The C-terminal self-binding helical peptide of human estrogen-related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists.

Orphan nuclear estrogen-related receptor γ (ERRγ) has been recognized as a potential therapeutic target for cancer, inflammation and metabolic disorder. The ERRγ contains a regulatory AF2 helical tail linked C-terminally to its ligand-binding domain (LBD), which is a self-binding peptide (SBP) and serves as molecular switch to dynamically regulate the receptor alternation between active and inactive states by binding to and unbinding from the AF2-binding site on ERRγ LBD surface, respectively. Traditional ERRγ modulators are all small-molecule chemical ligands that can be classified into agonists and inverse agonists in terms of their action mechanism; the agonists stabilize the AF2 in ABS site with an agonist conformation, while the inverse agonists lock the AF2 out of the site to largely abolish ERRγ transcriptional activity. Here, a class of ERRγ peptidic antagonists was described to compete with native AF2 for the ABS site, thus blocking the active state of AF2 binding to ERRγ LBD domain. Self-inhibitory peptide was derived from the SBP-covering AF2 region and we expected it can rebind potently to the ABS site by reducing its intrinsic disorder and entropy cost upon the rebinding. Hydrocarbon stapling was employed to do so, which employed an all-hydrocarbon bridge across the [i, i + 4]-anchor residue pair in the N-terminal, middle or C-terminal region of the self-inhibitory peptide. As might be expected, it is revealed that the stapled peptides are good binders of ERRγ LBD domain and can effectively compete with the native AF2 helical tail for ERRγ ABS site, which exhibit a basically similar binding mode with AF2 to the site and form diverse noncovalent interactions with the site, thus conferring stability and specificity to the domain-peptide complexes.

Molecular modeling and rational design of disulfide-stapled self-inhibitory peptides to target IL-17A/IL-17RA interaction.

Interleukin-17A (IL-17A) is a pro-inflammatory cytokine implicated in diverse autoimmune and inflammatory disorders such as psoriasis and Kawasaki disease. Mature IL-17A is a homodimer that binds to the extracellular type-III fibronectin D1:D2-dual domain of its cognate IL-17 receptor A (IL-17RA). In this study, we systematically examined the structural basis, thermodynamics property, and dynamics behavior of IL-17RA/IL-17A interaction and computationally identified two continuous hotspot regions separately from different monomers of IL-17A homodimer that contribute significantly to the interaction, namely I-shaped and U-shaped segments, thus rendered as a peptide-mediated protein-protein interaction (PmPPI). Self-inhibitory peptides (SIPs) are derived from the two segments to disrupt IL-17RA/IL-17A interaction by competitively rebinding to the IL-17A-binding pocket on IL-17RA surface, which, however, only have a weak affinity and low specificity for IL-17RA due to lack of the context support of intact IL-17A protein, thus exhibiting a large flexibility and intrinsic disorder when splitting from the protein context and incurring a considerable entropy penalty when rebinding to IL-17RA. The U-shaped segment is further extended, mutated and stapled by a disulfide bridge across its two strands to obtain a number of double-stranded cyclic SIPs, which are partially ordered and conformationally similar to their native status at IL-17RA/IL-17A complex interface. Experimental fluorescence polarization assays substantiate that the stapling can moderately or considerably improve the binding affinity of U-shaped segment-derived peptides by 2-5-fold. In addition, computational structural modeling also reveals that the stapled peptides can bind in a similar mode with the native crystal conformation of U-shaped segment in IL-17RA pocket, where the disulfide bridge is out of the pocket for avoiding intervene of the peptide binding.

Rational derivation, extension, and cyclization of self-inhibitory peptides to target TGF-ß/BMP signaling in ONFH.

The human transforming growth factor ß (TGF-ß)/bone morphogenic protein (BMP) signaling has been recognized as an attractive target to suppress fibroblast activation in osteonecrosis of the femoral head (ONFH). Here, we reported successful derivation of a self-inhibitory peptide from the crystal complex interface of TGF-ß with its cognate receptor TßRI using rational molecular design and in vitro binding assay. Computational modeling suggested that the peptide possesses a large flexibility and would incur considerable entropy penalty. To minimize the entropy effect, the peptide was extended and cyclized to obtain a modified version of cyclic peptide. Molecular dynamics (MD) simulations revealed that the cyclic peptide exhibits larger rigidity and lower thermal motion in unbound state as compared to its linear counterpart, thus causing less entropy penalty upon binding to TGF-ß. The computational findings were then substantiated by fluorescence polarization (FP) assays, that is, no binding affinity was detected for linear peptide (K d = n.d.), while cyclic version was determined to have a moderate affinity (K d = 76 ± 18 µM). Structural and energetic analysis identified two anchor residues Phe60 and Ser65 in cyclic peptide that can form a π-π stacking and a hydrogen bonding with the residues Trp30 and His68 of TGF-ß, respectively, conferring high stability and specificity to the complex system.

Structure-based rational design of self-inhibitory peptides to disrupt the intermolecular interaction between the troponin subunits C and I in neuropathic pain.

The troponin (Tn) is a ternary complex consisting of three subunits TnC, TnI and TnT; molecular disruption of the Tn complex has been recognized as an attractive strategy against neuropathic pain. Here, a self-inhibitory peptide is stripped from the switch region of TnI interaction interface with TnC, which is considered as a lead molecular entity and then used to generate potential peptide disruptors of TnC-TnI interaction based on a rational molecular design protocol. The region is a helical peptide segment capped by N- and C-terminal disorders. Molecular dynamics simulation and binding free energy analysis suggests that the switch peptide can interact with TnC in a structurally and energetically independent manner. Terminal truncation of the peptide results in a number of potent TnC binders with considerably simplified structure and moderately decreased activity relative to the native switch. We also employ fluorescence polarization assays to substantiate the computational findings; it is found that the rationally designed peptides exhibit moderate or high affinity to TnC with dissociation constants KD at micromolar level.

Rational design of EGFR dimerization-disrupting peptides: A new strategy to combat drug resistance in targeted lung cancer therapy.

Although a variety of tyrosine kinase inhibitors (TKIs) have been developed to target human epidermal growth factor receptor (EGFR) for lung cancer therapy, many patients treated with first-line small-molecule TKIs are clinically observed to eventually establish drug-resistant mutations T790 M and C797S around kinase active site, which play a primary role in development of acquired drug resistance to first-generation reversible and second-generation irreversible TKIs, respectively. Here, instead of developing small-molecule drugs to directly target the active site, we attempt to derive self-inhibitory peptides (SIPs) from the EGFR:EGFR asymmetric dimerization interface, where is separated from kinase active site and has a relatively low conservation as compared to the active site. It is found that the dimerization is a typical peptide-mediated protein interaction, where the first EGFR N-lobe adopts an N-terminal binding sequence (nBS) to interact with the dimerization interface of second EGFR C-lobe. A core binding sequence (nCBS, 676NQALLRILKE68) is identified in the nBS region as hotspot segment, which is then rationally optimized to generate a number of SIPs. Consequently, three designed SIPs are determined as promising candidates; they have high affinity to EGFR kinase domain, strong competitive potency with native nBS peptide for the dimerization interface, and effective cytotoxicity on human lung cancer cell lines. It is also demonstrated that these peptides are insensitive to drug-resistant EGFR T790 M/C797S mutation at molecular and cellular levels, and exhibit a good selectivity for EGFR over HER2 at molecular level.

Design, cyclization, and optimization of MMP13-TIMP1 interaction-derived self-inhibitory peptides against chondrocyte senescence in osteoarthritis.

The matrix metallopeptidase 13 (MMP13) is a central regulator of chondrocyte senescence that contributes to the development and progression of osteoarthritis (OA). In the present study, the native inhibitory structure of MMP13 in complex with its natural cognate inhibitor, the tissue inhibitor of metalloproteinases 1 (TIMP1), was modeled at atomic level using a grafting-based structural bioinformatics method with existing crystal structures. The modeled complex structure was then examined in detail, from which a TIMP1 inhibitory site that directly inserts into the active site of MMP13 enzyme was identified. The inhibitory site contains a coiled inhibitory loop (ILP) and a stretched N-terminal tail (NTT); they are highly structured in the intact MMP13-TIMP1 complex interface, but exhibit a large flexibility and intrinsic disorder when split from the interface context. In vitro binding assays demonstrated that the isolated ILP and NTT peptides cannot effectively rebind at the MMP13 active site (Kd > ~100 µM or = n.d.), although they have all key interacting residues in the enzyme inhibition. In silico simulations revealed that splitting of the peptide segments from TIMP1 inhibitory site does not influence the direct intermolecular interaction between MMP13 and the peptides substantially; instead, the large conformational flexibility of these isolated peptides in absence of interface context is primarily responsible for the affinity impairment, which would incur a considerable entropy penalty upon the peptide binding to MMP13. An extended version of ILP peptide, namely eILP (63TPAMESVCGY72), was redesigned with a rational strategy to derive a number of its cyclized counterparts by introducing a disulfide bridge across the peptide two-termini; the redesign reduces the peptide flexibility in free state and constrains the peptide pre-folding to a native-like conformation, which would help the peptide binding with minimized entropy penalty. Binding assays substantiated that the affinity Kd values of four designed cyclic peptides (, , and ) were improved to 23, 67, 42 and 18 µM, respectively, from the 96 µM of linear eILP peptide.

Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy.

The interaction event between programmed death receptor-1 (PD-1) and its ligand (PD-L1) functions as an essential immune checkpoint against cytotoxic T effector cell activation. Previously, a number of small-molecule inhibitors and antibody drugs have been successfully developed to block the PD1/PDL1 signaling axis for breast cancer immunotherapy. Here, we attempt to directly disrupt the formation of PD-1/PD-L1 complex by using a self-inhibitory peptide (SIP) strategy. In the procedure, the complex crystal structure is examined systematically with energetic analysis and alanine scanning. Two double-stranded segments I and II in PD-L1 active finger are identified as hotspot regions; they directly interact with the amphipathic pocket of PD-1 to form the complex system. The segments are derived from PD-L1 to define two SIP peptides, namely, DS-I and DS-II, which are thought to have capability of rebinding at the complex interface, thus disrupting PD-1/PD-L1 interaction as a new immune checkpoint blockade. A further analysis reveals that the free linear DS-I and DS-II peptides are highly flexible without protein context support, which would incur a large entropy penalty (unfavorable indirect readout effect) when rebinding to PD-1. Next, intramolecular cyclization is applied to constraining the intrinsically disordered conformation of free DS-II peptide into native ordered double-stranded configuration, which can be substantiated by molecular dynamics simulation and circular dichroism spectroscopy. Several cyclized counterparts of linear DS-II peptide are designed and their affinities to PD-1 are determined using fluorescence polarization assays. As might be expected, three designed cyclic peptides DS-II[c111-127], ΔDS-II[c111-127] and ΔDS-II[c110-128] exhibit considerably increased potency (Kd = 28.0 ±â€¯4.2, 17.5 ±â€¯3.1 and 11.6 ±â€¯2.3 µM, respectively) relative to linear DS-II peptide (Kd = 109 ±â€¯15 µM).

Rational redesign of a cation···π···π stacking at cardiovascular Fbw7-Skp1 complex interface and its application for deriving self-inhibitory peptides to disrupt the complex interaction.

The Fbw7-Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation ···π···π stacking system at the complex interface, which is formed by the Trp1159 residue of qGlu-peptide with the Lys2299 and His2359 residues of Fbw7 F-box domain. Both hybrid quantum mechanics/molecular mechanics (QM/MM) analysis of the real domain-peptide complex and electron-correlation ab initio calculation of the stacking system model suggested that the cation···π···π plays an important role in stabilizing the complex; substitution of peptide Trp1159 residue with aromatic Phe and Tyr would not cause a considerable effect on the configuration and energetics of cation···π···π stacking system, whereas His substitution seems to largely destabilize the system. Subsequently, the qGlu-peptide was stripped from the full-length Skp1 protein to define a so-called self-inhibitory peptide, which may rebind to the domain-peptide complex interface and thus disrupt the complex interaction. Fluorescence polarization (FP) assays revealed that the Trp1159Phe and Trp1159Tyr variants have a comparable or higher affinity (K d = 41 and 62 µM) than the wild-type qGlu-peptide (K d = 56 µM), while the Trp1159His mutation would largely impair the binding potency of qGlu-peptide to Fbw7 F-box domain (K d = 280 µM), confirming that the cation···π···π confers both affinity and specificity to the domain-peptide recognition, which can be reshaped by rational molecular design of the nonbonded interaction system. Graphical abstract Stereoview of the complex structure of Fbw7 with Skp1 (PDB: 2ovp), where the Trp1159 residue of Skp1 qGlu-peptide can form a cation···π···π stacking system with the Lys2299 and His2359 residues of Fbw7 F-box domain.

Derivation of Self-inhibitory Helical Peptides to Target Rho-kinase Dimerization in Cerebrovascular Malformation: Structural Bioinformatics Analysis and Peptide Binding Assay.

Rho-kinase dimerization is essential for its kinase activity and biological function; disruption of the dimerization has recently been established as a new and promising therapeutics strategy for cerebrovascular malformation (CM). Based on Rho-kinase dimer crystal structure we herein combined in silico analysis and in vitro assay to rationally derive self-inhibitory peptides from the dimerization interface. Three peptides namely Hlp1, Hlp2 and Hlp3 were successfully designed that have potential capability to rebind at the dimerization domain of Rho-kinase. Molecular dynamics (MD) simulations revealed that these peptides are helically structured when bound to Rho-kinase, but exhibit partially intrinsic disorder in unbound state. Binding free energy (BFE) analysis suggested that the peptides have a satisfactory energetic profile to interact with Rho-kinase. The computational findings were then substantiated by fluorescence anisotropy assays, conforming that the helical peptides can bind tightly to Rho-kinase with affinity KD at micromolar level. These designed peptides are considered as lead molecular entities that can be further modified and optimized to obtain more potent peptidomimetics as self-competitors to disrupt Rho-kinase dimerization in CM.

Structure-based design and confirmation of peptide ligands for neuronal polo-like kinase to promote neuroregeneration.

Neuronal polo-like kinase (nPLK) is an essential regular of cell cycle and differentiation in nervous system, and targeting nPLK has been established as a promising therapeutic strategy to treat neurological disorders and to promote neuroregeneration. The protein contains an N-terminal kinase domain (KD) and a C-terminal Polo-box domain (PBD) that are mutually inhibited by each other. Here, the intramolecular KD-PBD complex in nPLK was investigated at structural level via bioinformatics analysis, molecular dynamics (MD) simulation and binding affinity scoring. From the complex interface two regions representing separately two continuous peptide fragments in PBD domain were identified as the hot spots of KD-PBD interaction. Structural and energetic analysis suggested that one (PBD peptide 1) of the two peptides can bind tightly to a pocket nearby the active site of KD domain, which is thus potential as self-inhibitory peptide to target and suppress nPLK kinase activity. The knowledge harvesting from computational studies were then used to guide the structural optimization and mutation of PBD peptide 1. Consequently, two of three peptide mutants separately exhibited moderately and considerably increased affinity as compared to the native peptide. The computationally modeled complex structures of KD domain with these self-inhibitory peptides were also examined in detail to unravel the structural basis and energetic property of nPLK-peptide recognition and interaction.