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Amyloid beta-peptide (Abeta) is implicated as the major causative agent in Alzheimer's disease (AD). Abeta is produced by the processing of the amyloid precursor protein (APP) by BACE1 (beta-secretase) and gamma-secretase. Many inhibitors have been developed for the secretases. However, the inhibitors will interfere with the processing of not only APP but also of other secretase substrates. In this study, we describe the development of inhibitors that prevent production of Abeta by specific binding to the beta-cleavage site of APP. We used the hydropathic complementarity (HC) approach for the design of short peptide inhibitors. Some of the HC peptides were bound to the substrate peptide (Sub W) corresponding to the beta-cleavage site of APP and blocked its cleavage by recombinant human BACE1 (rhBACE1) in vitro. In addition, HC peptides specifically inhibited the cleavage of Sub W, and not affecting other BACE1 substrates. Chemical modification allowed an HC peptide (CIQIHF) to inhibit the processing of APP as well as the production of Abeta in the treated cells. Such novel APP-specific inhibitors will provide opportunity for the development of drugs that can be used for the prevention and treatment of AD with minimal side effects.

A kinase-anchoring proteins (AKAPs) coordinate cAMP-mediated signaling by binding and localizing cAMP-dependent protein kinase (PKA), using an amphipathic helical docking motif. Peptide disruptors of PKA localization that mimic this helix have been used successfully to assess the involvement of PKA in specific signaling pathways. However, these peptides were developed as disruptors for the type II regulatory subunit (RII) even though both RI and RII isoforms can bind to AKAPs and have discrete functions. To evaluate the effects of each localized isoform, we designed peptides that specifically bind to either RI or RII. Using a peptide array, we have defined the minimal binding sequence of dual specific-AKAP 2 ( d -AKAP2), which binds tightly to both RI and RII. Side-chain requirements for affinity and isoform specificity were evaluated by using a peptide substitution array where each position along the A kinase binding domain of d -AKAP2 was substituted by the other 19 l -amino acids. This array comprises 513 single-site substitution analogs of the d -AKAP2 sequence. Peptides containing single and multiple mutations were evaluated in a quantitative fluorescence binding assay and a cell-based colocalization assay. This strategy has allowed us to design peptides with high affinity ( K D = 1–2 nM) and high specificity for RIα versus RIIα. These isoform-specific peptides will be invaluable tools to evaluate functional differences between localized RI and RII PKA and are RIα-specific disruptors. This array-based analysis also provides a foundation for biophysical analysis of this docking motif.

The X-ray crystal structure of a complex between the human class II major histocompatibility complex (MHC) protein HLA-DR1 and a bispyrrolinone−peptide hybrid ligand has been determined to 2.7 A resolution. The bispyrrolinone segment of the ligand closely mimics the polyproline type II conformation of peptide ligands bound to class II MHC molecules, emphasizing the considerable versatility of this peptidomimetic scaffold. Most hydrogen bonds conserved in all peptide/class II complexes are formed, and the side chains of the bispyrrolinone segment project into the same spaces as those occupied by side chains of bound peptides. Molecular modeling used in the design of the hybrid ligand was remarkably accurate in predicting the observed molecular interactions.

1,2,5-Thiadiazolidin-3-one 1,1-dioxide derivatives (±)-1a – d and (±)-2 were designed by molecular modeling as MHC (major histocompatibility complex) class-II inhibitors. They were prepared from the unsymmetrically N,N′-disubstituted acyclic sulfamides (±)-4a – d (Scheme 1) and (±)-11 (Scheme 2). These N-alkyl-N′-arylsulfamide precursors were synthesized by nucleophilic substitution of either a sulfamoyl-chloride or a N-sulfamoyloxazolidinone. Extension of base-induced cyclization methods from aliphatic to aromatic sulfamides gave access to the desired target molecules. The N-alkyl-1,2,5-thiadiazolidin-3-one 1,1-dioxide derivatives (±)-3a – c were also prepared by the oxazolidinone route (Scheme 4) for coupling to a tetrapeptide fragment. The X-ray crystal structure of 1,2,5-thiadiazolidin-3-one 1,1-dioxide (±)-21a was solved, and the directionality of the H-bond donor (N−H) and acceptor (SO2) groups of the cyclic scaffold determined (Figs. 1 and 2). The pKa value of the N−H group in (±)-21a was determined by 1H-NMR titration as 11.9 (Fig. 3). Compounds (±)-1a – d were shown to inhibit competition peptide binding to HLA-DR4 molecules in the single-digit millimolar concentration range.

The design and synthesis of two pyrrolinone−peptide hybrid ligands (3 and 20) for the rheumatoid arthritis-associated class II MHC HLA-DR1 protein are described. The hybrids incorporate bispyrrolinones 4 and 21 as tetrapeptide mimics for amino acids VKQN (residues 309−312) of the virus hemagglutinin peptide HA 306−318 (PKYVKQNTLKLAT). Ligand construction employed our polypyrrolinone synthetic protocol, in conjunction with Fmoc-based solid-phase peptide synthesis. Bioaffinity studies reveal that hybrid ligand 3 bound the HLA-DR1 protein with affinity (IC50 = 137 nM) comparable to those of both the native HA 306−318 peptide (IC50 = 89 nM) and a control peptide (IC50 = 176 nM). This result demonstrates that the polypyrrolinone scaffold can be employed in the construction of bioactive peptide hybrid ligands, thus considerably expanding the scope and utility of the pyrrolinone scaffold.

A compendium of compounds designed as dipeptide mimetics was collected from the literature. Conformational space available to these molecules was evaluated to obtain distance and torsion angle parameters to aid in selection of mimetics for specific target peptides or to explore diversity strategies. Conformations were searched using the RandomSearch algorithm in SYBYL. Data were collected for conformations of each molecule falling within 5 kcal/mol of the minimum. The distance between capping groups on the N- and C-termini of the molecules was measured as well as the pseudotorsion angle about a virtual bond between these two points. Molecules are classified based on the torsion angle space occupied and range of distances spanned by the resulting conformations. A large percentage of the dipeptide mimetics studied here have redundant conformational properties. The distribution of distances for all molecules covers an overall range of 3–15 A, the majority falling between 5–8 A. The angles for the majority of the molecules cover a wide range of torsional space with essentially no gaps in the values they can occupy, although these molecules can be subdivided by the average distance spanned by the allowed conformations. A smaller group of molecules have torsion angles that are restricted to a range of ±60° about the cis position (0°). Representative examples of each group are shown. We conclude that despite the significant effort to devise unique molecular structures as dipeptide mimetics, there is a need for more conformationally restricted compounds to mimic specific peptide conformations, and to complement molecular diversity strategies. © 1997 John Wiley & Sons, Inc. Biopoly 43: 191–217, 1997

Peptide mimetics of thyrotropin-releasing hormone (TRH) in which the peptide backbone is replaced by cyclohexane were synthesized from the cyclohexenone precursor 7. The aromatic side chains of the mimetics were derived from the corresponding aldehydes which were attached to the cyclohexenone via the Wittig reagent 8. The TRH mimetics are active in a mouse model of cognitive performance.

The cyclic peptide 1 , containing a 2,7-disubstituted naphthalene spacer, was designed to mimic an exposed Ω-loop present in interleukin-1α, an important mediator of immune and inflammatory responses. The synthesis of this cyclic peptide was accomplished via solution phase fragment condensation methodology. The three dimensional characterization using 2D-NMR techniques revealed it to be an excellent mimic for the Ω-loop sequence 41–48 in interleukin -1α.

A nine-membered-ring lactam system (1) has been chosen as a framework for the development of non-peptide molecules to mimic structural features of peptide and protein {beta}-turns. The synthesis of model di- and tetrapeptide mimetics starting from 1,5-cyclooctadiene derivatives is reported. In the model dipeptide mimetic (9), the amide linkages is trans (NMR, X-ray) and functional groups at positions adjacent to the lactam amide bond correspond closely to the side-chain positions of residues i + 1 and i + 2 of classical type II{prime} {beta}-turns. In the model tetrapeptide mimetic (30), all four side chains of low-energy trans amide conformers of the mimetic are well matched to their peptide counterparts.

We previously identified TRAIL-inducing compound 10 (TIC10), also known as NSC-350625, as a small molecule being developed under the name ONC201 that has potent anti-tumor efficacy and a benign safety profile in preclinical cancer models. Further investigation of the preclinical profile of this drug candidate led in early 2014 to the FDA acceptance of the investigational drug application (IND) for oral ONC201 to treat patients with advanced cancer. The initially disclosed chemical structure of ONC201 provided by Stahle et. al in an expired patent was described as an imidazo[1,2-a]pyrido[4,3-d]pyrimidine derivative. Our first report of its anticancer activity by Allen et. al. included mass spectrometry and 1H NMR that indicated both were consistent with the structure depicted by Stahle et. al and the National Cancer Institute. A recent publication reported that the structure of ONC201 differs from the initial description and is in fact an angular [3,4-e] isomer of the previously depicted structure. Here, we report X-ray crystallography and other structural studies of ONC201 produced by Oncoceutics in a dihydrochloride salt form for clinical use that confirm the angular [3,4-e] structure and indicate that the material is not a mixture of the two isomers. Furthermore, we confirm that although fragmentation by mass spectrometry for the isomers is identical, the angular [3,4-e] isomer can be definitively identified as ONC201 by implementing specific various spectroscopy techniques to identify differences between ONC201 and the linear isomer. In accordance with our structural analysis, in vitro activity assays in cancer cells indicate that the previously disclosed anti-cancer activity and mechanism of action are indeed associated exclusively with the [3,4-e] structure and not the [4,3-d] linear isomer. Together these studies confirm the angular [3,4-e] structure of ONC201 as the highly active and pure anti-cancer drug candidate that was utilized in prior preclinical pharmacology studies and is now entering clinical trials in several oncology indications. Citation Format: Jessica Wagner, Christina Leah Kline, Richard S. Pottorf, Bhaskara Rao Nallaganchu, Gary L. Olson, David T. Dicker, Joshua E. Allen, Wafik S. El-Deiry. Cytotoxicity, biochemical activity, and structural analysis of ONC201 and comparisons to a biologically inactive isomer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4499. doi:10.1158/1538-7445.AM2015-4499

Molecular features of ligand binding to MHC class II HLA-DR molecules have been elucidated through a combination of peptide structure-activity studies and structure-based drug design, resulting in analogues with nanomolar affinity in binding assays. Stabilization of lead compounds against cathepsin B cleavage by N-methylation of noncritical backbone NH groups or by dipeptide mimetic substitutions has generated analogues that compete effectively against protein antigens in cellular assays, resulting in inhibition of T-cell proliferation. Crystal structures of four ternary complexes of different peptide mimetics with the rheumatoid arthritis-linked MHC DRB10401 and the bacterial superantigen SEB have been obtained. Peptide-sugar hybrids have also been identified using a structure-based design approach in which the sugar residue replaces a dipeptide. These studies illustrate the complementary roles played by phage display library methods, peptide analogue SAR, peptide mimetics substitutions, and structure-based drug design in the discovery of inhibitors of antigen presentation by MHC class II HLA-DR molecules.

Previous work indicates that both the C-terminal phenylalanine amide and the tryptophan moieties of cholecystokinin (CCK) are critical pharmacophores for interaction with either the A or B receptor subtypes. We have examined a series of analogs of Ac-CCK-7 [Ac-Tyr(SO3H)-Met-Gly-Trp-Met-Asp-Phe33-NH2] (2) in which the phenyl ring of the C-terminal Phe-NH2 has been modified. Compounds were assessed in binding assays using homogenated rat pancreatic membranes and bovine striatum as the source of CCK-A and CCK-B receptors respectively and for anorectic activity after intraperitoneal administration to rats. Substitution of a number of cycloalkyl or bicyclic aryl moieties for the phenyl ring of phenylalanine33 including cyclopentyl (20), cyclohexyl (21), cyclooctyl (23), 2-(5,6,7,8-tetrahydro)naphthyl (26), 2-naphthyl (27), and 1-naphthyl (29) led to analogs with 10-70 times the anorectic potency of 2. The anorectic activity of 21 was blocked by the specific CCK-A receptor antagonist MK-329. Other bulky aliphatic groups in place of the phenylalanine33 aromatic ring such as isopropyl, 2-adamantyl and cyclohexylmethyl gave derivatives similar to 2 in potency. While most of the new compounds were comparable to CCK in binding assays, 23, 26, 27 and 29 were exceptionally potent with IC50s 10(-11)-10(-14) M in the pancreas. Compounds 23 and 29 were further evaluated for their ability to stimulate amylase secretion and found to have potencies similar to that of CCK. The dissociation between potency in the binding and amylase secretion assays suggests that they may interact with a high affinity binding site which is not coupled to amylase secretion. We conclude that CCK receptors possess a generous hydrophobic pocket capable of accommodating large alkyl groups in place of the side chain of phenylalanine33 and that the pharmacological profile of CCK analogs can be tailored by appropriate exploitation of this finding.

An efficient synthesis of all-(E) vitamin A acetate from 2,2,6-trimethyl-cyclohexanone has been achieved via the intermediacy of 1-(9-acetoxy-3, 7-dimethyl-nona-3,5,7-trien-1-ynyl)-2,2,6-trimethyl-cyclohexanol (25), readily prepared in high yield by allylic rearrangement of tertiary propenols with glacial acetic acid. The key step in the synthesis is the transformation of 25 to the unsaturated ketone 27 (9-acetoxy-3,7-dimethyl-1-(2,6,6-trimethyl-cyclohex-1-enyl)-nona-3,5,7-trien- 2-one) using a novel vanadium(V)-catalysed rearrangement reaction. The carbonyl in 27 affords the means for the essential isomerization of the adjacent double bond to the (E) isomer and the product is readily transformed into the polyene by reduction and elimination. An overall yield of 18–31% of vitamin A acetate from 2,2,6-trimethyl-cyclohexanone has been realized.