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1.
Constrained Peptides with Target‐Adapted Cross‐Links as Inhibitors of a Pathogenic Protein–Protein Interaction 下载免费PDF全文
Dr. Gernot Hahne Dr. Christoph Rademacher Dr. Christian Ottmann Dr. Tom N. Grossmann 《Angewandte Chemie (International ed. in English)》2014,53(9):2489-2493
Bioactive conformations of peptides can be stabilized by macrocyclization, resulting in increased target affinity and activity. Such macrocyclic peptides proved useful as modulators of biological functions, in particular as inhibitors of protein–protein interactions (PPI). However, most peptide‐derived PPI inhibitors involve stabilized α‐helices, leaving a large number of secondary structures unaddressed. Herein, we present a rational approach towards stabilization of an irregular peptide structure, using hydrophobic cross‐links that replace residues crucially involved in target binding. The molecular basis of this interaction was elucidated by X‐ray crystallography and isothermal titration calorimetry. The resulting cross‐linked peptides inhibit the interaction between human adaptor protein 14‐3‐3 and virulence factor exoenzyme S. Taking into consideration that irregular peptide structures participate widely in PPIs, this approach provides access to novel peptide‐derived inhibitors. 相似文献
2.
Victor Adebomi Ryan D. Cohen Rachel Wills Holland Andrew Hays Chavers Gary E. Martin Monika Raj 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2019,131(52):19249-19256
Here, we report a novel “CyClick” strategy for the macrocyclization of peptides that works in an exclusively intramolecular fashion thereby precluding the formation of dimers and oligomers via intermolecular reactions. The CyClick chemistry is highly chemoselective for the N‐terminus of the peptide with a C‐terminal aldehyde. In this protocol, the peptide conformation internally directs activation of the backbone amide bond and thereby facilitates formation of a stable 4‐imidazolidinone‐fused cyclic peptide with high diastereoselectivity (>99 %). This method is tolerant to a variety of peptide aldehydes and has been applied for the synthesis of 12‐ to 23‐membered rings with varying amino acid compositions in one pot under mild reaction conditions. The reaction generated peptide macrocycles featuring a 4‐imidazolidinone in their scaffolds, which acts as an endocyclic control element that promotes intramolecular hydrogen bonding and leads to macrocycles with conformationally rigid turn structures. 相似文献
3.
Rajkumar Misra Sanjit Dey Rahi M. Reja Prof. Dr. Hosahudya N. Gopi 《Angewandte Chemie (International ed. in English)》2018,57(4):1057-1061
Double helices are not common in polypeptides and proteins except in the peptide antibiotic gramicidin A and analogous l,d ‐peptides. In contrast to natural polypeptides, remarkable β‐double‐helical structures from achiral γ‐peptides built from α,β‐unsaturated γ‐amino acids have been observed. The crystal structures suggest that they adopted parallel β‐double helical structures and these structures are stabilized by the interstrand backbone amide H‐bonds. Furthermore, both NMR spectroscopy and fluorescence studies support the existence of double‐helical conformations in solution. Although a variety of folded architectures featuring distinct H‐bonds have been discovered from the β‐ and γ‐peptide foldamers, this is the first report to show that achiral γ‐peptides can spontaneously intertwine into β‐double helical structures. 相似文献
4.
α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers 下载免费PDF全文
Dr. Juliette Fremaux Laura Mauran Dr. Karolina Pulka‐Ziach Dr. Brice Kauffmann Dr. Benoit Odaert Dr. Gilles Guichard 《Angewandte Chemie (International ed. in English)》2015,54(34):9816-9820
Short α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides. 相似文献
5.
John L. Kulp III Dr. Thomas D. Clark Dr. 《Chemistry (Weinheim an der Bergstrasse, Germany)》2009,15(44):11867-11877
β Helices—helices formed by alternating d,l ‐peptides and stabilized by β‐sheet hydrogen bonding—are found naturally in only a handful of highly hydrophobic peptides. This paper explores the scope of β‐helical structure by presenting the first design and biophysical characterization of a hydrophilic d,l ‐peptide, 1 , that forms a β helix in methanol. The design of 1 is based on the β‐hairpin/β helix—a new supersecondary that had been characterized previously only for hydrophobic peptides in nonpolar solvents. Incorporating polar residues in 1 provided solubility in methanol, in which the peptide adopts the expected β‐hairpin/β‐helical structure, as evidenced by CD, analytical ultracentrifugation (AUC), NMR spectroscopy, and NMR‐based structure calculations. Upon titration with water (at constant peptide concentration), the structure in methanol ( 1 m ) transitions cooperatively to an extended conformation ( 1 w ) resembling a cyclic β‐hairpin; observation of an isodichroic point in the solvent‐dependent CD spectra indicates that this transition is a two‐state process. In contrast, neither 1 m nor 1 w show cooperative thermal melting; instead, their structures appear intact at temperatures as high as 65 °C; this observation suggests that steric constraint is dominant in stabilizing these structures. Finally, the 1H NMR CαH spectroscopic resonances of 1 m are downfield‐shifted with respect to random‐coil values, a hitherto unreported property for β helices that appears to be a general feature of these structures. These results show for the first time that an appropriately designed β‐helical peptide can fold stably in a polar solvent; furthermore, the structural and spectroscopic data reported should prove useful in the future design and characterization of water‐soluble β helices. 相似文献
6.
Dr. Kirtikumar B. Jadhav Dr. Roman J. Lichtenecker Anke Bullach Dr. Bhubaneswar Mandal Prof. Dr. Hans‐Dieter Arndt 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(15):5898-5908
D ‐/L ‐Peptides such as gramicidin A (gA) adopt unique dimeric β‐helical structures of different topologies. To overcome their conformational promiscuity and enrich individual components, a dynamic combinatorial approach assisted by thiol tags was developed. This method led to identification of the preferential formation of antiparallel dimers under a broad range of conditions, which was independent of peptide side‐chain polarity. Exclusive formation of an antiparallel cyclic dimer was achieved in the presence of cesium ions. 相似文献
7.
Qizhao Li Masatoshi Ishida Hiroto Kai Tingting Gu Chengjie Li Xin Li Glib Baryshnikov Xu Liang Weihua Zhu Hans gren Hiroyuki Furuta Yongshu Xie 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2019,131(18):5986-5990
A hybrid thia‐norhexaphyrin comprising a directly linked N‐confused pyrrole and thiophene unit ( 1 ) revealed unique macrocycle transformations to afford multiply inner‐annulated aromatic macrocycles. Oxidation with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone triggered a cleavage of the C?S bond of the thiophene unit, accompanied with skeletal rearrangement to afford unique π‐conjugated products: a thiopyrrolo‐pentaphyrin embedded with a pyrrolo[1,2]isothiazole ( 2 ), a sulfur‐free pentaphyrin incorporating an indolizine moiety ( 3 ), and a thiopyranyltriphyrinoid containing a 2H‐thiopyran unit ( 4 ). Furthermore, 2 underwent desulfurization reactions to afford a fused pentaphyrin containing a pyrrolizine moiety ( 5 ) under mild conditions. Using expanded porphyrin scaffolds, oxidative thiophene cleavage and desulfurization of the hitherto unknown N‐confused core‐modified macrocycles would be a practical approach for developing unique polypyrrolic aromatic macrocycles. 相似文献
8.
Sebastian Dengler Pradeep K. Mandal Lars Allmendinger Cline Douat Ivan Huc 《Chemical science》2021,12(33):11004
Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer–peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.When peptides and helical aromatic foldamers are combined in a macrocycle, an interplay of their properties is observed, including helix handedness bias, helix stabilisation, peptide stretching and peptide resistance to proteolytic degradation. 相似文献
9.
Dr. Timothy A. Hill Dr. Nicholas E. Shepherd Dr. Frederik Diness Prof. Dr. David P. Fairlie 《Angewandte Chemie (International ed. in English)》2014,53(48):13020-13041
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well‐defined three‐dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein‐like structures in water. However, short peptides can be induced to fold into protein‐like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine‐tune three‐dimensional structure. Such constrained cyclic peptides can have protein‐like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three‐dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties. 相似文献
10.
Dr. Koushik Chandra Dr. Tapta Kanchan Roy Dr. Deborah E. Shalev Prof. Abraham Loyter Prof. Chaim Gilon Prof. R. Benny Gerber Prof. Assaf Friedler 《Angewandte Chemie (International ed. in English)》2014,53(36):9450-9455
We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N‐terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid‐phase synthesis of peptides and organic molecules. 相似文献
11.
Sriram Mahesh Victor Adebomi Zilma P. Muneeswaran Monika Raj 《Angewandte Chemie (International ed. in English)》2020,59(7):2793-2801
Nitroalkanes react specifically with aldehydes, providing rapid, stable, and chemoselective protein bioconjugation. These nitroalkylated proteins mimic key post‐translational modifications (PTMs) of proteins and can be used to understand the role of these PTMs in cellular processes. Demonstrated here is the substrate scope of this bioconjugation by attaching a variety of tags, such as NMR tags, fluorescent tags, affinity tags, and alkyne tags, to proteins. The structure and enzymatic activity of modified proteins remain conserved after labeling. Notably, the nitroalkane group leads to easy characterization of proteins by mass spectrometry because of its distinct fingerprint pattern. Importantly, the nitro‐alkylated peptides provide a new handle for site‐selective fluorination of peptides, thus installing a specific probe to study peptide–protein interactions by 19F NMR spectroscopy. Furthermore, nitroalkane reagents can be used for the late‐stage diversification of peptides and for the synthesis of peptide staples. 相似文献
12.
Dr. Giang K. T. Nguyen Dr. Xinya Hemu Jun‐Ping Quek Prof. Dr. James P. Tam 《Angewandte Chemie (International ed. in English)》2016,55(41):12802-12806
Macrocyclic compounds have received increasing attention in recent years. With their large surface area, they hold promise for inhibiting protein–protein interactions, a chemical space that was thought to be undruggable. Although many chemical methods have been developed for peptide macrocyclization, enzymatic methods have emerged as a promising new economical approach. Thus far, most enzymes have been shown to act on l ‐peptides; their ability to cyclize d ‐amino‐acid‐containing peptides has rarely been documented. Herein we show that macrocycles consisting of d ‐amino acids, except for the Asn residue at the ligating site, were efficiently synthesized by butelase 1, an Asn/Asp‐specific ligase. Furthermore, by using a peptide‐library approach, we show that butelase 1 tolerates most of the d ‐amino acid residues at the P1′′ and P2′′ positions. 相似文献
13.
Dr. Emilia Oueis Prof. Marcel Jaspars Prof. Nicholas J. Westwood Prof. James H. Naismith 《Angewandte Chemie (International ed. in English)》2016,55(19):5842-5845
The macrocyclization of linear peptides is very often accompanied by significant improvements in their stability and biological activity. Many strategies are available for their chemical macrocyclization, however, enzyme‐mediated methods remain of great interest in terms of synthetic utility. To date, known macrocyclization enzymes have been shown to be active on both peptide and protein substrates. Here we show that the macrocyclization enzyme of the cyanobactin family, PatGmac, is capable of macrocyclizing substrates with one, two, or three 1,4‐substituted 1,2,3‐triazole moieties. The introduction of non‐peptidic scaffolds into macrocycles is highly desirable in tuning the activity and physical properties of peptidic macrocycles. We have isolated and fully characterized nine non‐natural triazole‐containing cyclic peptides, a further ten molecules are also synthesized. PatGmac has now been shown to be an effective and versatile tool for the ring closure by peptide bond formation. 相似文献
14.
V. Haridas Harinder Singh Yogesh K. Sharma Kashmiri Lal 《Journal of Chemical Sciences》2007,119(3):219-230
The design and synthesis of figure-eight macrocycles are very scarce owing to the intricacies and lack of predictability from
first principles. This review emphasizes on discrete macrocyclic systems both synthetic and natural with a defined figure
eight knotted topology. In almost all the helical macrocycles, the helical arrangement is held by intramolecular hydrogen
bonding or as a backbone requirement, but in all cases, a planar graph can be drawn and so these compounds are trivial from
the topological stand point. Nature presents great deal of complexity in terms of structures in macromolecules like DNA and
proteins and also displays intriguing topology in simple natural products. Patellamide, tawicyclamides, nosiheptide and thiostrepton
are natural products with figure eight topology which shows interesting biological activity. Expanded porphyrins, Cu(II) complexes
of thiomacrocycles, cyclic peptides and oligoesters are synthetic macrocycles showing intriguing topology. Analysis of structure
and folding behaviour will enable chemists to design molecules with intriguing topology. 相似文献
15.
Zhang Y Zhang H Cui W Chen H 《Journal of the American Society for Mass Spectrometry》2011,22(9):1610-1621
Our previous study showed that selenamide reagents such as ebselen and N-(phenylseleno)phthalimide (NPSP) can be used for selective and rapid derivatization of protein/peptide thiols in high conversion
yield. This paper reports the systematic investigation of MS/MS dissociation behaviors of selenamide-derivatized peptide ions
upon collision induced dissociation (CID) and electron transfer dissociation (ETD). In the positive ion mode, derivatized
peptide ions exhibit tag-dependent CID dissociation pathways. For instance, ebselen-derivatized peptide ions preferentially
undergo Se–S bond cleavage upon CID to produce a characteristic fragment ion, the protonated ebselen (m/z 276), which allows selective identification of thiol peptides from protein digest as well as selective detection of thiol
proteins from protein mixture using precursor ion scan (PIS). In contrast, NPSP-derivatized peptide ions retain their phenylselenenyl
tags during CID, which is useful in sequencing peptides and locating cysteine residues. In the negative ion CID mode, both
types of tags are preferentially lost via the Se–S cleavage, analogous to the S–S bond cleavage during CID of disulfide-containing
peptide anions. In consideration of the convenience in preparing selenamide-derivatized peptides and the similarity of Se–S
of the tag to the S–S bond, we also examined ETD of the derivatized peptide ions to probe the mechanism for electron-based
ion dissociation. Interestingly, facile cleavage of Se–S bond occurs to the peptide ions carrying either protons or alkali
metal ions, while backbone cleavage to form c/z ions is severely inhibited. These results are in agreement with the Utah-Washington mechanism proposed for depicting electron-based
ion dissociation processes. 相似文献
16.
Lee M Lee Y Kang M Park H Seong Y Sung BJ Moon B Oh HB 《Journal of mass spectrometry : JMS》2011,46(8):830-839
The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSn tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at Cβ by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at Cα is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd. 相似文献
17.
López GE Colón-Díaz I Cruz A Ghosh S Nicholls SB Viswanathan U Hardy JA Auerbach SM 《The journal of physical chemistry. A》2012,116(4):1283-1288
We report gas-phase electronic structure calculations on helical peptides that act as scaffolds for imidazole-based hydrogen-bonding networks (proton wires). We have modeled various 21-residue polyalanine peptides substituted at regular intervals with histidines (imidazole-bearing amino acids), using a hybrid approach with a semiempirical method (AM1) for peptide scaffolds and density functional theory (B3LYP) for proton wires. We have computed energy landscapes including barriers for Grotthuss-shuttling-type proton motions though wires supported on 3(10)-, α- and π-helical structures, showing the 3(10)- and α-helices to be attractive targets in terms of high proton affinities, low Grotthuss shuttling barriers, and high stabilities. Moreover, bias forces provided by the helical dipole moments were found to promote unidirectional proton translocation. 相似文献
18.
Kuntrapakam Hema Kana M. Sureshan 《Angewandte Chemie (International ed. in English)》2020,59(23):8854-8859
Protein‐mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein‐mimics containing triazole linkages as peptide‐bond surrogate by topochemical azide‐alkyne cycloaddition (TAAC) polymerization of azide‐ and alkyne‐modified peptides. The rationally designed dipeptide N3‐CH2CO‐Phe‐NHCH2CCH ( 1 ) crystallized in a parallel β‐sheet arrangement and are head‐to‐tail aligned in a direction perpendicular to the β‐sheet‐direction. Upon heating, crystals of 1 underwent single‐crystal‐to‐single‐crystal polymerization forming a triazole‐linked pseudoprotein with Gly‐Phe‐Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical‐sheet orientation in the crystal resembles the cross‐α‐amyloids, where α‐helices are arranged laterally as sheets. 相似文献
19.
《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2017,129(36):10865-10869
The design and synthesis of head‐to‐tail linked artificial macrocycles using the Ugi‐reaction has been developed. This synthetic approach of just two steps is unprecedented, short, efficient and works over a wide range of medium (8–11) and macrocyclic (≥12) loop sizes. The substrate scope and functional group tolerance is exceptional. Using this approach, we have synthesized 39 novel macrocycles by two or even one single synthetic operation. The properties of our macrocycles are discussed with respect to their potential to bind to biological targets that are not druggable by conventional, drug‐like compounds. As an application of these artificial macrocycles we highlight potent p53–MDM2 antagonism. 相似文献
20.
Zengbing Bai Chuangxu Cai Wangjian Sheng Yuxiang Ren Huan Wang 《Angewandte Chemie (International ed. in English)》2020,59(34):14686-14692
Transition‐metal‐catalyzed C?H activation has shown potential in the functionalization of peptides with expanded structural diversity. Herein, the development of late‐stage peptide macrocyclization methods by palladium‐catalyzed site‐selective C(sp2)?H olefination of tryptophan residues at the C2 and C4 positions is reported. This strategy utilizes the peptide backbone as endogenous directing groups and provides access to peptide macrocycles with unique Trp–alkene crosslinks. 相似文献