanol typically used to fix cells for microscopy significantly alter the cellular localization of these DNA-binding ligands.
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95
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Sengle G, Eisenführ A, Arora PS, Nowick JS, Famulok M. Novel RNA catalysts for the Michael reaction. ACTA ACUST UNITED AC 2001; 8:459-73. [PMID: 11358693 DOI: 10.1016/s1074-5521(01)00026-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND In vitro selected ribozymes with nucleotide synthase, peptide and carbon-carbon bond forming activity provide insight into possible scenarios on how chemical transformations may have been catalyzed before protein enzymes had evolved. Metabolic pathways based on ribozymes may have existed at an early stage of evolution. RESULTS We have isolated a novel ribozyme that mediates Michael-adduct formation at a Michael-acceptor substrate, similar to the rate-limiting step of the mechanistic sequence of thymidylate synthase. The kinetic characterization of this catalyst revealed a rate enhancement by a factor of approximately 10(5). The ribozyme shows substrate specificity and can act as an intermolecular catalyst which transfers the Michael-donor substrate onto an external 20-mer RNA oligonucleotide containing the Michael-acceptor system. CONCLUSION The ribozyme described here is the first example of a catalytic RNA with Michael-adduct forming activity which represents a key mechanistic step in metabolic pathways and other biochemical reactions. Therefore, previously unforeseen RNA-evolution pathways can be considered, for example the formation of dTMP from dUMP. The substrate specificity of this ribozyme may also render it useful in organic syntheses.
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Sengle G, Jenne A, Arora PS, Seelig B, Nowick JS, Jäschke A, Famulok M. Synthesis, incorporation efficiency, and stability of disulfide bridged functional groups at RNA 5'-ends. Bioorg Med Chem 2000; 8:1317-29. [PMID: 10896110 DOI: 10.1016/s0968-0896(00)00080-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Modified guanosine monophosphates have been employed to introduce various functional groups onto RNA 5'-ends. Applications of modified RNA 5'-ends include the generation of functionalized RNA libraries for in vitro selection of catalytic RNAs, the attachment of photoaffinity-tags for mapping RNA-protein interactions or active sites in catalytic RNAs, or the nonradioactive labeling of RNA molecules with fluorescent groups. While in these and in similar applications a stable linkage is desired, in selection experiments for generating novel catalytic RNAs it is often advantageous that a functional group is introduced reversibly. Here we give a quantitative comparison of the different strategies that can be applied to reversibly attach functional groups via disulfide bonds to RNA 5'-ends. We report the preparation of functional groups with disulfide linkages, their incorporation efficiency into an RNA library, and their stability under various conditions.
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97
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Arora PS, Van QN, Famulok M, Shaka AJ, Nowick JS. Design and synthesis of a transition state analogue for the Diels-Alder reaction. Bioorg Med Chem 1998; 6:1421-8. [PMID: 9801813 DOI: 10.1016/s0968-0896(98)00072-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This paper describes the design and synthesis of a tricationic transition state analogue (TSA 1) for the Diels-Alder reaction. TSA 1 contains a bicyclo[2.2.1]heptene ring system that mimics the boat conformation of the Diels-Alder transition state and is designed to bind tightly to antibodies, nucleic acids, and imprinted polymers by means of hydrogen bonds and salt-bridges. This paper also describes the syntheses of the Diels-Alder reaction substrates (diene 2 and dienophile 3) and a sensitive HPLC assay to monitor the formation of Diels-Alder product 4. In contrast to previously reported TSAs and dienophiles for the Diels-Alder reaction that are based upon maleimides, TSA 1 and dienophile 3 are based upon fumaramide. The fumaramide system should destabilize the initially formed boat conformer of Diels-Alder product 4 and stabilize a half-chair conformer. The conversion of the initially formed boat conformer to the half-chair conformer is designed to help prevent Diels-Alder product 4 from binding strongly to catalysts selected to strongly bind TSA 1. This feature should minimize product inhibition, which can be a problem in the catalysis of the Diels-Alder reaction.
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98
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Handa R, Bhatia S, Wali JP, Kumar L, Kochupillai V, Mohindra M, Arora PS. Acute leukemia presenting as pericardial effusion--a case report. Singapore Med J 1997; 38:491-2. [PMID: 9550912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report a patient with acute lymphoblastic leukemia, who presented with pericardial effusion. There was no haematologic evidence of leukemia at the time of presentation. The pericardial effusion resolved with chemotherapy. Although a common finding at autopsy, clinically evident pericardial effusion is rare in leukemia. It is also extremely rare for pericardial effusion to be the presenting feature or to antedate haematologic evidence of leukemia. Physician awareness is important to make a correct diagnosis.
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Arora PS, Robjohns HL, Bell TN, Dunlop PJ. Use of binary diffusion and second virial coefficients to predict viscosities of gaseous systems. Aust J Chem 1980. [DOI: 10.1071/ch9801993] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Accurate binary diffusion
coefficients measured over the temperature range 275-323 K, together with some
excellent virial coefficients in the literature, have
been used to derive (m,6,8) potential parameters for the systems He-CH4,
He-CF4, He-O2, Ar-O2, CH4-C2H6,
CH4-C3H8 and CH4-C4H10.
These parameters predict quite well the viscosities reported for these systems
by Kestin and coworkers. The results indicate that
binary diffusion coefficients can be used to predict viscosities more
accurately than binary viscosities can be used to predict diffusion
coefficients.
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