Rational Strategy for Designing Peptidomimetic Small Molecules Based on Cyclic Peptides Targeting Protein-Protein Interaction between CTLA-4 and B7-1.

Currently, various pharmaceutical modalities are being developed rapidly. Targeting protein-protein interactions (PPIs) is an important objective in such development. Cyclic peptides, because they have good specificity and activity, have been attracting much attention as an alternative to antibody drugs. However, cyclic peptides involve some difficulties, such as oral availability and cell permeability. Therefore, while small-molecule drugs still present many benefits, the screening of functional small-molecule compounds targeting PPIs requires a great deal of time and effort, including structural analysis of targets and hits. In this study, we investigated a rational two-step strategy to design small-molecule compounds targeting PPIs. First, we obtained inhibitory cyclic peptides that bind to cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) by ribosomal display using PUREfrex® (PUREfrex®RD) to get structure-activity relation (SAR) information. Based on that information, we converted cyclic peptides to small molecules using PepMetics® scaffolds that can mimic the α-helix or ß-turn of the peptide. Finally, we succeeded in generating small-molecule compounds with good IC50 (single-digit µM values) against CTLA-4. This strategy is expected to be a useful approach for small-molecule design targeting PPIs, even without having structural information such as that associated with X-ray crystal structures.

Visualized and Quantitative Conformational Analysis of Peptidomimetics.

Protein-protein interactions (PPIs) are fundamentally important and challenging drug targets. Peptidomimetic molecules of various types have been developed to modulate PPIs. A particularly promising drug discovery strategy, structural peptidomimetics, was designed based on special mimicking of side-chain Cα-Cß bonds. It is simple and versatile. Nevertheless, no quantitative method has been established to evaluate its similarity to a target peptide motif. We developed two methods that enable visual, comprehensive, and quantitative analysis of peptidomimetics: peptide conformation distribution (PCD) plot and peptidomimetic analysis (PMA) map. These methods specifically examine multiple side-chain Cα-Cß bonds of a peptide fragment motif and their corresponding bonds (pseudo-Cα-Cß bonds) in a mimetic molecule instead of φ and ψ angles of a single amino acid in the traditional Ramachandran plot. The PCD plot is an alignment-free method, whereas the PMA map is an alignment-based method providing distinctive and complementary analysis. Results obtained from analysis using these two methods indicate our multifacial α-helix mimetic scaffold 12 as an excellent peptidomimetic that can precisely mimic the spatial positioning of side-chain functional groups of α-helix. These methods are useful for visualized and quantified evaluation of peptidomimetics and for the rational design of new mimetic scaffolds.

Isostearyl Mixed Anhydrides for the Preparation of N-Methylated Peptides Using C-Terminally Unprotected N-Methylamino Acids.

Sustainable and efficient manufacturing methods for N-methylated peptides remain underexplored despite growing interest in therapeutic N-methylated peptides within the pharmaceutical industry. A methodology for the coupling of C-terminally unprotected N-methylamino acids mediated by an isostearic acid halide (ISTAX) and silylating reagent has been developed. This approach allows for the coupling of a wide variety of amino acids and peptides in high yields under mild conditions without the need for a C-terminal deprotection step in the process of C-terminal elongation. These advantages make this a useful synthetic method for the production of peptide therapeutics and diagnostics containing N-methylamino acids.

Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches.

Fibrodysplasia ossificans progressiva (FOP) is a rare but severe genetic disorder in which acute inflammation elicits progressive heterotopic ossification in the muscles, tendons, and ligaments. Classic FOP is caused by the R206H mutation in ALK2/ACVR1. While several activin receptor-like kinase 2 (ALK2) inhibitors were found to be efficacious in animal models of FOP, most of the ALK2 (R206H) inhibitors lacked sufficient oral bioavailability for efficacy. Previously, the synthesis of a series of novel bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitors that achieved both substantial potency and an improved ADMET profile was reported. In the present study, the detailed procedure of the in silico approach employed to identify the initial bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitor RK-59638 and the analysis of the ALK2 (R206H) RK-59638 complex structure to guide the synthetic optimization of the chemical series, obtaining RK-71807 showing improved potency and metabolic stability, were described. According to the initial in silico screening, the screening efficiencies and chemical diversity of the hit compounds of both ligand-based and structure-based methods were evaluated. Then, X-ray structures of ALK2 (R206H) and the inhibitors were analyzed to assess the structure-activity relationships of the synthesized compounds. The 3D-RISM analysis indicated the existence of the additional hydrogen bond via water molecules restricting the attachment point in the pyrazole scaffold. The quantum mechanics calculation of the newly determined ALK2 (R206H) RK-71807 complex structure using a fragment molecular orbital method and pair interaction energy decomposition analysis was employed to evaluate the interaction energies between the inhibitor and each of the amino acid residues and decompose them to electrostatic, exchange-repulsion, and charge transfer energies. The pattern of decomposed interaction energies was then compared to that formed by RK-59638 and LDN-193189 to investigate the structural basis of ALK2 (R206H) inhibition.

Bis-Heteroaryl Pyrazoles: Identification of Orally Bioavailable Inhibitors of Activin Receptor-Like Kinase-2 (R206H).

Mutant activin receptor-like kinase-2 (ALK2) was reported to be closely associated with the pathogenesis of fibrodysplasia ossificans progressiva (FOP) and diffuse intrinsic pontine glioma (DIPG), and therefore presents an attractive target for therapeutic intervention. Through in silico virtual screenings and structure-activity relationship studies assisted by X-ray crystallographic analyses, a novel series of bis-heteroaryl pyrazole was identified as potent inhibitors of ALK2 (R206H). Derived from in silico hit compound RK-59638 (6a), compound 18p was identified as a potent inhibitor of ALK2 (R206H) with good aqueous solubility, liver microsomal stability, and oral bioavailability.

Enantiospecific synthesis and filed evaluation of four stereoisomers of 10,14-dimethyloctadec-1-ene, a sex pheromone component secreted by female moths of the apple leafminer.

All four stereoisomers of 10,14-dimethyloctadec-1-ene, a sex pheromone component of the apple leafminer (Lyonetia prunifoliella: Lepidoptera), were synthesized starting from (R)- and (S)-propylene oxide by applying stereospecific inversion of chiral secondary tosylates as a key step. Field evaluation showed that male moths of the Japanese population were selectively attracted by the (10S,14S)-isomer and that the activity was not inhibited by the enantiomer.

Synthesis and field evaluation of stereoisomers and analogues of 5-methylheptadecan-7-ol, an unusual sex pheromone component of the lichen moth, Miltochrista calamina.

Females of the lichen moth, Miltochrista calamina (Arctiidae, Lithosiinae), were previously shown to produce 5-methylheptadecan-7-ol (1) as a sex pheromone. In field tests, males were attracted only by the (5R,7R)-isomer of the four stereoisomers that were prepared by separation from two mixtures of diastereoisomers. A new route to (5R,7R)-1 starting from (S)-propylene oxide was developed utilizing the SN2 reaction of an optically active secondary tosylate and the Jacobsen hydrolytic kinetic resolution of an epoxide intermediate as key steps. Enantioselective HPLC analysis of the product and the antipode synthesized from (R)-propylene oxide confirmed their high enantiomeric excess (> 99 %). Using this stereospecific synthesis, six analogues with the same configuration as (5R,7R)-1 but with different alkyl chain(s) connected to the stereogenic centers were prepared in order to obtain GC/MS data and to examine the ability of M. calamina males to discriminate between them. The mass spectra of the synthetic analogues revealed characteristic fragment ions derived by cleavage around the methyl group in addition to that at the hydroxyl group. In field trapping tests, five out of the six compounds were attractive to male M. calamina moths, indicating that the males distinguished the configurations of methyl and hydroxyl groups but were less able to perceive differences in the lengths of the two alkyl chains in the pheromone.

Improved synthesis of three methyl-branched pheromone components produced by the female lichen moth.

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produce a novel sex pheromone composed of three methyl-branched ketones: 6-methyl-2-octadecanone (I), 14-methyl-2-octadecanone (II), and 6,14-dimethyl-2-octadecanone (III). Their structures were confirmed by syntheses accomplished by a different route for each component. In order to obtain a sufficient amount of the synthetic pheromone, we developed new routes via methyl-branched 1-alkenes: 6-methyl-1-octadecene (1), 14-methyl-1-octadecene (2), and 6,14-dimethyl-1-octadecene (3). Compound 1 was synthesized by coupling between a C(10)-chain bromide and a 3-methyl-branched C(8) unit (A) prepared from 3-methyl-1,5-pentanediol, 2, by coupling between a C(11)-chain bromide and a 3-methyl-branched C(7) unit (B) prepared from 2-hexanone, and 3, by connecting A and B, using propargyl alcohol as a C(3) linchpin. The use of 3-chloro-1-propanol and tert-butyl acetoacetate as the linchpin was also examined to connect the two synthetic blocks in the synthesis of 3. Components I-III were obtained by Wacker oxidation of the corresponding 1-alkenes 1-3 in good yields.

Synthesis and field evaluation of methyl-branched ketones, sex pheromone components produced by Lithosiinae female moths in the family of Arctiidae.

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produce a novel sex pheromone composed of three methyl-branched ketones (I-III) in a ratio of 2:1:1. In order to confirm the structure of III (6,14-dimethyl-2-octadecanone), a mixture of its four stereoisomers was synthesized via chain elongation by two Wittig reactions, starting from 1,7-hexanediol. GC-MS data of the synthetic III were satisfactorily coincident with those of the natural component. In addition to the racemic mixtures of I (6-methyl-2-octadecanone) and II (14-methyl-2-octadecanone), previously synthesized, the activity of III was evaluated in the Iriomote Islands, and effective male attraction was observed for the 2:1:1 mixture of I-III. This result indicates that the females do not produce only one stereoisomer for each component or that the response of the males is not disturbed by the other stereoisomers of natural isomers produced by the females. The field test also revealed that the two-component lure of I and II captured as many males as the mixture of I-III, while lures baited with two components in other combinations and with only one component scarcely exhibited any male attraction ability.