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Journal articles on the topic 'Constrained peptides'

Author: Grafiati

Published: 10 December 2022

Last updated: 31 July 2025

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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 (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 modu

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2

Real, Eléonore, Jean-Christophe Rain, Véronique Battaglia, et al. "Antiviral Drug Discovery Strategy Using Combinatorial Libraries of Structurally Constrained Peptides." Journal of Virology 78, no. 14 (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 proce

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3

Gisemba, Solomon A., Michael J. Ferracane, Thomas F. Murray, and Jane V. Aldrich. "A Bicyclic Analog of the Linear Peptide Arodyn Is a Potent and Selective Kappa Opioid Receptor Antagonist." Molecules 29, no. 13 (2024): 3109. http://dx.doi.org/10.3390/molecules29133109.

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Kappa opioid receptor (KOR) antagonists have potential therapeutic applications in the treatment of stress-induced relapse to substance abuse and mood disorders. The dynorphin A analog arodyn (Ac[Phe1,2,3,Arg4,D-Ala8]dynorphin A-(1–11)-NH2) exhibits potent and selective kappa opioid receptor antagonism. Multiple cyclizations in longer peptides, such as dynorphin and its analogs, can extend the conformational constraint to additional regions of the peptide beyond what is typically constrained by a single cyclization. Here, we report the design, synthesis, and pharmacological evaluation of a bic

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4

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 (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 si

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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 (1996): C249. http://dx.doi.org/10.1107/s0108767396089489.

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6

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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7

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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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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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 (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 ant

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9

Zhou, Lijuan, Fei Cai, Yanjie Li, et al. "Disulfide-constrained peptide scaffolds enable a robust peptide-therapeutic discovery platform." PLOS ONE 19, no. 3 (2024): e0300135. http://dx.doi.org/10.1371/journal.pone.0300135.

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Peptides present an alternative modality to immunoglobulin domains or small molecules for developing therapeutics to either agonize or antagonize cellular pathways associated with diseases. However, peptides often suffer from poor chemical and physical stability, limiting their therapeutic potential. Disulfide-constrained peptides (DCP) are naturally occurring and possess numerous desirable properties, such as high stability, that qualify them as drug-like scaffolds for peptide therapeutics. DCPs contain loop regions protruding from the core of the molecule that are amenable to peptide enginee

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10

Kuepper, Arne, Niall M. McLoughlin, Saskia Neubacher, et al. "Constrained peptides mimic a viral suppressor of RNA silencing." Nucleic Acids Research 49, no. 22 (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 ligand

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11

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 (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 advanta

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12

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 (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 hydr

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13

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

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14

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

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15

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

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16

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

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17

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 (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 PS

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18

Qing, Xiaoyu, Qian Wang, Hanyu Xu, Pei Liu, and Luhua Lai. "Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase." Molecules 28, no. 17 (2023): 6430. http://dx.doi.org/10.3390/molecules28176430.

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Although loop epitopes at protein-protein binding interfaces often play key roles in mediating oligomer formation and interaction specificity, their binding sites are underexplored as drug targets owing to their high flexibility, relatively few hot spots, and solvent accessibility. Prior attempts to develop molecules that mimic loop epitopes to disrupt protein oligomers have had limited success. In this study, we used structure-based approaches to design and optimize cyclic-constrained peptides based on loop epitopes at the human phosphoglycerate dehydrogenase (PHGDH) dimer interface, which is

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19

BLANES-MIRA, Clara, Maria T. PASTOR, Elvira VALERA та ін. "Identification of SNARE complex modulators that inhibit exocytosis from an α-helix-constrained combinatorial library". Biochemical Journal 375, № 1 (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 appr

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20

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

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21

Jiang, Hongbing, Yidong Xu, Li Li, et al. "Inhibition of Influenza Virus Replication by Constrained Peptides Targeting Nucleoprotein." Antiviral Chemistry and Chemotherapy 22, no. 3 (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 in

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22

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 (2008): 565–67. http://dx.doi.org/10.1016/j.bmcl.2007.11.096.

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23

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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24

Cai, Fei, Yuehua Wei, Daniel Kirchhofer, Andrew Chang, and Yingnan Zhang. "Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds." PLOS Computational Biology 20, no. 11 (2024): e1012609. http://dx.doi.org/10.1371/journal.pcbi.1012609.

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Peptides are an emerging modality for developing therapeutics that can either agonize or antagonize cellular pathways associated with disease, yet peptides often suffer from poor chemical and physical stability, which limits their potential. However, naturally occurring disulfide-constrained peptides (DCPs) and de novo designed Hyperstable Constrained Peptides (HCPs) exhibiting highly stable and drug-like scaffolds, making them attractive therapeutic modalities. Previously, we established a robust platform for discovering peptide therapeutics by utilizing multiple DCPs as scaffolds. However, w

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25

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 (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 D

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26

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

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27

He, Jian, Randal Eckert, Thanh Pharm, et al. "Novel Synthetic Antimicrobial Peptides against Streptococcus mutans." Antimicrobial Agents and Chemotherapy 51, no. 4 (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

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28

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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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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29

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 (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

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30

Bai, Zengbing, and Huan Wang. "Backbone-Enabled Peptide Macrocyclization through Late-Stage Palladium-Catalyzed C–H Activation." Synlett 31, no. 03 (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 b

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31

Tian, Yuan, Xiangze Zeng, Jingxu Li, et al. "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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32

TJERNBERG, Lars O., Agneta TJERNBERG, Niklas BARK та ін. "Assembling amyloid fibrils from designed structures containing a significant amyloid β-peptide fragment". Biochemical Journal 366, № 1 (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 aggre

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33

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

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34

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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35

Fabris, Laura, Sabrina Antonello, Lidia Armelao, et al. "Gold Nanoclusters Protected by Conformationally Constrained Peptides." Journal of the American Chemical Society 128, no. 1 (2006): 326–36. http://dx.doi.org/10.1021/ja0560581.

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36

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 (2014): 5434–37. http://dx.doi.org/10.1021/ol5026684.

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37

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

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38

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

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39

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

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40

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

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41

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

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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 (2000): 10095–98. http://dx.doi.org/10.1016/s0040-4039(00)01795-0.

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43

Nagarajan, Balaji, and Nehru Viji Sankaranarayanan. "Exploring the Energy Landscape of Conformationally Constrained Peptides in Vacuum and in the Presence of an Explicit Solvent Using the MOLS Technique." Sci 7, no. 3 (2025): 93. https://doi.org/10.3390/sci7030093.

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This research represents the first application of the MOLS method to characterize the conformational energy landscape of an antimicrobial peptide within a solvent environment, providing a novel approach to understanding peptide behavior in solution. This method’s exhaustive nature ensures that all minimum-energy conformations for a given amino acid sequence are sampled. In this work, we employed a combination of MOLS and VMD software to generate structural models of a cyclic peptide, both solvated and non-solvated, and then utilized the CHARMM force field to conduct energy calculations through

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44

Eaholtz, Galen, Anita Colvin, Daniele Leonard, Charles Taylor, and William A. Catterall. "Block of Brain Sodium Channels by Peptide Mimetics of the Isoleucine, Phenylalanine, and Methionine (IFM) Motif from the Inactivation Gate." Journal of General Physiology 113, no. 2 (1999): 279–94. http://dx.doi.org/10.1085/jgp.113.2.279.

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Inactivation of sodium channels is thought to be mediated by an inactivation gate formed by the intracellular loop connecting domains III and IV. A hydrophobic motif containing the amino acid sequence isoleucine, phenylalanine, and methionine (IFM) is required for the inactivation process. Peptides containing the IFM motif, when applied to the cytoplasmic side of these channels, produce two types of block: fast block, which resembles the inactivation process, and slow, use-dependent block stimulated by strong depolarizing pulses. Fast block by the peptide ac-KIFMK-NH2, measured on sodium chann

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Roy, Siddhartha, Piya Ghosh, Israr Ahmed, Madhumita Chakraborty, Gitashri Naiya та Basusree Ghosh. "Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions". Biomedicines 6, № 4 (2018): 118. http://dx.doi.org/10.3390/biomedicines6040118.

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Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as “undruggable”. Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these

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46

Miles, Jennifer A., David J. Yeo, Philip Rowell, et al. "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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47

Zheng, Zihao, Aisha M. Mergaert, Irene M. Ong, Miriam A. Shelef, and Michael A. Newton. "MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing." Bioinformatics 37, no. 17 (2021): 2637–43. http://dx.doi.org/10.1093/bioinformatics/btab162.

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Abstract Summary Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local FDR statistics and local false sign rate statistics when provided with data on estimated effects

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48

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 (1993): 2569–71. http://dx.doi.org/10.1021/jm00069a016.

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49

Ma, He, Peiju Qiu, Peta J. Harvey, et al. "In Silico Design of MDM2‐Targeting Peptides from a Naturally Occurring Constrained Peptide." ChemMedChem 14, no. 19 (2019): 1710–16. http://dx.doi.org/10.1002/cmdc.201900366.

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

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