1
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McCann S, Roe WE, Agnew HE, Knipe PC. Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers. Angew Chem Int Ed Engl 2023; 62:e202307180. [PMID: 37414732 PMCID: PMC10952507 DOI: 10.1002/anie.202307180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.
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Affiliation(s)
- Sinead McCann
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - William E. Roe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Hannah E. Agnew
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
| | - Peter C. Knipe
- School of Chemistry and Chemical EngineeringQueen's University BelfastDavid Keir Building, Stranmillis RoadBelfastBT9 5AGUK
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2
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Roe WE, Warnock TMC, Knipe PC. A spirocyclic backbone accesses new conformational space in an extended, dipole-stabilized foldamer. Commun Chem 2023; 6:71. [PMID: 37069245 PMCID: PMC10110530 DOI: 10.1038/s42004-023-00868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Most aromatic foldamers adopt uniform secondary structures, offering limited potential for the exploration of conformational space and the formation of tertiary structures. Here we report the incorporation of spiro bis-lactams to allow controlled rotation of the backbone of an iteratively synthesised foldamer. This enables precise control of foldamer shape along two orthogonal directions, likened to the aeronautical yaw and roll axes. XRD, NMR and computational data suggest that homo-oligomers adopt an extended right-handed helix with a pitch of over 30 Å, approximately that of B-DNA. Compatibility with extant foldamers to form hetero-oligomers is demonstrated, allowing greater structural complexity and function in future hybrid foldamer designs.
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Affiliation(s)
- William Edward Roe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Toyah Mary Catherine Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Peter Clarke Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK.
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3
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Xie Y, Luo D, Wiener J, Tang S, Chepyshev S, Schafmeister C. Development of Fmoc-Protected Bis-Amino Acids toward Automated Synthesis of Highly Functionalized Spiroligomers. Org Lett 2022; 24:3421-3425. [PMID: 35499925 PMCID: PMC9113113 DOI: 10.1021/acs.orglett.2c01295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report the fluorenylmethoxycarbonyl (Fmoc) protection of functionalized bis-amino acid building blocks using a temporary Cu2+ complexation strategy, together with an efficient multikilogram-scale synthesis of bis-amino acid precursors. This allows the synthesis of stereochemically and functionally diverse spiroligomers utilizing solid-phase Fmoc/tBu chemistry to facilitate the development of applications. Four tetramers were assembled on a semiautomated microwave peptide synthesizer. We determined their secondary structures with two-dimensional nuclear magnetic resonance spectroscopy.
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4
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Hurley MFD, Northrup JD, Ge Y, Schafmeister CE, Voelz VA. Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. J Chem Inf Model 2021; 61:2818-2828. [PMID: 34125519 DOI: 10.1021/acs.jcim.1c00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to preorganize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies to predict and design conformational and binding properties of macrocycles as functional scaffolds for peptidomimetics. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly preorganized all-trans amide conformation, whose formation is likely limited by the slow rate of cis/trans isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na+ has a higher affinity to the macrocycle than K+, with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.
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Affiliation(s)
- Matthew F D Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Justin D Northrup
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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5
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Northrup JD, Wiener JA, Hurley MFD, Hou CFD, Keller TM, Baxter RHG, Zdilla MJ, Voelz VA, Schafmeister CE. Metal-Binding Q-Proline Macrocycles. J Org Chem 2021; 86:4867-4876. [PMID: 33635647 DOI: 10.1021/acs.joc.1c00116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We introduce the efficient Fmoc-SPPS and peptoid synthesis of Q-proline-based, metal-binding macrocycles (QPMs), which bind metal cations and display nine functional groups. Metal-free QPMs are disordered, evidenced by NMR and a crystal structure of QPM-3 obtained through racemic crystallization. Upon addition of metal cations, QPMs adopt ordered structures. Notably, the addition of a second functional group at the hydantoin amide position (R2) converts the proline ring from Cγ-endo to Cγ-exo, due to steric interactions.
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Affiliation(s)
- Justin D Northrup
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States.,ThirdLaw Molecular, 512 Township Line Road, Blue Bell, Pennsylvania 19422, United States
| | - Jesse A Wiener
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Matthew F D Hurley
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Chun-Feng David Hou
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of Medicine, Temple University, 3440 North Broad Street, Philadelphia Pennsylvania 19140, United States
| | - Taylor M Keller
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Richard H G Baxter
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of Medicine, Temple University, 3440 North Broad Street, Philadelphia Pennsylvania 19140, United States
| | - Michael J Zdilla
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Christian E Schafmeister
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States.,ThirdLaw Molecular, 512 Township Line Road, Blue Bell, Pennsylvania 19422, United States
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6
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Wang X, Kohl B, Rominger F, Elbert SM, Mastalerz M. A Triptycene-Based Enantiopure Bis(Diazadibenzoanthracene) by a Chirality-Assisted Synthesis Approach. Chemistry 2020; 26:16036-16042. [PMID: 32648593 PMCID: PMC7756852 DOI: 10.1002/chem.202002781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Indexed: 12/14/2022]
Abstract
By applying a chirality-assisted synthesis (CAS) approach enantiopure diaminodibromotriptycenes were converted to rigid chiral helical diazadibenzoanthracenes, which show besides pronounced Cotton effects in circular dichroism spectra higher photoluminescence quantum yields as comparable carbacyclic analogues. For the enantiopure building blocks, a protocol was developed allowing the large scale synthesis without the necessity of separation via HPLC.
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Affiliation(s)
- Xubin Wang
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Bernd Kohl
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Frank Rominger
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Sven M. Elbert
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Michael Mastalerz
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
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7
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Northrup JD, Mach RH, Sellmyer MA. Radiochemical Approaches to Imaging Bacterial Infections: Intracellular versus Extracellular Targets. Int J Mol Sci 2019; 20:E5808. [PMID: 31752318 PMCID: PMC6888724 DOI: 10.3390/ijms20225808] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 02/03/2023] Open
Abstract
The discovery of penicillin began the age of antibiotics, which was a turning point in human healthcare. However, to this day, microbial infections are still a concern throughout the world, and the rise of multidrug-resistant organisms is an increasing challenge. To combat this threat, diagnostic imaging tools could be used to verify the causative organism and curb inappropriate use of antimicrobial drugs. Nuclear imaging offers the sensitivity needed to detect small numbers of bacteria in situ. Among nuclear imaging tools, radiolabeled antibiotics traditionally have lacked the sensitivity or specificity necessary to diagnose bacterial infections accurately. One reason for the lack of success is that the antibiotics were often chelated to a radiometal. This was done without addressing the ramifications of how the radiolabeling would impact probe entry to the bacterial cell, or the mechanism of binding to an intracellular target. In this review, we approach bacterial infection imaging through the lens of bacterial specific molecular targets, their intracellular or extracellular location, and discuss radiochemistry strategies to guide future probe development.
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Affiliation(s)
- Justin D. Northrup
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert H. Mach
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
| | - Mark A. Sellmyer
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.D.N.); (R.H.M.)
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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8
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Saito F, Trapp N, Bode JW. Iterative Assembly of Polycyclic Saturated Heterocycles from Monomeric Building Blocks. J Am Chem Soc 2019; 141:5544-5554. [PMID: 30845799 DOI: 10.1021/jacs.9b01537] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polycyclic saturated heterocycles with predictable shapes and structures are assembled by iterative couplings of bifunctional stannyl amine protocol (SnAP) reagents and a single morpholine-forming assembly reaction. Combinations of just a few monomers enable the programmable construction of rotationally restricted, nonplanar heterocyclic arrays with discrete sizes and molecular shapes. The three-dimensional structures of these constrained scaffolds can be quickly and reliably predicted by DFT calculations and the target structures immediately decompiled into the constituent building blocks and assembly sequences. As a demonstration, in silico combinations of the building blocks predict saturated heptacyclic structures with elementary shapes including helices, S-turns and U-turns, which are synthesized in 5-6 steps from the monomers using just three chemical reactions.
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Affiliation(s)
- Fumito Saito
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH-Zürich , 8093 Zürich , Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH-Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH-Zürich , 8093 Zürich , Switzerland
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9
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Utilization of the p-nitrobenzyloxycarbonyl (pNZ) amine protecting group and pentafluorophenyl (Pfp) esters for the solid phase synthesis of spiroligomers. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Shin YH, Gellman SH. Impact of Backbone Pattern and Residue Substitution on Helicity in α/β/γ-Peptides. J Am Chem Soc 2018; 140:1394-1400. [PMID: 29350033 DOI: 10.1021/jacs.7b10868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have evaluated the impact of changes in the chemical structure of peptidic oligomers containing α-, β-, and γ-amino acid residues (α/β/γ-peptides) on the propensities of these oligomers to adopt helical conformations in aqueous and alcoholic solutions. These studies were inspired by our previous discovery that α/β/γ-peptides containing a regular αγααβα hexad repeat adopt an α-helix-like conformation in which the β and γ residues are aligned in a stripe along one side, and the remainder of the helix surface is defined by the α residues. This helix was found to be most stable when the β and γ residues were rigidified with specific cyclic constraints. Relaxation of the β residue constraints caused profound conformational destabilization, but relaxation of the γ residue constraints led to only a moderate drop in helicity. The new work more broadly characterizes the effect of γ residue substitution on helix stability, based on circular dichroism and two-dimensional NMR measurements. We find that even a fully unsubstituted γ residue (derived from γ-aminobutyric acid) supports a moderate helical propensity, which is surprising in light of the strong destabilizing effect of glycine residues on α-helix stability. Additional studies examine the effects of altering sequence in terms of amino acid type, by comparing a prototype with the αγααβα hexad pattern to isomers with irregular arrangements of the α, β, and γ residues along the backbone. The data indicate that the strong helix-forming propensity previously discovered for α/β/γ-peptide 12-mers is retained when sequence is varied, with small variations detected across diverse α-β-γ placements. These structural findings suggest that α/β/γ-peptide scaffolds represent versatile scaffolds for the design of peptidic foldamers that display specific functions.
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Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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11
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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem 2017; 10:8-16. [DOI: 10.1038/nchem.2894] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/20/2017] [Indexed: 12/19/2022]
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12
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Northrup JD, Purcell CR, Schafmeister CE. One-Pot Synthesis of Chiral, Spirocyclic 4-Hydantoin-Proline Derivatives for Incorporation into Spiroligomer-Based Macromolecules. J Org Chem 2017; 82:3223-3231. [PMID: 27690253 DOI: 10.1021/acs.joc.6b01773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Derivatives of 4-hydantoin-proline have been synthesized via a direct two-step alkylation method. This method is valuable in the development of applications of N,N'-disubstituted hydantoin bearing α-amino acids by improving yields, reducing the time and number of steps required to synthesize these substituted molecules, and enabling late stage functionalization of spiroligomer termini. Over 20 unique electrophiles have been tested, highlighting the inherent versatility of this chemistry.
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Affiliation(s)
- J D Northrup
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Claire R Purcell
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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13
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Cheong JE, Pfeiffer CT, Northrup JD, Parker MF, Schafmeister CE. An improved, scalable synthesis of bis-amino acids. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Kudryavtsev KV, Mantsyzov AB, Ivantcova PM, Sokolov MN, Churakov AV, Bräse S, Zefirov NS, Polshakov VI. Control of Azomethine Cycloaddition Stereochemistry by CF3 Group: Structural Diversity of Fluorinated β-Proline Dimers. Org Lett 2016; 18:4698-701. [PMID: 27574905 DOI: 10.1021/acs.orglett.6b02327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Proline-functionalized dimers consisting of homochiral monomeric units were synthesized by a non-peptidic coupling method for the first time. The applied synthetic methodology is based on 1,3-dipolar cycloaddition chemistry of azomethine ylides and provides absolute control over the β-proline backbone stereogenic centers. An o-(trifluoromethyl)phenyl substituent contributes to appropriate stabilization of the definite acrylamide chiral cis conformation and to achieve the dipole reactivity that is not observed for aryl groups lacking strong electronegative character.
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Affiliation(s)
- Konstantin V Kudryavtsev
- Department of Chemistry, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation.,Institute of Physiologically Active Compounds, Russian Academy of Sciences , Chernogolovka, Moscow Region 142432, Russian Federation
| | - Alexey B Mantsyzov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University , Lomonosovsky Ave 31/5, Moscow 119992, Russian Federation
| | - Polina M Ivantcova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Mikhail N Sokolov
- Department of Chemistry, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Andrei V Churakov
- Institute of General and Inorganic Chemistry, Russian Academy of Sciences , Leninskii prosp. 31, Moscow 119991, Russian Federation
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology , Fritz-Haber-Weg 6, Karlsruhe 76131, Germany.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology , Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany
| | - Nikolay S Zefirov
- Department of Chemistry, Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation.,Institute of Physiologically Active Compounds, Russian Academy of Sciences , Chernogolovka, Moscow Region 142432, Russian Federation
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University , Lomonosovsky Ave 31/5, Moscow 119992, Russian Federation.,NMR Laboratory, Institute of Physics, Kazan Federal University , Kremlevskaya 18, Kazan 420008, Russian Federation
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15
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Qi M, Hülsmann M, Godt A. Spacers for Geometrically Well-Defined Water-Soluble Molecular Rulers and Their Application. J Org Chem 2016; 81:2549-71. [DOI: 10.1021/acs.joc.6b00125] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mian Qi
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Miriam Hülsmann
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and
Center for Molecular Materials (MC2), Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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16
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Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis. Angew Chem Int Ed Engl 2015; 54:12772-6. [DOI: 10.1002/anie.201506793] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 12/15/2022]
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18
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Abstract
We demonstrate the synthesis and characterization of the solution conformations of a collection of functionalized spiroligomer-based macrocycles. These macrocycles contain 14 independently controllable stereocenters and four independently controllable functional groups on a highly preorganized scaffold. These molecules are being developed to display complex, preorganized surfaces for binding proteins and to create enzyme-like active sites. In this work, we demonstrate the convergent synthetic approach to this new class of macrocycles and demonstrate that the conformational properties of these molecules can be changed by altering the configuration stereocenters within the backbone.
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Affiliation(s)
- Qingquan Zhao
- Department of Chemistry, Temple University , 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Christian E Schafmeister
- Department of Chemistry, Temple University , 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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19
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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20
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Parker ML, Osuna S, Bollot G, Vaddypally S, Zdilla MJ, Houk KN, Schafmeister CE. Acceleration of an aromatic Claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad. J Am Chem Soc 2014; 136:3817-27. [PMID: 24456160 PMCID: PMC4004270 DOI: 10.1021/ja409214c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 01/03/2023]
Abstract
A series of hydrogen-bonding catalysts have been designed for the aromatic Claisen rearrangement of a 1,1-dimethylallyl coumarin. These catalysts were designed as mimics of the two-point hydrogen-bonding interaction present in ketosteroid isomerase that has been proposed to stabilize a developing negative charge on the ether oxygen in the migration of the double bond.1 Two hydrogen bond donating groups, a phenol alcohol and a carboxylic acid, were grafted onto a conformationally restrained spirocyclic scaffold, and together they enhance the rate of the Claisen rearrangement by a factor of 58 over the background reaction. Theoretical calculations correctly predict the most active catalyst and suggest that both preorganization and favorable interactions with the transition state of the reaction are responsible for the observed rate enhancement.
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Affiliation(s)
- Matthew
F. L. Parker
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sílvia Osuna
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Guillaume Bollot
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Shivaiah Vaddypally
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
| | - Michael J. Zdilla
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Christian E. Schafmeister
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
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22
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Abstract
Piperazinediones1that incorporate three geometrically and chemically independent recognition elements can assemble predictably into a solid.
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Affiliation(s)
- Eugene A. Mash
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson, USA
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23
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Nair RV, Kotmale AS, Dhokale SA, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Formation of a pseudo-β-hairpin motif utilizing the Ant–Pro reverse turn: consequences of stereochemical reordering. Org Biomol Chem 2014; 12:774-82. [DOI: 10.1039/c3ob42016g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a special case of pseudo-β-hairpin formation by tetrapeptide sequences featuring a two-residue Ant–Pro dipeptide motif (Ant = anthranilic acid and Pro = proline) at the loop region.
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Affiliation(s)
- Roshna V. Nair
- Division of Organic Synthesis
- National Chemical Laboratory
- Pune 411 008, India
| | - Amol S. Kotmale
- Central Material Characterization Division
- National Chemical Laboratory
- Pune 411 008, India
| | - Snehal A. Dhokale
- Central Material Characterization Division
- National Chemical Laboratory
- Pune 411 008, India
| | - Rupesh L. Gawade
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008, India
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24
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Deregulations in the cyclin-dependent kinase-9-related pathway in cancer: implications for drug discovery and development. ISRN ONCOLOGY 2013; 2013:305371. [PMID: 23840966 PMCID: PMC3690251 DOI: 10.1155/2013/305371] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/19/2013] [Indexed: 12/21/2022]
Abstract
The CDK9-related pathway is an important regulator of mammalian cell biology and is also involved in the replication cycle of several viruses, including the human immunodeficiency virus type 1. CDK9 is present in two isoforms termed CDK9-42 and CDK9-55 that bind noncovalently type T cyclins and cyclin K. This association forms a heterodimer, where CDK9 carries the enzymatic site and the cyclin partner functions as a regulatory subunit. This heterodimer is the main component of the positive transcription elongation factor b, which stabilizes RNA elongation via phosphorylation of the RNA pol II carboxyl terminal domain. Abnormal activities in the CDK9-related pathway were observed in human malignancies and cardiac hypertrophies. Thus, the elucidation of the CDK9 pathway deregulations may provide useful insights into the pathogenesis and progression of human malignancies, cardiac hypertrophy, AIDS and other viral-related maladies. These studies may lead to the improvement of kinase inhibitors for the treatment of the previously mentioned pathological conditions. This review describes the CDK9-related pathway deregulations in malignancies and the development of kinase inhibitors in cancer therapy, which can be classified into three categories: antagonists that block the ATP binding site of the catalytic domain, allosteric inhibitors, and small molecules that disrupt protein-protein interactions.
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25
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Shin YH, Mortenson DE, Satyshur KA, Forest KT, Gellman SH. Differential impact of β and γ residue preorganization on α/β/γ-peptide helix stability in water. J Am Chem Soc 2013; 135:8149-52. [PMID: 23701135 PMCID: PMC3815483 DOI: 10.1021/ja403319q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cyclic constraints have proven to be very effective for preorganizing β-amino acid residues and thereby stabilizing β- and α/β-peptide helices, but little is known about possible preorganization effects among γ residues. Here we assess and compare the impact of cyclic preorganization of β and γ residues in the context of a specific α/β/γ-peptide helix. The results show that β residue preorganization is critical for helix stability but that γ residue preorganization is less important.
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Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - David E. Mortenson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Kenneth A. Satyshur
- Department of Bacteriology and Biophysics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Katrina T. Forest
- Department of Bacteriology and Biophysics, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
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26
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Vaddypally S, Xu C, Zhao S, Fan Y, Schafmeister CE, Zdilla MJ. Architectural spiroligomers designed for binuclear metal complex templating. Inorg Chem 2013; 52:6457-63. [PMID: 23668771 DOI: 10.1021/ic4003498] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first structurally, spectroscopically, and electronically characterized metal-spiroligomer complexes are reported. The binuclear [M2L2](4+) ions (M = Mn, Zn) are macrocyclic "squares" and are characterized by X-ray diffraction, (1)H and (13)C NMR, electronic absorption, emission, and mass spectroscopies. The manganese complex contains two spin-independent Mn(II) ions and is additionally characterized using EPR and CD spectroscopies and CV.
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Affiliation(s)
- Shivaiah Vaddypally
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania, USA
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27
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González-Esguevillas M, Adrio J, Carretero JC. Enantioselective synthesis of 4-aminopyrrolidine-2,4-dicarboxylate derivatives via Ag-catalyzed cycloaddition of azomethine ylides with alkylidene azlactones. Chem Commun (Camb) 2013; 49:4649-51. [DOI: 10.1039/c3cc41663a] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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28
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29
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Kheirabadi M, Çelebi-Ölçüm N, Parker MFL, Zhao Q, Kiss G, Houk KN, Schafmeister CE. Spiroligozymes for Transesterifications: Design and Relationship of Structure to Activity. J Am Chem Soc 2012; 134:18345-53. [DOI: 10.1021/ja3069648] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahboubeh Kheirabadi
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia,
Pennsylvania 19122, United States
| | - Nihan Çelebi-Ölçüm
- Department of Chemistry and
Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569, United States
| | - Matthew F. L. Parker
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia,
Pennsylvania 19122, United States
| | - Qingquan Zhao
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia,
Pennsylvania 19122, United States
| | - Gert Kiss
- Department of Chemistry and
Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569, United States
| | - K. N. Houk
- Department of Chemistry and
Biochemistry, University of California at Los Angeles, Los Angeles, California 90095-1569, United States
| | - Christian E. Schafmeister
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia,
Pennsylvania 19122, United States
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30
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Brown ZZ, Akula K, Arzumanyan A, Alleva J, Jackson M, Bichenkov E, Sheffield JB, Feitelson MA, Schafmeister CE. A spiroligomer α-helix mimic that binds HDM2, penetrates human cells and stabilizes HDM2 in cell culture. PLoS One 2012; 7:e45948. [PMID: 23094022 PMCID: PMC3475717 DOI: 10.1371/journal.pone.0045948] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/23/2012] [Indexed: 11/19/2022] Open
Abstract
We demonstrate functionalized spiroligomers that mimic the HDM2-bound conformation of the p53 activation domain. Spiroligomers are stereochemically defined, functionalized, spirocyclic monomers coupled through pairs of amide bonds to create spiro-ladder oligomers [1]. Two series of spiroligomers were synthesized, one of structural analogs and one of stereochemical analogs, from which we identified compound 1, that binds HDM2 with a Kd value of 400 nM. The spiroligomer 1 penetrates human liver cancer cells through passive diffusion and in a dose-dependent and time-dependent manner increases the levels of HDM2 more than 30-fold in Huh7 cells in which the p53/HDM2 negative feed-back loop is inoperative. This is a biological effect that is not seen with the HDM2 ligand nutlin-3a. We propose that compound 1 modulates the levels of HDM2 by stabilizing it to proteolysis, allowing it to accumulate in the absence of a p53/HDM2 feedback loop.
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Affiliation(s)
- Zachary Z. Brown
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Kavitha Akula
- Chemistry Department, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Alla Arzumanyan
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jennifer Alleva
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
| | - Marcus Jackson
- Chemistry Department, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Eugeney Bichenkov
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Joel B. Sheffield
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Mark A. Feitelson
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Christian E. Schafmeister
- Chemistry Department, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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31
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Zhu N, Yan Q, Luo Z, Zhai Y, Zhao D. Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain-Length Dependence, Solvent Effects, and Intermolecular Assembly. Chem Asian J 2012; 7:2386-93. [DOI: 10.1002/asia.201200430] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Indexed: 11/11/2022]
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32
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Zhao Q, Lam YH, Kheirabadi M, Xu C, Houk KN, Schafmeister CE. Hydrophobic substituent effects on proline catalysis of aldol reactions in water. J Org Chem 2012; 77:4784-92. [PMID: 22500641 PMCID: PMC3589585 DOI: 10.1021/jo300569c] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Derivatives of 4-hydroxyproline with a series of hydrophobic groups in well-defined orientations have been tested as catalysts for the aldol reactions. All of the modified proline catalysts carry out the intermolecular aldol reaction in water and provide high diastereoselectivity and enantioselectivity. Modified prolines with aromatic groups syn to the carboxylic acid are better catalysts than those with small hydrophobic groups (1a is 43.5 times faster than 1f). Quantum mechanical calculations provide transition structures, TS-1a(water) and TS-1f(water), that support the hypothesis that a stabilizing hydrophobic interaction occurs with 1a.
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Affiliation(s)
- Qingquan Zhao
- Department of Chemistry, Temple University, 1901 N. 13 Street, Philadelphia, PA 19122
| | - Yu-hong Lam
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - Mahboubeh Kheirabadi
- Department of Chemistry, Temple University, 1901 N. 13 Street, Philadelphia, PA 19122
| | - Chongsong Xu
- Department of Chemistry, Temple University, 1901 N. 13 Street, Philadelphia, PA 19122
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
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33
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Johnson LM, Mortenson DE, Yun HG, Horne WS, Ketas TJ, Lu M, Moore JP, Gellman SH. Enhancement of α-helix mimicry by an α/β-peptide foldamer via incorporation of a dense ionic side-chain array. J Am Chem Soc 2012; 134:7317-20. [PMID: 22524614 DOI: 10.1021/ja302428d] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report a new method for preorganization of α/β-peptide helices, based on the use of a dense array of acidic and basic side chains. Previously we have used cyclically constrained β residues to promote α/β-peptide helicity; here we show that an engineered ion pair array can be comparably effective, as indicated by mimicry of the CHR domain of HIV protein gp41. The new design is effective in biochemical and cell-based infectivity assays; however, the resulting α/β-peptide is susceptible to proteolysis. This susceptibility was addressed via introduction of a few cyclic β residues near the cleavage site, to produce the most stable, effective α/β-peptide gp41 CHR analogue identified. Crystal structures of an α- and α/β-peptide (each involved in a gp41-mimetic helix bundle) that contain the dense acid/base residue array manifest disorder in the ionic side chains, but there is little side-chain disorder in analogous α- and α/β-peptide structures with a sparser ionic side-chain array. These observations suggest that dense arrays of complementary acidic and basic residues can provide conformational stabilization via Coulombic attractions that do not require entropically costly ordering of side chains.
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Affiliation(s)
- Lisa M Johnson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, USA
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34
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Brown ZZ, Alleva J, Schafmeister CE. Solid-phase synthesis of functionalized bis-peptides. Biopolymers 2012; 96:578-85. [PMID: 22180905 DOI: 10.1002/bip.21591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We demonstrate the first solid-phase synthesis of highly functionalized bis-peptides. Bis-peptides are ladder oligomers composed of stereochemically pure, cyclic bis-amino acids joined by substituted diketopiperazine linkages. They have a shape-programmable backbone that is controlled by controlling the stereochemistry and sequence of the monomers within each oligomer. Functionalized bis-peptides are assembled using a new amide bond forming reaction (acyl-transfer coupling) that we have previously developed and a novel activation strategy that allows the sequential formation of penta- and hexa-substituted diketopiperazines from extremely hindered N-alkyl-alpha,alpha-disubstituted amino acids. We present mechanistic evidence that acyl-transfer coupling is competitive with direct acylation in the formation of hindered amide bonds. We also detail the synthesis of four functionalized bis-peptides, and that by combining bis-peptides with amino acids through diketopiperazine linkages, bis-peptides can mimic the display of residues i, i+4, i+7 of an alpha-helical peptide.
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Affiliation(s)
- Zachary Z Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA
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35
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Zhang S, Zhao Y. Flexible oligocholate foldamers as membrane transporters and their guest-dependent transport mechanism. Org Biomol Chem 2012; 10:260-6. [DOI: 10.1039/c1ob06364b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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36
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Priya G, Kotmale AS, Gawade RL, Mishra D, Pal S, Puranik VG, Rajamohanan PR, Sanjayan GJ. Helical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding. Chem Commun (Camb) 2012; 48:8922-4. [DOI: 10.1039/c2cc33235c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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37
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Ramesh VVE, Priya G, Kotmale AS, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Multifaceted folding in a foldamer featuring highly cooperative folds. Chem Commun (Camb) 2012; 48:11205-7. [DOI: 10.1039/c2cc35649j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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38
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Krow GR, Yu F, Sender M, Gandla D, Lin G, DeBrosse C, Ross CW. Introduction of C(5/6) side chains onto 2-azabicyclo[2.1.1]hexanes via a 6-anti-bromo-5-anti-hydroxy derivative. CAN J CHEM 2012. [DOI: 10.1139/v11-112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oxidation of the title bromoalcohol provided the strained ketone, 5-bromo-6-oxo-2-azabicyclo[2.1.1]hexane. Additions of nucleophiles to either this or the debrominated ketone have been used to introduce 5(6)-syn-alkyl and aryl groups, 5(6)-alkylidene linkages, and 5(6)-anti-alkyl and acyl substituents. Facial selectivity is for additions to the 6-bromo-5-ketone and 5-alkylidene azabicycles to occur from the face syn to the nitrogen atom. The bromine atom of the title alcohol has also been replaced by a 6-anti-(1-hydroxyethyl) substituent using a directed radical addition process. The stereoselective functionalization reactions expand the range of available methano-bridged pyrrolidines.
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Affiliation(s)
- Grant R. Krow
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Fang Yu
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Matthew Sender
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Deepa Gandla
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Guoliang Lin
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Charles DeBrosse
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Charles W. Ross
- Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., Inc., West Point, PA 19486-004, USA
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39
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Boersma MD, Haase HS, Peterson-Kaufman KJ, Lee EF, Clarke OB, Colman PM, Smith BJ, Horne WS, Fairlie WD, Gellman SH. Evaluation of diverse α/β-backbone patterns for functional α-helix mimicry: analogues of the Bim BH3 domain. J Am Chem Soc 2011; 134:315-23. [PMID: 22040025 DOI: 10.1021/ja207148m] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β(3)-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β(3)-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β(3)-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide.
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Affiliation(s)
- Melissa D Boersma
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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40
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Aquino C, Sarkar M, Chalmers MJ, Mendes K, Kodadek T, Micalizio GC. A biomimetic polyketide-inspired approach to small-molecule ligand discovery. Nat Chem 2011; 4:99-104. [PMID: 22270625 PMCID: PMC3266625 DOI: 10.1038/nchem.1200] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/14/2011] [Indexed: 02/06/2023]
Abstract
The discovery of new compounds for the pharmacological manipulation of protein function often embraces the screening of compound collections, and it is widely recognized that natural products offer beneficial characteristics as protein ligands. Much effort has therefore been focused on “natural product-like” libraries, yet the synthesis and screening of such libraries is often limited by one or more of the following: modest library sizes and structural diversity, conformational heterogeneity, and the costs associated with the substantial infrastructure of modern high-throughput screening centers. Here, we describe the design and execution of an approach to this broad problem by merging principles associated biologically-inspired oligomerization and the structure of polyketide-derived natural products. A novel class of chiral and conformationally-constrained oligomers is described (termed “chiral oligomers of pentenoic amides” – COPAs) that offers compatibility with split-and-pool methods and can be screened en masse in a batch mode. We demonstrate that a COPA library containing 160,000 compounds is a useful source of novel protein ligands by identifying a non-covalent synthetic ligand to the DNA-binding domain of the p53 transcription factor.
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Affiliation(s)
- Claudio Aquino
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA
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41
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic Structural Parameters for the γ-Peptide 14-Helix: Importance of Subunit Preorganization. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101301] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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42
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic structural parameters for the γ-peptide 14-helix: importance of subunit preorganization. Angew Chem Int Ed Engl 2011; 50:5843-6. [PMID: 21567680 DOI: 10.1002/anie.201101301] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI 53706, USA
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43
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Synthesis of the (2S,4S)-stereoisomers of 4-(indol-1-yl) and 4-arylamino derivatives of 5-oxoproline, proline, and 2-hydroxymethylpyrrolidine. Russ Chem Bull 2011. [DOI: 10.1007/s11172-011-0137-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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44
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Vigorov AY, Nizova IA, Sadretdinova LS, Ezhikova MA, Kodess MI, Ganebnykh IN, Krasnov VP. Chemoselectivity in the Reduction of (2S,4S)-4-Amino-5-oxoproline Derivatives with Borane Complexes. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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45
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Minozzi M, Monesi A, Nanni D, Spagnolo P, Marchetti N, Massi A. An insight into the radical thiol/yne coupling: the emergence of arylalkyne-tagged sugars for the direct photoinduced glycosylation of cysteine-containing peptides. J Org Chem 2010; 76:450-9. [PMID: 21175145 DOI: 10.1021/jo101906j] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An explorative study of the Thiol-Yne Coupling (TYC) reaction has been carried out using an aliphatic (1-octyne) and an aromatic alkyne (phenylacetylene) and two alkanethiols (methyl thioglycolate and N-acetyl-L-cysteine methyl ester). The outcomes of the TYC reactions strongly depend on the experimental conditions (e.g., temperature, solvent, and alkyne/thiol ratio), but these can be properly adjusted to achieve selective production of either mono- or bis-coupling products. With respect to 1-octyne, phenylacetylene undergoes notably easier radical hydrothiolation, further showing a notably higher aptitude for monohydrothiolation exclusive of bis-hydrothiolation. The overall findings were exploited in glycosylation of cysteine derivatives as well as of cysteine-containing peptides. A sugar featuring an arylacetylene moiety gave rise to a true click-reaction, that is, glycosylation of the tripeptide glutathione in its native form, by means of virtually equimolar amounts of reagents. This reaction was successfully applied, under physiological conditions, to a cysteine-containing nonapeptide with marked advantages over the analogous Thiol-Ene Coupling (TEC) derivatization. A TYC/TEC sequence affording bis-armed cysteine derivatives through dual functionalization of an alkynyl sugar was additionally devised.
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Affiliation(s)
- Matteo Minozzi
- Dipartimento di Chimica Organica A. Mangini, Università di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
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46
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Ressurreição ASM, Delatouche R, Gennari C, Piarulli U. Bifunctional 2,5‐Diketopiperazines as Rigid Three‐Dimensional Scaffolds in Receptors and Peptidomimetics. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001330] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Sofia M. Ressurreição
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
- Universidade de Lisboa, iMed. UL, Faculdade de Farmácia, Av. Prof. Gama Pinto, 649‐003 Lisboa, Portugal
| | - Régis Delatouche
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
| | - Cesare Gennari
- Università degli Studi di Milano, Dipartimento di ChimicaOrganica e Industriale, via G. Venezian 21, 20133 Milano, Italy
| | - Umberto Piarulli
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
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Cho H, Zhao Y. Environmental Effects Dominate the Folding of Oligocholates in Solution, Surfactant Micelles, and Lipid Membranes. J Am Chem Soc 2010; 132:9890-9. [DOI: 10.1021/ja103694p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hongkwan Cho
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111
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Brown ZZ, Schafmeister CE. Synthesis of hexa- and pentasubstituted diketopiperazines from sterically hindered amino acids. Org Lett 2010; 12:1436-9. [PMID: 20218644 DOI: 10.1021/ol100048g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Steric hindrance assists in the formation of hindered diketopiperazines using acyl-transfer coupling. In acyl-transfer coupling, the carboxylate of an unprotected N-alkylamino acid attacks an active ester to form a transient anhydride that undergoes an O,N acyl transfer to form a tertiary amide. If the active ester is part of an N-alkylamino acid it will form a diketopiperazine. It is demonstrated here that acyl-transfer coupling can assemble highly functionalized bis-peptides bearing a functional group on every monomer.
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Affiliation(s)
- Zachary Z Brown
- Chemistry Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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49
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Affiliation(s)
- Changsik Song
- Department of Chemistry
- Institute for Soldier Nanotechnologies
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50
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Ni BB, Yan Q, Ma Y, Zhao D. Recent advances in arylene ethynylene folding systems: Toward functioning. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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