High Specificity in Protein Recognition by Hydrogen‐Bond‐Surrogate α‐Helices: Selective Inhibition of the p53/MDM2 Complex

Henchey, Laura K.; Porter, Jason R.; Ghosh, Indraneel; Arora, Paramjit S.

doi:10.1002/cbic.201000378

Cited by 91 publications

(91 citation statements)

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“…The p53 sequence was chosen because it has relatively few side-chain contacts such as ionic bridges, which may bias the results. We have previously characterized a number of p53 HBS analogs by CD and NMR spectroscopies allowing us to predict potential aggregation issues that can affect stabilized constructs (36)(37)(38). The bisthiol p53 peptide is weakly helical in aqueous buffers at 295 K. CD spectroscopy ( Fig.…”

Section: Significancementioning

confidence: 99%

Effects of side chains in helix nucleation differ from helix propagation

Miller

Watkins

Kallenbach

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Helix-coil transition theory connects observable properties of the α-helix to an ensemble of microstates and provides a foundation for analyzing secondary structure formation in proteins. Classical models account for cooperative helix formation in terms of an energetically demanding nucleation event (described by the σ constant) followed by a more facile propagation reaction, with corresponding s constants that are sequence dependent. Extensive studies of folding and unfolding in model peptides have led to the determination of the propagation constants for amino acids. However, the role of individual side chains in helix nucleation has not been separately accessible, so the σ constant is treated as independent of sequence. We describe here a synthetic model that allows the assessment of the role of individual amino acids in helix nucleation. Studies with this model lead to the surprising conclusion that widely accepted scales of helical propensity are not predictive of helix nucleation. Residues known to be helix stabilizers or breakers in propagation have only a tenuous relationship to residues that favor or disfavor helix nucleation.synthetic helices | helix propensity T he α-helix is the most prevalent secondary structure in proteins and can form extremely rapidly. Helix formation is thus crucial in early steps of protein folding, and a complete description of the kinetics and thermodynamics of α-helix formation is fundamental for understanding protein folding (1). Theoretical models of the helix-coil transition consider helix formation to proceed in two steps: initial nucleation of a helical sequence, denoted by the parameter σ in the Zimm-Bragg notation (2), followed by more favorable helix propagation, denoted by s parameters. This distinction identifies the energetically unfavorable organization of three consecutive amino acid residues to form a helical nucleus as the slow step in helix formation (2-4). Helix propagation, in contrast, refers to the addition of the next hydrogen bond to a preformed helix (Fig. 1A). Zimm-Bragg or equivalent theories posit that formation of short peptide helices in water is unfavorable because the large decrease in entropy required for nucleation is not adequately compensated by the enthalpic gain from forming a small number of hydrogen bonds.The ability of different peptide sequences to adopt helical conformations has been rigorously investigated, and the stability of α-helices can be estimated from widely used scales of helical propensity (5). These scales are important for our understanding of protein structure, folding, and function. The classical studies for determination of helix propensities have used peptides, coiled-coils, and protein models for host-guest studies in which a guest residue is systematically substituted at a site in a host structure (6-12). Helix-coil transition theory then relates changes in the conformational stability to microscopic helix propensities or s constants for individual residues. The results provide a quantitative basis for evaluating t...

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Section: Significancementioning

confidence: 99%

Effects of side chains in helix nucleation differ from helix propagation

Miller

Watkins

Kallenbach

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…[19][20][21][22][23][24][27][28][29] and 62 for reviews) for the modulation a plethora of intracellular targets (i.e. Bcl2-family, 19,[22][23][24]43,47,48,58,[67][68][69][70][71]76,77,83,92,93,98 p53:MDM2/X, 42,57,65,66,72,79,81,82,87,89,94,95 MAML:Notch, 49 eIF4E, 158 ERa/ERb, 50 IRS1, 84 HIF-1:p300, 56,90 RAS:SOS, 59 Rab-GTPase, 96 b-catenin, 64,78,80 protein kinase-A, 91 RPA, 97 HIV-1 integrase, …”

Section: Stapled Peptide Modulation Of Drug Target Spacementioning

confidence: 99%

“…With respect to stapled peptides, mounting evidence from numerous studies [19][20][21][22][23][24]43,44,[47][48][49]56,57,64, has implicated active transport processes to underlie cellular uptake as demonstrated by intracellular on-target engagement and/or fluorescence microscopy (i.e. visualization of fluorescently labeled stapled peptide analogs).…”

Section: Understanding the Cell Penetration Properties Of Macrocyclicmentioning

confidence: 99%

“…Historically, numerous strategies have emerged to create novel synthetic a-helical secondary structure proteomimetics. [19][20][21][22][23][24]43,44,47,48,56,57,64,[118][119][120][121][122] Albeit not detailed in this focused review, such strategies have included N-terminal helicalinducing capping moieties, [123][124][125] non-peptide foldamers/oligomers 126,127 and small-molecule mimetics. [128][129][130][131][132][133][134][135][136] Unquestionably, the most rewarding strategy has been proven to be the synthesis of macrocyclic a-helical peptides utilizing a variety of linkers, including disulfide, 118 Pioneering studies on macrocylic a-helical peptides first demonstrated 118,119 the effective use of disulfide-bridged and bis-lactam-bridged macrocyclic peptides 1 and 2 ( Figure 9.2), respectively, and focused on model systems wherein a-helicity properties were confirmed by circular dichroism and/or NMR spectroscopy.…”

Section: Structural Diversity and Chemistry Of Macrocyclicmentioning

confidence: 99%

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Macrocyclic α-Helical Peptide Drug Discovery

Sawyer

Guerlavais

Darłak

et al. 2014

Macrocycles in Drug Discovery

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Macrocyclic α-helical peptides have emerged as a promising new drug class and within the scope of hydrocarbon-stapled peptides such molecules have advanced into the clinic. The overarching concept of designing proteomimetics of an α-helical ‘ligand’ which binds its cognate ‘target’ relative to α-helical interfacing protein-protein interactions has been well-validated and expanded through numerous investigations for a plethora of therapeutic targets oftentimes referred to as “undruggable” with respect to other modalities (e.g., small-molecule or proteins). This chapter highlights the evolution of macrocyclic α-helical peptides in terms of target space, biophysical and computational chemistry, structural diversity and synthesis, drug design and chemical biology. It is noteworthy that hydrocarbon-stapled peptides have successfully risen to the summit of such drug discovery campaigns.

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“…Drugging strategy P53 N-terminal peptide [40] MDM2 p53 hydrogen-bond-surrogate α-helix [85] p53 hydrocarbon-stapled α-helix (3V3B) [86] p53-mimicking small molecule Nutlin (1RV1) [87] cell-penetrable spiroligomer α-helix [88] p53-based small molecule MI-219 [89] p53 peptidomimetic trisaccharide [90] P53 N-terminal peptide [91] MDM4 Optimized p53 peptide [92] targeting MDM2/MDM4 P53 peptide from tetramerisation domain [93] CDK2-Cyclin A/B Based on CDK2 docking site P53 C-terminal peptide [94] Core domain of P53 mutant…”

Section: Molecule Ligandmentioning

confidence: 99%

Evolution of Conformational Disorder & Diversity of the P53 Interactome

Huart¹,

Hupp²

2013

Biodiscovery

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The tumour suppressor p53 is now known to be an ancient transcription factor that had already evolved interaction sites with its partner protein MDM2 at the dawn of multi-cellular eukaryotic animal life. The billionyear life history of the p53-MDM2 axis has permitted significant time for the proteins to integrate into a distinct range of cellular pathways including binding to hundreds of genomic promoters and regulatory protein-protein interactions with hundreds of distinct functions. This long age of p53 allows us to understand how the protein can regulate a range of functions such as energy generation of the cell, cell motility, genome integrity, virus infection, immune cell response, ageing, and oxidative stress. Due to this deep integration of p53 into the core of eukaryotic life, it is not surprising that the p53 pathway requires inactivation in order for human cancer cells to evade the normal growth controlling processes that have been shaped through evolution by natural selection. This review will focus on the emerging concepts in the protein science field that shed light on p53 protein evolution and function including the nature of thermodynamically unstable regulatory proteins and the growing realisation that the majority of protein-protein interactions in complex eukaryotic cells are driven by intrinsically unstructured and weakly interacting peptide motifs. These concepts help to explain how the vast number of dynamic and specific protein-protein interactions in the p53 pathway evolved, suggest how amino acid modifications like phosphorylation or acetylation in turn evolved to regulate dynamically the p53 interactome, and finally reveal therapeutic strategies for targeting the p53 interactome in human cancers. Intrinsic disorder: the rise of a new dogma in protein science that impacts upon our understanding of p53As biologists or biochemists, we have all learned the structure-function paradigm that proteins display different levels of organisation: a "primary" linear sequence on which depends local spatial "secondary" arrangements stabilised by a three dimensional compact structure, usually referred as globular protein or called native fold, i.e. the biologically active form of the protein. Upon this structure-function concept several protein-protein interaction (PPI) models have been developed such as the recent Nobel Prize awarded on solving the structure of a ribosome. It is perhaps not a co-incidence that a major advance on the road to acquire the structure of this prokaryotic multi-protein complex was the decision to switch to purifying ribosomal proteins from thermophilic bacteria which are more suitable to form stable structures using current experimental methodologies. More "unstable" ribosomal complexes from, for example, higher eukaryotes are not suitable for such crystallographic

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High Specificity in Protein Recognition by Hydrogen‐Bond‐Surrogate α‐Helices: Selective Inhibition of the p53/MDM2 Complex

Cited by 91 publications

References 50 publications

Effects of side chains in helix nucleation differ from helix propagation

Effects of side chains in helix nucleation differ from helix propagation

Macrocyclic α-Helical Peptide Drug Discovery

Evolution of Conformational Disorder & Diversity of the P53 Interactome

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