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Статті в журналах з теми "Constrained peptides"

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Автор: Grafiati

Опубліковано: 10 грудня 2022

Оновлено: 28 січня 2023

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1

Bozovičar, Krištof, and Tomaž Bratkovič. "Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties." International Journal of Molecular Sciences 22, no. 4 (February 5, 2021): 1611. http://dx.doi.org/10.3390/ijms22041611.

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The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.

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2

Deschamps, J. R., C. George, C. Moore, R. Cudney, and J. L. Flippen-Anderson. "Constrained linear opioid peptides." Acta Crystallographica Section A Foundations of Crystallography 52, a1 (August 8, 1996): C249. http://dx.doi.org/10.1107/s0108767396089489.

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3

Bode, S. A., and D. W. P. M. Löwik. "Constrained cell penetrating peptides." Drug Discovery Today: Technologies 26 (December 2017): 33–42. http://dx.doi.org/10.1016/j.ddtec.2017.11.005.

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4

Yin, Hang. "Constrained Peptides as Miniature Protein Structures." ISRN Biochemistry 2012 (September 26, 2012): 1–15. http://dx.doi.org/10.5402/2012/692190.

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Анотація:

This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.

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5

Moll, Gert N., Anneke Kuipers, Rick Rink, Tjibbe Bosma, Louwe de Vries, and Pawel Namsolleck. "Biosynthesis of lanthionine-constrained agonists of G protein-coupled receptors." Biochemical Society Transactions 48, no. 5 (October 14, 2020): 2195–203. http://dx.doi.org/10.1042/bst20200427.

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The conformation with which natural agonistic peptides interact with G protein-coupled receptor(s) (GPCR(s)) partly results from intramolecular interactions such as hydrogen bridges or is induced by ligand–receptor interactions. The conformational freedom of a peptide can be constrained by intramolecular cross-links. Conformational constraints enhance the receptor specificity, may lead to biased activity and confer proteolytic resistance to peptidic GPCR agonists. Chemical synthesis allows to introduce a variety of cross-links into a peptide and is suitable for bulk production of relatively simple lead peptides. Lanthionines are thioether bridged alanines of which the two alanines can be introduced at different distances in chosen positions in a peptide. Thioether bridges are much more stable than disulfide bridges. Biosynthesis of lanthionine-constrained peptides exploiting engineered Gram-positive or Gram-negative bacteria that contain lanthionine-introducing enzymes constitutes a convenient method for discovery of lanthionine-stabilized GPCR agonists. The presence of an N-terminal leader peptide enables dehydratases to dehydrate serines and threonines in the peptide of interest after which a cyclase can couple the formed dehydroamino acids to cysteines forming (methyl)lanthionines. The leader peptide also guides the export of the formed lanthionine-containing precursor peptide out of Gram-positive bacteria via a lanthipeptide transporter. An engineered cleavage site in the C-terminus of the leader peptide allows to cleave off the leader peptide yielding the modified peptide of interest. Lanthipeptide GPCR agonists are an emerging class of therapeutics of which a few examples have demonstrated high efficacy in animal models of a variety of diseases. One lanthipeptide GPCR agonist has successfully passed clinical Phase Ia.

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6

Real, Eléonore, Jean-Christophe Rain, Véronique Battaglia, Corinne Jallet, Pierre Perrin, Noël Tordo, Peggy Chrisment, Jacques D'Alayer, Pierre Legrain, and Yves Jacob. "Antiviral Drug Discovery Strategy Using Combinatorial Libraries of Structurally Constrained Peptides." Journal of Virology 78, no. 14 (July 15, 2004): 7410–17. http://dx.doi.org/10.1128/jvi.78.14.7410-7417.2004.

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ABSTRACT We have developed a new strategy for antiviral peptide discovery by using lyssaviruses (rabies virus and rabies-related viruses) as models. Based on the mimicry of natural bioactive peptides, two genetically encoded combinatorial peptide libraries composed of intrinsically constrained peptides (coactamers) were designed. Proteomic knowledge concerning the functional network of interactions in the lyssavirus transcription-replication complex highlights the phosphoprotein (P) as a prime target for inhibitors of viral replication. We present an integrated, sequential drug discovery process for selection of peptides with antiviral activity directed against the P. Our approach combines (i) an exhaustive two-hybrid selection of peptides binding two phylogenetically divergent lyssavirus P's, (ii) a functional analysis of protein interaction inhibition in a viral reverse genetic assay, coupled with a physical analysis of viral nucleoprotein-P complex by protein chip mass spectrometry, and (iii) an assay for inhibition of lyssavirus infection in mammalian cells. The validity of this strategy was demonstrated by the identification of four peptides exhibiting an efficient antiviral activity. Our work highlights the importance of P as a target in anti-rabies virus drug discovery. Furthermore, the screening strategy and the coactamer libraries presented in this report could be considered, respectively, a general target validation strategy and a potential source of biologically active peptides which could also help to design pharmacologically active peptide-mimicking molecules. The strategy described here is easily applicable to other pathogens.

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7

Kuepper, Arne, Niall M. McLoughlin, Saskia Neubacher, Alejandro Yeste-Vázquez, Estel Collado Camps, Chandran Nithin, Sunandan Mukherjee, et al. "Constrained peptides mimic a viral suppressor of RNA silencing." Nucleic Acids Research 49, no. 22 (December 6, 2021): 12622–33. http://dx.doi.org/10.1093/nar/gkab1149.

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Abstract The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.

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8

Corr, M., L. F. Boyd, S. R. Frankel, S. Kozlowski, E. A. Padlan, and D. H. Margulies. "Endogenous peptides of a soluble major histocompatibility complex class I molecule, H-2Lds: sequence motif, quantitative binding, and molecular modeling of the complex." Journal of Experimental Medicine 176, no. 6 (December 1, 1992): 1681–92. http://dx.doi.org/10.1084/jem.176.6.1681.

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To gain insight into the rules that govern the binding of endogenous and viral peptides to a given major histocompatibility complex (MHC) class I molecule, we characterized the amino acid sequences of a set of self peptides bound by a soluble analogue of murine H-2Ld, H-2Lds. We tested corresponding synthetic peptides quantitatively for binding in several different assays, and built three-dimensional computer models of eight peptide/H-2Lds complexes, based on the crystallographic structure of the human HLA-B27/peptide complex. Comparison of primary and tertiary structures of bound self and antigenic peptides revealed that residues 2 and 9 were not only restricted in sequence and tolerant of conservative substitutions, but were spatially constrained in the three-dimensional models. The degree of sequence variability of specific residues in MHC-restricted peptides reflected the lack of structural constraint on those amino acids. Thus, amino acid residues that define a peptide motif represent side chains required or preferred for a close fit with the MHC class I heavy chain.

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9

Willick, Gordon, Paul Morley, and James Whitfield. "Constrained Analogs of Osteogenic Peptides." Current Medicinal Chemistry 11, no. 21 (November 1, 2004): 2867–81. http://dx.doi.org/10.2174/0929867043364153.

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10

Ladner, Robert C. "Constrained peptides as binding entities." Trends in Biotechnology 13, no. 10 (October 1995): 426–30. http://dx.doi.org/10.1016/s0167-7799(00)88997-0.

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11

Morrison, Chris. "Constrained peptides' time to shine?" Nature Reviews Drug Discovery 17, no. 8 (July 30, 2018): 531–33. http://dx.doi.org/10.1038/nrd.2018.125.

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12

Kennedy, Eileen J. "Constrained peptides and biological targets." Bioorganic & Medicinal Chemistry 26, no. 6 (March 2018): 1117. http://dx.doi.org/10.1016/j.bmc.2018.02.046.

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13

Pineda-Castañeda, Héctor M., Diego S. Insuasty-Cepeda, Víctor A. Niño-Ramírez, Hernando Curtidor, and Zuly J. Rivera-Monroy. "Designing Short Peptides: A Sisyphean Task?" Current Organic Chemistry 24, no. 21 (December 7, 2020): 2448–74. http://dx.doi.org/10.2174/1385272824999200910094034.

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Over the last few years, short peptides have become a powerful tool in basic and applied research, with different uses like diagnostic, antimicrobial peptides, human health promoters or bioactive peptides, therapeutic treatments, templates for peptidomimetic design, and peptide-based vaccines. In this endeavor, different approaches and technologies have been explored, such as bioinformatics, large-scale peptide synthesis, omics sciences, structure-activity relationship studies, and a biophysical approach, among others, seeking to obtain the shortest sequence with the best activity. The advantage of short peptides lies in their stability, ease of production, safety, and low cost. There are many strategies for designing short peptides with biomedical and industrial applications (targeting the structure, length, charge, or polarity) or as a starting point for improving their properties (sequence data base, de novo sequences, templates, or organic scaffolds). In peptide design, it is necessary to keep in mind factors such as the application (peptidomimetic, immunogen, antimicrobial, bioactive, or protein-protein interaction inhibitor), the expected target (membrane cell, nucleus, receptor proteins, or immune system), and particular characteristics (shorter, conformationally constrained, cycled, charged, flexible, polymerized, or pseudopeptides). This review summarizes the different synthetic approaches and strategies used to design new peptide analogs, highlighting the achievements, constraints, and advantages of each.

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14

Rizo, Josep, and Lila M. Gierasch. "Constrained Peptides: Models of Bioactive Peptides and Protein Substructures." Annual Review of Biochemistry 61, no. 1 (June 1992): 387–416. http://dx.doi.org/10.1146/annurev.bi.61.070192.002131.

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15

SHEPHERD, Craig M., Hans J. VOGEL, and D. Peter TIELEMAN. "Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations." Biochemical Journal 370, no. 1 (February 15, 2003): 233–43. http://dx.doi.org/10.1042/bj20021255.

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Molecular-dynamics simulations covering 30ns of both a natural and a synthetic antimicrobial peptide in the presence of a zwitterionic lipid bilayer were performed. In both simulations, copies of the peptides were placed in an α-helical conformation on either side of the bilayer about 10Å (1Å = 0.1nm) from the interface, with either the hydrophobic or the positively charged face of the helix directed toward the bilayer surface. The degree of peptide—lipid interaction was dependent on the starting configuration: surface binding and subsequent penetration of the bilayer was observed for the hydrophobically oriented peptides, while the charge-oriented peptides demonstrated at most partial surface binding. Aromatic residues near the N-termini of the peptides appear to play an important role in driving peptide—lipid interactions. A correlation between the extent of peptide—lipid interactions and helical stability was observed in the simulations. Insertion of the peptides into the bilayer caused a dramatic increase in the lateral area per lipid and decrease in the bilayer thickness, resulting in substantial disordering of the lipid chains. Results from the simulations are consistent with early stages of proposed mechanisms for the lytic activity of antimicrobial peptides. In addition to these ‘free’ simulations, 25ns simulations were carried out with the peptides constrained at three different distances relative to the bilayer interface. The constraint forces are in agreement with the extent of peptide—bilayer insertion observed in the free simulations.

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16

Lupold, Shawn E., and Ronald Rodriguez. "Disulfide-constrained peptides that bind to the extracellular portion of the prostate-specific membrane antigen." Molecular Cancer Therapeutics 3, no. 5 (May 1, 2004): 597–603. http://dx.doi.org/10.1158/1535-7163.597.3.5.

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Abstract The prostate-specific membrane antigen (PSMA) is a well-characterized surface antigen, overexpressed in the most advanced, androgen-resistant human prostate cancer cells. We sought to exploit PSMA cell surface properties as a target for short peptides that will potentially guide protein-based therapeutics, such as viral vectors, to prostate cancer cells. Two separate phage display peptide strategies were applied, in parallel, to purified PSMA protein bound to two separate substrates. We reasoned that peptide sequences common to both substrate selections would be specific binders of PSMA. Additionally, the design allowed for stringent cross-selections, where phage populations from one selection condition could be applied to the alternative substrate. These strategies resulted in a series of phage displayed peptides able to bind to PSMA by ELISA and direct binding assays, both with purified protein and in prostate cancer cells. Cell binding is competitively inhibited by purified PSMA. The synthesized peptides are capable of enhancing PSMA carboxypeptidase enzymatic activity, suggesting protein folding stabilization. The discovery of these peptides provides the foundation for subsequent development of peptide targeted therapeutics against prostate cancer.

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17

BLANES-MIRA, Clara, Maria T. PASTOR, Elvira VALERA, Gregorio FERNÁNDEZ-BALLESTER, Jaime M. MERINO, Luis M. GUTIERREZ, Enrique PEREZ-PAYÁ та Antonio FERRER-MONTIEL. "Identification of SNARE complex modulators that inhibit exocytosis from an α-helix-constrained combinatorial library". Biochemical Journal 375, № 1 (1 жовтня 2003): 159–66. http://dx.doi.org/10.1042/bj20030509.

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Synthetic peptides patterned after the proteins involved in vesicle fusion [the so-called SNARE (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor) proteins] are potent inhibitors of SNARE complex assembly and neuronal exocytosis. It is noteworthy that the identification of peptide sequences not related to the SNARE proteins has not been accomplished yet; this is due, in part, to the structural constraints and the specificity of the protein interactions that govern the formation of the SNARE complex. Here we have addressed this question and used a combinatorial approach to identify peptides that modulate the assembly of the SNARE core complex and inhibit neuronal exocytosis. An α-helix-constrained, mixture-based, 17-mer combinatorial peptide library composed of 137180 sequences was synthesized in a positional scanning format. Peptide mixtures were assayed for their ability to prevent the formation of the in vitro-reconstituted SDS-resistant SNARE core complex. Library deconvolution identified eight peptides that inhibited the assembly of the SNARE core complex. Notably, the most potent 17-mer peptide (acetyl-SAAEAFAKLYAEAFAKG-NH2) abolished both Ca2+-evoked catecholamine secretion from detergent-permeabilized chromaffin cells and l-glutamate release from intact hippocampal primary cultures. Collectively, these findings indicate that amino acid sequences that prevent SNARE complex formation are not restricted to those that mimic domains of SNARE proteins, thus expanding the diversity of molecules that target neuronal exocytosis. Because of the implication of neurosecretion in the aetiology of several human neurological disorders, these newly identified peptides may be considered hits for the development of novel anti-spasmodic drugs.

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18

Burns, Virginia A., Benjamin G. Bobay, Anne Basso, John Cavanagh, and Christian Melander. "Targeting RNA with cysteine-constrained peptides." Bioorganic & Medicinal Chemistry Letters 18, no. 2 (January 2008): 565–67. http://dx.doi.org/10.1016/j.bmcl.2007.11.096.

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19

Levy, Yaakov, and Oren M. Becker. "Energy landscapes of conformationally constrained peptides." Journal of Chemical Physics 114, no. 2 (2001): 993. http://dx.doi.org/10.1063/1.1329646.

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20

Jiang, Hongbing, Yidong Xu, Li Li, Leiyun Weng, Qiang Wang, Shijian Zhang, Baosen Jia, et al. "Inhibition of Influenza Virus Replication by Constrained Peptides Targeting Nucleoprotein." Antiviral Chemistry and Chemotherapy 22, no. 3 (December 2011): 119–30. http://dx.doi.org/10.3851/imp1902.

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Background: Because of high mutation rates, new drug-resistant viruses are rapidly evolving, thus making the necessary control of influenza virus infection difficult. Methods: We screened a constrained cysteine-rich peptide library mimicking μ-conotoxins from Conus geographus and a proline-rich peptide library mimicking lebocin 1 and 2 from Bombyx mori by using influenza virus RNA polymerase (PB1, PB2 and PA) and nucleoprotein (NP) as baits. Results: Among the 22 peptides selected from the libraries, we found that the NP-binding proline-rich peptide, PPWCCCSPMKRASPPPAQSDLPATPKCPP, inhibited influenza replicon activity to mean ±SD 40.7% ±15.8% when expressed as a GFP fusion peptide in replicon cells. Moreover, when the GFP fusion peptide was transduced into cells by an HIV-TAT protein transduction domain sequence, the replication of influenza virus A/WSN/33 (WSN) at a multiplicity of infection of 0.01 was inhibited to 20% and 69% at 12 and 24 h post-infection, respectively. In addition, the TAT-GFP fusion peptide was able to slightly protect Balb/c mice from WSN infection when administrated prior to the infection. Conclusions: These results suggest the potential of this peptide as the seed of an anti-influenza drug and reveal the usefulness of the constrained peptide strategy for generating inhibitors of influenza infection. The results also suggest that influenza NP, which is conserved among the influenza A viruses, is a good target for influenza inhibition, despite being the most abundant protein in infected cells.

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21

Koopmanschap, Gijs, Eelco Ruijter, and Romano VA Orru. "Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics." Beilstein Journal of Organic Chemistry 10 (March 4, 2014): 544–98. http://dx.doi.org/10.3762/bjoc.10.50.

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In the recent past, the design and synthesis of peptide mimics (peptidomimetics) has received much attention. This because they have shown in many cases enhanced pharmacological properties over their natural peptide analogues. In particular, the incorporation of cyclic constructs into peptides is of high interest as they reduce the flexibility of the peptide enhancing often affinity for a certain receptor. Moreover, these cyclic mimics force the molecule into a well-defined secondary structure. Constraint structural and conformational features are often found in biological active peptides. For the synthesis of cyclic constrained peptidomimetics usually a sequence of multiple reactions has been applied, which makes it difficult to easily introduce structural diversity necessary for fine tuning the biological activity. A promising approach to tackle this problem is the use of multicomponent reactions (MCRs), because they can introduce both structural diversity and molecular complexity in only one step. Among the MCRs, the isocyanide-based multicomponent reactions (IMCRs) are most relevant for the synthesis of peptidomimetics because they provide peptide-like products. However, these IMCRs usually give linear products and in order to obtain cyclic constrained peptidomimetics, the acyclic products have to be cyclized via additional cyclization strategies. This is possible via incorporation of bifunctional substrates into the initial IMCR. Examples of such bifunctional groups are N-protected amino acids, convertible isocyanides or MCR-components that bear an additional alkene, alkyne or azide moiety and can be cyclized via either a deprotection–cyclization strategy, a ring-closing metathesis, a 1,3-dipolar cycloaddition or even via a sequence of multiple multicomponent reactions. The sequential IMCR-cyclization reactions can afford small cyclic peptide mimics (ranging from four- to seven-membered rings), medium-sized cyclic constructs or peptidic macrocycles (>12 membered rings). This review describes the developments since 2002 of IMCRs-cyclization strategies towards a wide variety of small cyclic mimics, medium sized cyclic constructs and macrocyclic peptidomimetics.

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22

Toniolo, C. "Structure of conformationally constrained peptides: From model compounds to bioactive peptides." Biopolymers 28, no. 1 (January 1989): 247–57. http://dx.doi.org/10.1002/bip.360280125.

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23

Yin, Liusong, Peter Trenh, and Lawrence Stern. "MHC II-peptide complex conformation constrained by interactions throughout the peptide binding groove determines HLA-DM susceptibility (P5014)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 41.8. http://dx.doi.org/10.4049/jimmunol.190.supp.41.8.

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Abstract HLA-DM (DM) mediates the exchange of peptides loaded onto MHC II. However, the determinants of DM-mediated peptide release remain unclear and controversial. In this study, we synthesized a series of peptides derived from HLA-A2104-117 and measured their kinetic stabilities when bound to HLA-DR1 (DR1) in the absence or presence of DM. As expected from previous work, we found that peptides with non-optimal pocket 1 residues were highly DM susceptible. Surprisingly we found that substitution of the pocket 9 residue can counteract the low binding affinity, low kinetic stability and high DM-susceptibility of peptides containing non-optimal pocket 1 residues. Surface Plasmon Resonance demonstrated that DM bound well to DR1 loaded with a peptide variant with pocket 1 alanine (A1), while no binding was observed for a rescue variant with leucine at pocket 9 (A1L9) or for the wild-type peptide (W1Q9). We determined the crystal structure of DR1-A1L9 to 2.3Å resolution, confirming the expected binding frame with alanine at pocket 1. DR1-A1 appeared to adopt a different conformation which can be better detected and edited by DM, as evidenced by the sodium dodecyl sulfate-resistance and recognition by a conformation-specific monoclonal antibody UL-5A1. Together with the results that multiple substitutions influence DM-susceptibility, our data suggest that conformation of MHC II-peptide complex constrained by interactions throughout the peptide binding site determines DM-susceptibility.

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24

Cary, Douglas R., Masaki Ohuchi, Patrick C. Reid, and Keiichi Masuya. "Constrained Peptides in Drug Discovery and Development." Journal of Synthetic Organic Chemistry, Japan 75, no. 11 (2017): 1171–78. http://dx.doi.org/10.5059/yukigoseikyokaishi.75.1171.

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25

Fabris, Laura, Sabrina Antonello, Lidia Armelao, Robert L. Donkers, Federico Polo, Claudio Toniolo, and Flavio Maran. "Gold Nanoclusters Protected by Conformationally Constrained Peptides." Journal of the American Chemical Society 128, no. 1 (January 2006): 326–36. http://dx.doi.org/10.1021/ja0560581.

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26

Kang, Chang Won, Sujeewa Ranatunga, Matthew P. Sarnowski, and Juan R. Del Valle. "Solid-Phase Synthesis of Tetrahydropyridazinedione-Constrained Peptides." Organic Letters 16, no. 20 (October 8, 2014): 5434–37. http://dx.doi.org/10.1021/ol5026684.

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27

McDevitt, T. C., K. E. Nelson, and P. S. Stayton. "Constrained Cell Recognition Peptides Engineered into Streptavidin." Biotechnology Progress 15, no. 3 (June 4, 1999): 391–96. http://dx.doi.org/10.1021/bp990043n.

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28

McDowell, Robert S., and Thomas R. Gadek. "Structural studies of potent constrained RGD peptides." Journal of the American Chemical Society 114, no. 24 (November 1992): 9245–53. http://dx.doi.org/10.1021/ja00050a001.

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29

Skowron, Kornelia J., Thomas E. Speltz, and Terry W. Moore. "Recent structural advances in constrained helical peptides." Medicinal Research Reviews 39, no. 2 (October 11, 2018): 749–70. http://dx.doi.org/10.1002/med.21540.

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30

Farrow, Blake, Andrew G. Wang, David N. Bunck, and James R. Heath. "Mimicking Protein Functions with Entropically Constrained Peptides." Biophysical Journal 110, no. 3 (February 2016): 203a. http://dx.doi.org/10.1016/j.bpj.2015.11.1134.

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31

Helton, Leah G., and Eileen J. Kennedy. "Targeting Plasmodium with constrained peptides and peptidomimetics." IUBMB Life 72, no. 6 (February 10, 2020): 1103–14. http://dx.doi.org/10.1002/iub.2244.

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32

Tóth, Gábor K., Zoltán Kele, and Ferenc Fülöp. "Synthesis of conformationally constrained peptides via solid-phase incorporation of the constraints." Tetrahedron Letters 41, no. 51 (December 2000): 10095–98. http://dx.doi.org/10.1016/s0040-4039(00)01795-0.

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33

Bag, Subhendu Sekhar, Subhashis Jana, Afsana Yashmeen та Suranjan De. "Triazolo-β-aza-ε-amino acid and its aromatic analogue as novel scaffolds for β-turn peptidomimetics". Chemical Communications 51, № 25 (2015): 5242–45. http://dx.doi.org/10.1039/c4cc08414d.

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Анотація:

Triazolo-β-aza-ε-amino acid and its aromatic analogue (AlTAA/ArTAA) in the peptide backbone mark a novel class of conformationally constrained molecular scaffolds to induce β-turn conformations. This was demonstrated in a Leu-enkephalin analogue and in other designed peptides.

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34

He, Jian, Randal Eckert, Thanh Pharm, Maurice D. Simanian, Chuhong Hu, Daniel K. Yarbrough, Fengxia Qi, Maxwell H. Anderson, and Wenyuan Shi. "Novel Synthetic Antimicrobial Peptides against Streptococcus mutans." Antimicrobial Agents and Chemotherapy 51, no. 4 (February 12, 2007): 1351–58. http://dx.doi.org/10.1128/aac.01270-06.

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ABSTRACT Streptococcus mutans, a common oral pathogen and the causative agent of dental caries, has persisted and even thrived on the tooth surface despite constant removal and eradication efforts. In this study, we generated a number of synthetic antimicrobial peptides against this bacterium via construction and screening of several structurally diverse peptide libraries where the hydrophobicity and charge within each library was varied incrementally in order to generate a collection of peptides with different biochemical characteristics. From these libraries, we identified multiple peptides with robust killing activity against S. mutans. To further improve their effectiveness, the most bactericidal peptides from each library were synthesized together as one molecule, in various combinations, with and without a flexible peptide linker between each antimicrobial region. Many of these “fusion” peptides had enhanced killing activities in comparison with those of the original nonconjoined molecules. The results presented here illustrate that small libraries of biochemically constrained peptides can be used to generate antimicrobial peptides against S. mutans, several of which may be likely candidates for the development of anticaries agents.

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TJERNBERG, Lars O., Agneta TJERNBERG, Niklas BARK, Yuan SHI, Bela P. RUZSICSKA, Zimei BU, Johan THYBERG та David J. E. CALLAWAY. "Assembling amyloid fibrils from designed structures containing a significant amyloid β-peptide fragment". Biochemical Journal 366, № 1 (15 серпня 2002): 343–51. http://dx.doi.org/10.1042/bj20020229.

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The amyloid plaque, consisting of amyloid β-peptide (Aβ) fibrils surrounded by dystrophic neurites, is an invariable feature of Alzheimer's disease. The determination of the molecular structure of Aβ fibrils is a significant goal that may lead to the structure-based design of effective therapeutics for Alzheimer's disease. Technical challenges have thus far rendered this goal impossible. In the present study, we develop an alternative methodology. Rather than determining the structure directly, we design conformationally constrained peptides and demonstrate that only certain ‘bricks’ can aggregate into fibrils morphologically identical to Aβ fibrils. The designed peptides include variants of a decapeptide fragment of Aβ, previously shown to be one of the smallest peptides that (1) includes a pentapeptide sequence necessary for Aβ—Aβ binding and aggregation and (2) can form fibrils indistinguishable from those formed by full-length Aβ. The secondary structure of these bricks is monitored by CD spectroscopy, and electron microscopy is used to study the morphology of the aggregates formed. We then made various residue deletions and substitutions to determine which structural features are essential for fibril formation. From the constraints, statistical analysis of side-chain pair correlations in β-sheets and experimental data, we deduce a detailed model of the peptide strand alignment in fibrils formed by these bricks. Our results show that the constrained decapeptide dimers rapidly form an intramolecular, antiparallel β-sheet and polymerize into amyloid fibrils at low concentrations. We suggest that the formation of an exposed β-sheet (e.g. an Aβ dimer formed by interaction in the decapeptide region) could be a rate-limiting step in fibril formation. A theoretical framework that explains the results is presented in parallel with the data.

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36

Bai, Zengbing, and Huan Wang. "Backbone-Enabled Peptide Macrocyclization through Late-Stage Palladium-Catalyzed C–H Activation." Synlett 31, no. 03 (December 9, 2019): 199–204. http://dx.doi.org/10.1055/s-0039-1691495.

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Peptide macrocycles are widely used in fields ranging from medicinal chemistry to materials science. Efficient chemical methods for the synthesis of cyclic peptides with novel three-dimensional structures are highly desired to facilitate the development of this unique class of compounds. However, the range of methods available for constructing peptide macrocycles is limited compared with that for small molecules. We recently developed new methods for synthesizing highly constrained cyclic peptides with C–C crosslinks through Pd-catalyzed C–H activation reactions. These methods use endogenous backbone amides as directing groups and, therefore, have the potential for use in late-stage functionalization of peptide natural products.

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37

Tian, Yuan, Xiangze Zeng, Jingxu Li, Yanhong Jiang, Hui Zhao, Dongyuan Wang, Xuhui Huang, and Zigang Li. "Achieving enhanced cell penetration of short conformationally constrained peptides through amphiphilicity tuning." Chem. Sci. 8, no. 11 (2017): 7576–81. http://dx.doi.org/10.1039/c7sc03614k.

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We synthesized a panel of conformationally constrained peptides with either α-helix or β-hairpin conformations. We tuned the amphiphilicity of these constrained peptides with different distributions of charged or hydrophobic residues and compared their cellular uptake efficiencies in different cell lines.

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38

Zhang, Dingwa, Deyong He, Xiaoliang Pan, and Lijun Liu. "Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface." Protein & Peptide Letters 27, no. 10 (November 2, 2020): 999–1006. http://dx.doi.org/10.2174/0929866527666200414160723.

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Background: The Yes-Associated Protein (YAP) is a central regulator of Hippo pathway involved in carcinogenesis, which functions through interaction with TEA Domain (TEAD) transcription factors. Pharmacological disruption of YAP–TEAD4 complexes has been recognized as a potential therapeutic strategy against diverse cancers by suppressing the oncogenic activity of YAP. Objective: Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein. Dynamics simulations, energetics analyses and fluorescence polarizations are employed to characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to TEAD4 protein. Methods: Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein. Dynamics simulations, energetics analyses and fluorescence polarizations are employed to characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to TEAD4 protein. Result: The native conformation of PS-2 peptide is a cyclic loop, which is supposed to be constrained by adding a disulfide bond across the spatially vicinal residue pair Arg87-Phe96 or Met86- Phe95 at the peptide’s two ends, consequently resulting in two intramolecular cyclized counterparts of linear PS-2 peptide, namely PS-2(cyc87,96) and PS-2(cyc86,95). The linear PS-2 peptide is determined as a weak binder of TEAD4 (Kd = 190 μM), while the two cyclic PS-2(cyc87,96) and PS-2(cyc86,95) peptides are measured to have moderate or high affinity towards TEAD4 (Kd = 21 and 45 μM, respectively). Conclusion: PS-1 and PS-2 peptides are highly flexible and cannot maintain in native active conformation when splitting from the interfacial context, and thus would incur a considerable entropy penalty upon rebinding to the interface. Cyclization does not influence the direct interaction between PS-2 peptide and TEAD4 protein, but can largely reduce the intrinsic disorder of PS-2 peptide in free state and considerably minimize indirect entropy effect upon the peptide binding.

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39

Miles, Jennifer A., David J. Yeo, Philip Rowell, Silvia Rodriguez-Marin, Christopher M. Pask, Stuart L. Warriner, Thomas A. Edwards, and Andrew J. Wilson. "Hydrocarbon constrained peptides – understanding preorganisation and binding affinity." Chemical Science 7, no. 6 (2016): 3694–702. http://dx.doi.org/10.1039/c5sc04048e.

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40

Willick, Gordon. "Preface [ Constrained Peptides (Guest Editor: Gordon E. Willick)]." Current Medicinal Chemistry 11, no. 21 (November 1, 2004): i. http://dx.doi.org/10.2174/0929867043364216.

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41

Sia, S. K., P. A. Carr, A. G. Cochran, V. N. Malashkevich, and P. S. Kim. "Short constrained peptides that inhibit HIV-1 entry." Proceedings of the National Academy of Sciences 99, no. 23 (November 4, 2002): 14664–69. http://dx.doi.org/10.1073/pnas.232566599.

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42

Bhardwaj, Gaurav, Vikram Khipple Mulligan, Christopher D. Bahl, Jason M. Gilmore, Peta J. Harvey, Olivier Cheneval, Garry W. Buchko, et al. "Accurate de novo design of hyperstable constrained peptides." Nature 538, no. 7625 (September 14, 2016): 329–35. http://dx.doi.org/10.1038/nature19791.

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43

Dantas de Araujo, Aline, Samuel R. Perry, and David P. Fairlie. "Chemically Diverse Helix-Constrained Peptides Using Selenocysteine Crosslinking." Organic Letters 20, no. 5 (February 20, 2018): 1453–56. http://dx.doi.org/10.1021/acs.orglett.8b00233.

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44

Arimoto, Rieko, Oleg G. Kisselev, Gergely M. Makara, and Garland R. Marshall. "Rhodopsin-Transducin Interface: Studies with Conformationally Constrained Peptides." Biophysical Journal 81, no. 6 (December 2001): 3285–93. http://dx.doi.org/10.1016/s0006-3495(01)75962-0.

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45

K. Tiwari, Rakesh, and Keykavous Parang. "Conformationally Constrained Peptides as Protein Tyrosine Kinase Inhibitors." Current Pharmaceutical Design 18, no. 20 (May 1, 2012): 2852–66. http://dx.doi.org/10.2174/138161212800672714.

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46

Mayer, Bernd, and Giancarlo Marconi. "Circular dichroic constrained structure optimization of homoalanine peptides." Journal of Computational Chemistry 21, no. 4 (March 2000): 270–81. http://dx.doi.org/10.1002/(sici)1096-987x(200003)21:4<270::aid-jcc3>3.0.co;2-v.

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47

van Maarseveen, Jan H., and Peter Timmerman. "Editorial for the special issue on “constrained peptides”." Drug Discovery Today: Technologies 26 (December 2017): 1–2. http://dx.doi.org/10.1016/j.ddtec.2017.12.001.

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48

North, Michael. "Incorporation of Conformationally Constrained ?-Amino Acids into Peptides." Journal of Peptide Science 6, no. 7 (2000): 301–13. http://dx.doi.org/10.1002/1099-1387(200007)6:7<301::aid-psc260>3.0.co;2-1.

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49

Bakail, May, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. "Recognition of ASF1 by Using Hydrocarbon‐Constrained Peptides." ChemBioChem 20, no. 7 (February 13, 2019): 891–95. http://dx.doi.org/10.1002/cbic.201800633.

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50

Chakravarty, Sarvajit, Deidre Wilkins, and Donald J. Kyle. "Design of potent, cyclic peptide bradykinin receptor antagonists from conformationally constrained linear peptides." Journal of Medicinal Chemistry 36, no. 17 (August 1993): 2569–71. http://dx.doi.org/10.1021/jm00069a016.

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