Targeting oncogenic transcriptional corepressor Nac1 POZ domain with conformationally constrained peptides by cyclization and stapling

Rational design of stapled helical peptides as antidiabetic PPARγ antagonists to target coactivator site by decreasing unfavorable entropy penalty instead of increasing favorable enthalpy contribution

Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor belonging to the nuclear hormone receptor and has been exploited as a well-established druggable target for the treatment of diabetes mellitus (DM). Traditionally, small-molecule compounds have been developed to attack at the ligand site and Ser273 phosphorylation site of PPARγ. In this study, we derived helical peptide segments from the LXXLL motif region of coactivator proteins as antidiabetic PPARγ antagonists, which were expected to competitively disrupt the native interaction between PPARγ and its cognate coactivators by rebinding at PPARγ coactivator site. Structural analysis, dynamics simulation and energetics dissection revealed that these peptides cannot be well folded into active helical structure when splitting from the protein context of their parent coactivators and exhibit a large flexibility and intrinsic disorder in the free state, which would, therefore, incur a considerable entropy penalty upon rebinding to PPARγ. Hydrocarbon stapling strategy was employed to constrain these free coactivator peptides into ordered helical conformation, thus largely minimizing unfavorable entropy penalty but having only a moderate effect on favorable enthalpy contribution. The computational findings were further substantiated by fluorescence-based assays; the binding affinity of three potent SRC1, NCoA6 and p300 coactivator peptides to PPARγ was observed to be improved by 7.2-fold, 4.2-fold and 5.7-fold upon the stapling, which were also measured to have an efficient competitive potency with their unstapled counterparts for PPARγ coactivator site, with CC₅₀ = 0.096, 0.12 and 0.18 μM, respectively.

Structure-based analysis and rational design of human peroxiredoxin-1's C-terminus-derived peptides to target sulfiredoxin-1 in pancreatic cancer

Human peroxiredoxin (PRX) family of antioxidant enzymes reduces hydrogen peroxide and alkyl hydroperoxide involved in the redox signaling, among which the widely documented PRX1 is a versatile molecule regulating cell growth, differentiation and apoptosis, and has been implicated in the tumorigensis of pancreatic cancer. In this study, we systematically examined the complex crystal structure of PRX1 with its cognate interacting partner sulfiredoxin-1 (SRX1) at molecular level, and found that the PRX1-SRX1 association is a typical peptide-mediated protein-protein interaction, where a 18-mer C-terminal tail (CTT) segment of PRX1 was identified to be primarily responsible for the interaction, which contributes ~80% and ~ 55% to the total binding potency of SRX1 to PRX1 monomer and homodimer, respectively. We also demonstrated that the SRX1 exhibits a strong global selectivity for PRX1 CTT tail over other PRX family proteins. Next, the intermolecular interaction between PRX1 CTT tail and SRX1 was investigated at structural, energetic and dynamic levels, from which a 9-mer core region of PRX1 CTT tail was defined as the SRX1-binding hotspot. Biophysical assays substantiated that the CTT and CTTc peptides (out of PRX1 protein context) can bind in an independent manner and possess a close affinity to SRX1. Based on the CTTc sketch a computational combinatorial library consisting of 216 designed peptide derivatives was rationally generated, from which the top-5 hits were found to have comparable affinity with CTT peptide and improved affinity relative to CTTc peptide. They can be used as structurally reduced lead molecular entities to further develop new peptidic agents for therapeutic purpose to disrupt the native PRX1-SRX1 interaction by competing with PRX1 CTT tail for the peptide-binding pocket of SRX1.

Interleukin-1α, Interleukin-1β and Interleukin-1 Receptor Antagonist Share a Common U-shaped Recognition Epitope on Interleukin-1 Receptor Surface

Interleukin-1 (IL-1) plays a central role in the regulation of immune and inflammatory responses. There are two forms of IL-1 agonists (IL-1α and IL-1β) and one form of IL-1 antagonist (IL-1Ra); they share a similar binding mode to IL-1 receptor (IL-1R) but exhibit opposite biological functions on the receptor. In this study, the intermolecular interactions of IL-1R receptor with IL-1α, IL-1β and IL-1Ra ligands were systematically investigated at structural, energetic and dynamic levels. It was found that the receptor primarily adopts a U-shaped, double-stranded and linear/conformational-hybrid epitope to commonly interact with the three ligands. The epitope covers a common protein segment (residues 107-127), which is fully located within in the C2T2 subsdomain of IL-1R extracellular domain (ECD) and contributes ~40% to the total binding energy of IL-1R/ligand association. The epitope is natively folded into an ordered conformation in IL-1R protein context but would become largely disordered out of the context. Here, we adopted a disulfide bridge to staple U-shaped epitope-derived peptides, which can be effectively constrained into a native-like conformation and thus exhibit an improved affinity to ligands as compared to their unstapled counterpart, with affinity increase by up to ~15-fold. These disulfide bridges were designed to point out of ligand/peptide complex interface and thus would not disrupt the direct complex interaction. Energetic decomposition imparted that the stapling has only a modest influence on the interaction enthalpy and desolvation effect of ligand/peptide binding, but can substantially reduce entropy penalty upon the binding. For a peptide, the stapling-addressed entropic reduction can be roughly regarded as a constant, which only improves peptide affinity to these ligands, but does not change peptide selectivity over different ligands. This article is protected by copyright. All rights reserved.

Interleukin-25 recognition by its unique receptor IL-17Rb via two discrete linear and cyclic epitopes

Interleukin-17 (IL-17) is a family of pro-inflammatory cytokines and has been involved in the pathogenesis of chronic inflammatory and autoimmune diseases. The IL-17E, also known as IL-25, is a distinct member of this family that binds to its unique receptor IL-17Rb to induce the activation of nuclear factor kappa-light-chain enhancer of activated B cells. Here, we systematically examined the intermolecular recognition and association of IL-25 with IL-17Rb and demonstrated that the IL-25 primarily adopts two discrete linear and cyclic epitopes to interact with IL-17Rb. The two epitopes are separately located in the monomers 1 and 2 of IL-25 homodimer and cover sequences ¹²⁵ DPRGNSELLYHN¹³⁶ and ⁷⁷ ELDRDLNRLPQDLY⁹⁰ . They totally contribute 71.6% binding energy to the full-length IL-25. The linear epitope targets a site spanning over the extracellular fnIIID1 and fnIIID2 domains of IL-17Rb, while the cyclic epitope primarily binds at the fnIIID1 domain. In addition, we also found that the linear and cyclic epitopes are natively folded into ordered single-stranded and double-stranded conformations in IL-25 protein context, respectively, but would become largely disordered when splitting from the context to be free peptides, which, however, cannot bind effectively to IL-17Rb as them in the native state. In this respect, we extended the cyclic epitope to cover the whole IL-25 double-stranded region and added a disulfide bridge across its two strands at three selected anchor residue pairs. It is revealed that the disulfide-stapled peptides can be constrained into a native-like conformation and thus exhibit an improved binding potency to IL-17Rb as compared to their unstapled counterpart.

Computational design and experimental substantiation of conformationally constrained peptides from the complex interfaces of transcriptional enhanced associate domains with their cofactors in gastric cancer

Transcriptional enhanced associate domains (Teads) are the downstream effectors of the hippo signaling pathway and have been recognized as attractive druggable targets of gastric cancer. The biological function of Teads is regulated by diverse cofactors. In this study, the intermolecular interactions of Teads with their cognate cofactors were systematically characterized at structural, thermodynamic and dynamic levels. The Teads possess a double-stranded helical hairpin that is surrounded by three independent structural elements β-sheet, α-helix and Ω-loop of cofactor proteins and plays a central role in recognition and association with cofactors. A number of functional peptides were split from the hairpin region at Tead-cofactor complex interfaces, which, however, cannot maintain in native conformation without the support of protein context and would therefore incur a considerable entropy penalty upon competitively rebinding to the interfaces. Here, we further used disulfide and hydrocarbon bridges to cyclize and staple the hairpin and helical peptides, respectively. The chemical modification strategies were demonstrated to effectively constrain peptide conformation into active state and to largely reduce peptide flexibility in free state, thus considerably improving their affinity. Since the cyclization and stapling only minimize the indirect entropy cost but do not influence the direct enthalpy effect upon peptide binding, the designed conformationally constrained peptides can retain in their native selectivity over different cofactors. This is particularly interesting because it means that the cyclized/stapled, affinity-improved peptides can specifically compete with their parent Teads for the cofactor arrays as they share consistent target specificity.

Structure-based derivation and optimization of YAP-like coactivator-derived peptides to selectively target TEAD family transcription factors by hydrocarbon stapling and cyclization

Human transcriptional enhanced associate domain (TEAD) family consists of four paralogous transcription factors that function to modulate gene expression by interacting with YAP-like coactivators and have been recognized as potential therapeutic targets of diverse diseases including lung cancer and gastric tumor. Here, we attempt to explore the systematic interaction profile between the 4 TEAD proteins and the peptides derived from the binding sites of 8 known YAP-like coactivators, in order to analyze the binding affinity and recognition specificity of these peptides toward the TEAD family, and to design hydrocarbon-stapled/cyclized peptides that can target the specific interaction profile for each coactivator. Structural, energetic, and dynamic investigations of TEAD-coactivator interactions reveal that the coactivators adopt three independent secondary structure regions (β-strand, α-helix, and Ω-loop) to surround on the surface of TEAD proteins, in which the α-helical and Ω-loop regions are primarily responsible for the interactions. Five α-helical peptides and four Ω-loop peptides are derived from the 8 YAP-like coactivators, and their systematic binding profile toward the 4 TEAD proteins is created, and hydrocarbon stapling and cyclization strategies are employed to constrain the free α-helical and Ω-loop peptides into their native conformations, respectively, thus effectively promoting peptide binding to TEADs. The all-hydrocarbon and disulfide bridges are designed to point out the TEAD-peptide complex interface, which would not disrupt the direct intermolecular interaction between the TEAD and peptide. Therefore, the stapling and cyclization only improve peptide binding affinity to these TEADs, but do not alter peptide recognition specificity over different TEADs.

Revisiting bone morphogenetic protein-2 knuckle epitope and redesigning the epitope-derived peptides

The bone morphogenetic protein-2 (BMP2) plays a crucial role in bone formation, growth and regeneration, which adopts a conformational wrist epitope and a linear knuckle epitope to interact with its type-I (BRI) and type-II (BRII) receptors, respectively. In this study, we systematically examine the BRII-recognition site of BMP2 at structural, energetic and dynamic levels and accurately locate hotspots of the recognition at BMP2-BRII complex interface. It is revealed that the traditional knuckle epitope (BMP2 residue range 73-92) do fully match the identified hotspots; the BMP2-recognition site includes the C-terminal region of traditional knuckle epitope as well as its flanked β-strands. In addition, the protein context of full-length BMP2 is also responsible for the recognition by addressing conformational constraint on the native epitope segment. Therefore, we herein redefine the knuckle epitope to BMP2 residue range 84-102, which has a similar sequence length but is slid along the protein sequence by ~10 residues as compared to traditional knuckle epitope. The redefined one is also a linear epitope that is natively a double-stranded β-sheet with two asymmetric arms as compared to the natively single β-strand of the traditional version, although their sequences are partially overlapped to each other. It is revealed that the redefined epitope-derived peptide LN^84-102 exhibits an improved affinity by >3-fold relative to the traditional epitope-derived peptide KL^73-92 . Even so, the LN^84-102 peptide still cannot fully represent the BMP2 recognition event by BRII that has been reported to have a nanomolar affinity. We further introduce a disulfide bond across the two arms of double-stranded β-sheet to constrain the free LN^84-102 peptide conformation, which mimics the conformational constraint addressed by protein context. Consequently, several cyclic peptides are redesigned, in which the LN^84-102 (cyc89-101) is determined to exhibit a sub-micromolar affinity; this value is ~5-fold higher than its linear counterpart. Structural analysis also reveals that the cyclic peptide can interact with BRII in a similar binding mode with the redefined knuckle epitope region in full-length BMP2 protein.

Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner

Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.

Rational design and improvement of the dimerization-disrupting peptide selectivity between ROCK-I and ROCK-II kinase isoforms in cerebrovascular diseases

Human rho-associated coiled-coil forming kinases (ROCKs) ROCK-I and ROCK-II have been documented as attractive therapeutic targets for cerebrovascular diseases. Although ROCK-I and ROCK-II share a high degree of structural conservation and are both present in classic rho/ROCK signaling pathway, their downstream substrates and pathological functions may be quite different. Selective targeting of the two kinase isoforms with traditional small-molecule inhibitors is a great challenge due to their surprisingly high homology in kinase domain (~90%) and the full identity in kinase active site (100%). Here, instead of developing small-molecule drugs to selectively target the adenosine triphosphate (ATP) site of two isoforms, we attempt to design peptide agents to selectively disrupt the homo-dimerization event of ROCK kinases through their dimerization domains which have a relatively low conservation (~60%). Three helical peptides H1, H2, and H3 are split from the kinase dimerization domain, from which the isolated H2 peptide is found to have the best capability to rebind at the dimerization interface. A simulated annealing (SA) iteration method is used to improve the H2 peptide selectivity between ROCK-I and ROCK-II. The method accepts moderate degradation in peptide affinity in order to maximize the affinity difference between peptide binding to the two isoforms. Consequently, hundreds of parallel SA runs yielded six promising peptide candidates with ROCK-I over ROCK-II (I over II [IoII]) calculated selectivity and four promising peptide candidates with ROCK-II over ROCK-I (II over I [IIoI]) calculated selectivity. Subsequent anisotropy assays confirm that the selectivity values range between 13.2-fold and 83.9-fold for IoII peptides, and between 5.8-fold and 21.2-fold for IIoI peptides, which are considerably increased relative to wild-type H2 peptide (2.6-fold for IoII and 2.0-fold for IIoI). The molecular origin of the designed peptide selectivity is also analyzed at structural level; it is revealed that the peptide residues can be classified into conserved, non-conserved, and others, in which the non-conserved residues play a crucial role in defining peptide selectivity, while conserved residues confer stability to kinase-peptide binding.

Systematic profiling of clinical missence mutation effects on the intermolecular interaction between human growth hormone and its receptor in isolated growth hormone deficiency

Isolated growth hormone deficiency (IGHD) is the most common pituitary hormone deficiency and can result from congenital or acquired causes. Among the known factors, genetic mutations in human growth hormone (hGH) remain the most frequent cause of IGHD, which influence the binding of hGH to its cognate receptor (hGHbp). Although previous studies have systematically investigated the residue importance at hGH-hGHbp complex interface, the molecular role of IGHD-associated residue mutations in the complex function still remains largely unexplored. Here, a total of 21 known hGH naturally-occurring missence mutations that have been clinically observed to be involved in IGHD disorder are collected and confirmed by original literature; they effects on the conformation, energetics and dynamics of hGH-hGHbp recognition and interaction are dissected at molecular level by using atomistic dynamics simulations, binding energy calculations and fluorescence spectroscopy assays. A systematic profile of hGH-hGHbp binding response to these clinical missence mutations is created, based on which it is revealed that (i) most mutations have appreciably unfavorable effect on the binding, which potentially destabilize the complex interaction, while only very few are predicted as moderate stabilizers for the complex system, and (ii) these disease-related mutations can locate either at complex interface or in hGH protein interior far away from the interface; both can influence the complex binding through either direct interaction or indirect allostericity. Two mutations, E100K (non-interface) and G146R (interface), are identified to address potent destabilization effect on hGH-hGHbp complex system; they can reduce the complex binding affinity by 8-fold (K_d changes from 0.76 to 5.9 nM) and 46-fold (K_d changes from 0.76 to 34.7 nM), respectively.

Identification of a small-molecule compound that inhibits homodimerization of oncogenic NAC1 protein and sensitizes cancer cells to anticancer agents

Nucleus accumbens-associated protein-1 (NAC1) is a transcriptional repressor encoded by the NACC1 gene, which is amplified and overexpressed in various human cancers and plays critical roles in tumor development, progression, and drug resistance. NAC1 has therefore been explored as a potential therapeutic target for managing malignant tumors. However, effective approaches for effective targeting of this nuclear protein remain elusive. In this study, we identified a core unit consisting of Met⁷ and Leu⁹⁰ in NAC1's N-terminal domain (amino acids 1-130), which is critical for its homodimerization and stability. Furthermore, using a combination of computational analysis of the NAC1 dimerization interface and high-throughput screening (HTS) for small molecules that inhibit NAC1 homodimerization, we identified a compound (NIC3) that selectively binds to the conserved Leu-90 of NAC1 and prevents its homodimerization, leading to proteasomal NAC1 degradation. Moreover, we demonstrate that NIC3-mediated down-regulation of NAC1 protein sensitizes drug-resistant tumor cells to conventional chemotherapy and enhances the antimetastatic effect of the antiangiogenic agent bevacizumab both in vitro and in vivo These results suggest that small-molecule inhibitors of NAC1 homodimerization may effectively sensitize cancer cells to some anticancer agents and that NAC1 homodimerization could be further explored as a potential therapeutic target in the development of antineoplastic agents.

Is protein context responsible for peptide-mediated interactions?

Many cell signaling pathways are orchestrated by the weak, transient, and reversible peptide-mediated interactions (PMIs). Here, the role of protein context in contributing to the stability and specificity of PMIs is investigated systematically.

Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: A new strategy to improve therapeutic peptide activity against sepsis

Nrf2 is a critical regulator of innate immune response and survival during sepsis, which is constitutively degraded through binding to the Keap1 adapter protein of E3 ubiquitin ligase. Two linear peptides DLG and ETG derived from, respectively, the low-affinity and high-affinity motifs of Nrf2 binding site exhibit self-binding affinity to Keap1 central hole (active pocket); they can be exploited as therapeutic self-inhibitory peptides to disrupt the Nrf2-Keap1 interaction. Molecular dynamics simulation and binding energetics decomposition reveal that the two peptides possess large flexibility and intrinsic disorder in unbound free state, and thus would incur a considerable entropy penalty upon binding to Keap1. In order to improve Keap1-peptide binding affinity (or free energy ΔG), instead of traditionally increasing favorable enthalpy contribution (ΔH) we herein describe a rational peptide cyclization strategy to minimize unfavorable entropy penalty (ΔS) upon the binding of Nrf2-derived linear peptides to Keap1. Crystal structure analysis impart that the native active conformations of DLG and ETG peptides bound with Keap1 are folded into U-shape and hairpin configurations, respectively, and adopt their turning head to insert into the central hole of Keap1. Here, cyclization is designed by adding a disulfide bond across the two arms of DLG U-shape or ETG hairpin, which would not influence the direct intermolecular interaction between Keap1 and peptide as well as desolvation effect involved in the interaction, but can effectively constrain the conformational flexibility and disorder of the two peptides in free state, thus largely minimizing entropy penalty upon the binding. Both free energy calculation and binding affinity assay substantiate that the cyclization, as might be expected, can moderately or considerably enhance peptide binding potency to Keap1, with affinity (dissociation constant K_d) increase by 1.4-7.5-fold for designed cyclic peptides relative to their linear counterparts.