Modulation of Protein-Protein Interactions by Stabilizing/Mimicking Protein Secondary Structure Elements

Vega, M. Jesús Pérez de; Martı́n-Martı́nez, Mercedes; González‐Muñiz, Rosario

doi:10.2174/156802607779318325

Cited by 79 publications

(23 citation statements)

References 234 publications

(257 reference statements)

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“…As an initial examination of this process, we noted that the large macrocycle 8 carries the PatA recognition sequence, RSII. Recognition motifs within cyclic peptide scaffolds have been shown to hold potential in stabilizing these scaffolds for enhanced protein-protein interactions (Davidson et al, 2009; de Vega et al, 2007). Thus, we expected that the macrocyclic product 8 might be proteolysed by PatA, which in turn will produce a derivative with the thiazoline residue in an abnormal position.…”

Section: Resultsmentioning

confidence: 99%

Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides

Sardar

Lin

Schmidt

2015

Chemistry & Biology

143

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SUMMARY Macrocyclases and other posttranslational enzymes afford derived peptides with improved properties for pharmaceutical and biotechnological applications. Here, we asked whether multiple posttranslational modifications could be simultaneously controlled and matched to rationally generate new peptide derivatives. We reconstituted the cyanobactin peptide natural products in vitro with up to five different posttranslational enzymes in a single tube. By manipulating the order of addition and identity of enzymes and exploiting their broad-substrate tolerance, we engineered the production of highly unnatural derivatives, including an N-C peptide macrocycle of 22 amino acids in length. In addition to engineering, this work better defines the macrocyclization mechanism, provides the first biochemical demonstration of Ser/Thr posttranslational prenylation, and is the first example of reconstitution of a native, multistep RiPP pathway with multiple enzymes in one pot. Overall, this work demonstrates how the modularity of posttranslational modification enzymes can be used to design and synthesize desirable peptide motifs.

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Section: Resultsmentioning

confidence: 99%

Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides

Sardar

Lin

Schmidt

2015

Chemistry & Biology

143

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“…There are certain types of PPIs that have been more amenable to drug discovery than others (Scott et al, 2016). Particular success has emerged from strategies that attempt to mimic a peptide or protein ligand, such that small molecule leads directly compete with the native macromolecular ligand (de Vega et al, 2007). In the field of PPI research, structural and biophysical approaches play a key role, often in iterative cycles of ligand development (Scott et al, 2016).…”

Section: The Challenge Of Ligand Discovery and Design Targeting Prmentioning

confidence: 99%

Integrating Experimental and In Silico HTS in the Discovery of Inhibitors of Protein–Nucleic Acid Interactions

Constantino

Spies

2018

Methods in Enzymology

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Discovery of novel tool compounds and drug leads against a range of unorthodox protein targets has pushed both experimental screening methodologies as well as the field of structure based design to the limit in recent years. Increasingly, it has been recognized that some of the most desirable targets for the development of small molecule effectors are actually protein-protein and protein-nucleic acid interactions. There are numerous nontrivial challenges to pursuing small molecule lead compounds directed toward PPIs and PNIs: relatively shallow cavities, large surface areas that are natively complexed to macromolecules, complex patterns of interstitial waters, a paucity of “hot spots”, large conformational changes upon ligand binding, etc. Although there have been some notable successes targeting PPIs in the last decade, there has been distinctly less success in the realm of targeting PNIs. This chapter focuses on an approach, successfully applied by our group to address the challenge of gaining traction on the PPI target RAD52, which is a protein that binds both single stranded and double stranded DNA, and is an anti-cancer target for certain types of cancer. There are many approaches to tackling the difficult problems of finding effective small molecules that disrupt PPIs and PNIs, but the methods presented here offer a series of elegant solutions, which integrate experimental HTS, biophysical methods, docking and molecular dynamics in a powerful way. Additionally, the structural knowledge gained from these studies provides a means for rationally understanding what features lead to ligand affinity in these fascinating and highly unorthodox pockets.

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“…The simplest peptides are linear and disordered, assume structure only upon binding to a protein, and are prone to degradation by host proteases. Thus, peptide drug design strategies often seek to engineer structure into the peptide [5]. These approaches include induction of secondary structure such as β-turns, α-helices and β-hairpins [6]; head-to-tail cyclization [7, 8]; and incorporation of non-standard amino acid residues, as in peptoids [9].…”

Section: Introductionmentioning

confidence: 99%

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

et al. 2016

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BackgroundDisulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stability. A challenge in developing a DRP therapeutic is to engineer binding to a specific target. This challenge can be overcome by (i) sampling the large sequence space of a given scaffold through a phage display library and by (ii) panning multiple libraries encoding structurally distinct scaffolds. Here, we implement a protocol for defining these diverse scaffolds, based on clustering structurally defined DRPs according to their conformational similarity.ResultsWe developed and applied a hierarchical clustering protocol based on DRP structural similarity, followed by two post-processing steps, to classify 806 unique DRP structures into 81 clusters. The 20 most populated clusters comprised 85% of all DRPs. Representative scaffolds were selected from each of these clusters; the representatives were structurally distinct from one another, but similar to other DRPs in their respective clusters. To demonstrate the utility of the clusters, phage libraries were constructed for three of the representative scaffolds and panned against interleukin-23. One library produced a peptide that bound to this target with an IC50 of 3.3 μM.ConclusionsMost DRP clusters contained members that were diverse in sequence, host organism, and interacting proteins, indicating that cluster members were functionally diverse despite having similar structure. Only 20 peptide scaffolds accounted for most of the natural DRP structural diversity, providing suitable starting points for seeding phage display experiments. Through selection of the scaffold surface to vary in phage display, libraries can be designed that present sequence diversity in architecturally distinct, biologically relevant combinations of secondary structures. We supported this hypothesis with a proof-of-concept experiment in which three phage libraries were constructed and panned against the IL-23 target, resulting in a single-digit μM hit and suggesting that a collection of libraries based on the full set of 20 scaffolds increases the potential to identify efficiently peptide binders to a protein target in a drug discovery program.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1350-9) contains supplementary material, which is available to authorized users.

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Modulation of Protein-Protein Interactions by Stabilizing/Mimicking Protein Secondary Structure Elements

Cited by 79 publications

References 234 publications

Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides

Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides

Integrating Experimental and In Silico HTS in the Discovery of Inhibitors of Protein–Nucleic Acid Interactions

Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

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