An amide-to-chloroalkene substitution improves the peptide permeability

Sayuri Takeo, Chihiro Iio, Ai Sakakibara, Mio Takeda, Yuki Yamazaki, Kohei Sato, Nobuyuki Mase, Mizuki Watanabe, Tetsuo Narumi

Chem Rxiv, 2024. DOI: 10.26434/chemrxiv-2024-l36zv

This study highlights the novel application of Chloroalkene Dipeptide Isosteres (CADIs) in enhancing peptide membrane permeability. Replacing the peptide bond with CADIs in model dipeptides significantly improved passive permeability. This enhancement is attributed to the increased lipophilicity provided by the CADI substitution, as confirmed by AlogP calculations and HPLC retention times. Molecular dynamics simulations further indicated that CADI substitution reduces water interaction, potentially lowering hydration energy. Our findings demonstrate that CADI incorporation can effectively improve the permeability of peptides, offering a valuable approach for developing bioactive peptidomimetics with enhanced pharmacological properties including permeability and hydrolytic stability.

Identification of Peptide-Based Hepatitis B Virus Capsid Inhibitors Based on the Viral Core Protein

Kazutoshi Kawahara, Junko Fujimoto, Sayuri Takeo, Kohei Sato, Kenji Nakashima, Nobuyuki Mase, Masaru Yokoyama, Tetsuro Suzuki, Tetsuo Narumi 

Bioorg. Med. Chem. Lett. (accepted)

(Chemrxiv, DOI: https://doi.org/10.26434/chemrxiv-2024-p5jb1)

In this study, we have identified two novel peptides, 19Ac (comprising residues 91-105) and 20Ac (encompassing residues 96-110), from a systematically designed peptide library based on the Hepatitis B virus (HBV) core protein, that inhibit the assembly of HBV capsid. Peptide 20Ac exhibited about twofold the inhibitory potency of 19Ac and proved effective against both standard and morphothiadin (GLS4)-resistant HBV strains. Molecular dynamics simulations revealed that despite their overlapping sequence, 19Ac and 20Ac bonded to different regions of the core protein, thereby inhibiting capsid assembly through distinct mechanisms. These peptides could serve as valuable seed compounds for the further development of HBV capsid inhibitors, including GLS4-resistant strains.

Development of Novel Amino Acids Containing N-mercaptophenetyl (MPE)-type Auxiliary and Orthogonal Protecting Groups for Sequential Ligation of Multiple Peptides

Yoshinori Taguchi, Kohei Watanabe, Kohei Sato, Nobuyuki Mase, Tetsuo Narumi

ChemistrySelect 2024, 9, e202402339.

Novel amino acids containing N-mercaptophenethyl-type auxiliary and orthogonal protecting groups (tert-butyloxycarbonyl (Boc), 1,3-thiazolidine-4-carbonyl (Thz), and allyloxycarbonyl (Alloc)) were developed and applied to sequential ligation of multiple peptides in a one-pot fashion. The combination of these acids enables the synthesis of a branched peptide featuring a lysine side chain.

Substitution Effects of Alkene Dipeptide Isosteres on Adjacent Peptide Bond Rotation

Chihiro Iio, Kohei Sato, Nobuyuki Mase, Tetsuo Narumi

Chem. Pharm. Bull. 2024, 72, 596-599.

Alkene dipeptide isosteres (ADIs) are promising surrogates of peptide bonds that enhance the bioactive peptide resistance to enzymatic hydrolysis in medicinal chemistry. In this study, we investigated the substitution effects of an ADI on the energy barrier of cis–trans isomerization in the acetyl proline methyl ester (Ac-Pro-OMe) model. The (E)-alkene-type proline analog, which favors a cis-amide conformation, exhibits a lower rotational barrier than native Ac-Pro-OMe. A van’t Hoff analysis suggests that the energy barrier is primarily reduced by enthalpic repulsion. It was concluded that although carbon–carbon double bonds and pyrrolidine rings individually increase the rigidity of the incorporation site, their combination can provide structural flexibility and disrupt bioactive conformations. This work provides new insights into ADI-based drug design.

Amide-to-chloroalkene substitution for overcoming intramolecular acyl transfer challenges in hexapeptidic neuromedin U receptor 2 agonists

Tetsuo Narumi, Daichi Toyama, Junko Fujimoto, Ryuji Kyan, Kohei Sato, Kenji Mori, James T. Pearson, Nobuyuki Mase, Kentaro Takayama

Chem. Commun. 2024, 60, 3563-3566.

CPN-116 is a peptidic agonist that activates human neuromedin U receptor type 2 (NMUR2) but suffers from chemical instability due to inherent backbone isomerization on the Dap residue. To address this, a Leu-Dap-type (Z)-chloroalkene dipeptide isostere was synthesized diastereoselectively as a surrogate of the Leu-Dap peptide bond to develop a (Z)-chloroalkene analogue of CPN-116. The synthesized CPN-116 analogue is stable in 1.0 M phosphate buffer (pH 7.4) without backbone isomerization and can activate NMUR2 with similar potency to CPN-116 at nM concentrations (EC₅₀ = 1.0 nM).

Late-Stage Derivatization of Oleanolic Acid-Based Anti-HIV-1 Compounds

Reon Takeuchi, Junko Fujimoto, Yoshinori Taguchi, Ryuji Ide, Ryuji Kyan, Kohei Sato, Nobuyuki Mase, Masaru Yokoyama, Shigeyoshi Harada, Tetsuo Narumi

Chem. Pharm. Bull. 2024, 72, 330-335.

A 12-keto-type oleanolic acid derivative (4) has been identified as a potent anti-human immunodeficiency virus type-1 (HIV-1) compound that demonstrates synergistic effects with several types of HIV-1 neutralizing antibodies. In the present study, we used a common key synthetic intermediate to carry out the late-stage derivatization of an anti-HIV compound based on the chemical structure of a 12-keto-type oleanolic acid derivative. To execute this strategy, we designed a diketo-type oleanolic acid derivative (5) for chemoselective transformation, targeting the carboxy group and the hydroxyl group on the statine unit, as well as the 3-carbonyl group on the oleanolic acid unit, as orthogonal synthetic handles. We carried out four types of chemoselective transformations, leading to identification of the indole-type derivative (16) as a novel potent anti-HIV compound. In addition, further optimization of the β-hydroxyl group on the statine unit provided the R-4-isobutyl γ-amino acid-type derivative (6), which exhibited potent anti-HIV activity comparable to that of 4 but with reduced cytotoxicity.

Peptidomimetic Catalysts as Chemical Probes of Weak Intermolecular Forces: An Insight into The N-H…Cl-C H-Bonding Interaction

Chihiro Iio, Takuma Nishizawa, Takuya Chiba, Junko Fujimoto, Yuki Kodama, Kohei Sato, Nobuyuki Mase, Tetsuo Narumi

ChemRxiv, 2023. DOI: 10.26434/chmrxiv-2023-zp00r

Despite the widespread use of amide bond isosteres, there is only a limited understanding of their H-bonding mimicry of amides. With experimental and computational approaches, we have explored the hydrogen bonding acceptor potential of the chlorine substituent in chloroalkene dipeptide isosteres (CADIs). The (Z)-chloroalkene and (E)-methylalkene analogues of peptide catalysts were synthesized and employed as probe molecules to assess the H-bonding acceptor capabilities of CADIs. These peptidomimetic studies provide experimental evidence supporting the existence of an intermolecular H-bonding interaction between the chlorine substituent in CADIs and the amide proton of the carbamate substrate. These findings show the capability of peptide catalysts to experimentally evaluate weak intermolecular forces. DFT calculations elucidated that the chlorine substituent in CADIs prefers to form p-type hydrogen bonding interactions on the lateral portions of the chlorine atom, which is different from the carbonyl oxygen of amides which predominantly forms s-type H-bonds in peptide secondary structures.

Design, synthesis, and bio-evaluation of novel triterpenoid derivatives as anti-HIV-1 compounds

Reon Takeuchi, Kasumi Ogihara, Junko Fujimoto, Kohei Sato, Nobuyuki Mase, Kazuhisa Yoshimura, Shigeyoshi Harada, Tetsuo Narumi

Bioorganic & Medicinal Chemistry Letters  2022, 69, 128768.

https://doi.org/10.1016/j.bmcl.2022.128768

Two betulinic acid derivatives, RPR103611 (2) and IC9564 (3) were previously reported to be potent HIV-1 entry inhibitors. In this current study, a SAR study of the triterpenoid moiety of 2 and 3 has been performed and an oleanolic acid derivative (4) was identified as a novel HIV-1 entry inhibitor. In addition, the combination of 4 with several-type of HIV-1 neutralizing antibodies provided significant synergistic effects. The synthetic utility of the C=C double bond in the C-ring of 4 was also demonstrated to develop the 12-keto-type oleanolic acid derivative (5) as a potent anti-HIV compound. This simple transformation led to a significantly increased anti-HIV activity and a reduced cytotoxicity of the compound.

Synthesis and Structural Characterization of β-Turn Mimics Containing (Z)-Chloroalkene Dipeptide Isosteres

Yuki Kodama, Sayuri Takeo, Junko Fujimoto, Kohei Sato, Nobuyuki Mase, Tetsuo Narumi

J. Org. Chem. 2022, 87 (5), 2167–2177.

Described here is the synthetic, spectroscopic, crystallographic, and computational analysis of a series of peptidomimetics containing L-Xaa-D-Yaa-type (Z)-chloroalkene dipeptide isosteres (CADIs) that were measured in an investigation of the β-turn mimicry of this peptide bond surrogate. We found that the 1,3-allylic strain across the chloroalkene moiety engenders the hyperconjugative interactions between the chloroalkene moiety and the C–H bonding or antibonding orbitals of the C–H bonds in allylic positions. These effects contribute significantly to the stabilization of β-turn structures.