Takuya Kobayakawa

Stereoselective formation of trisubstituted (Z)-chloroalkenes adjacent to a tertiary carbon stereogenic center by organocuprate-mediated reduction/alkylation.

A robust and efficient method for the synthesis of trisubstituted (Z)-chloroalkenes is described. A one-pot reaction of γ,γ-dichloro-α,β-enoyl sultams involving organocuprate-mediated reduction/asymmetric alkylation affords α-chiral (Z)-chloroalkene derivatives in moderate to high yields with excellent diastereoselectivity, and allylic alkylation of internal allylic gem-dichlorides is also demonstrated. This study provides the first examples of the use of allylic gem-dichlorides adjacent to the chiral center for novel 1,4-asymmetric induction.

Remote Stereoinduction in the Organocuprate-Mediated Allylic Alkylation of Allylic gem-Dichlorides: Highly Diastereoselective Synthesis of (Z)-Chloroalkene Dipeptide Isosteres

Highly diastereoselective synthesis of (Z)-chloroalkene dipeptide isosteres has been achieved by 1,4-asymmetric induction in the organocuprate-mediated allylic alkylation adjacent to the chiral center of allylic gem-dichlorides. The reaction proceeds with a variety of heterocuprates prepared from CuCN and various organometallic reagents. It allows rapid construction of valuable architectures of L,D-type and L,L-type (Z)-chloroalkene dipeptide isosteres from the corresponding (E)- and (Z)-allylic gem-dichlorides in high yields, with excellent (Z)-selectivity and diastereoselectivity.

Low‐Molecular‐Weight CXCR4 Ligands with Variable Spacers

Low‐molecular‐weight CXCR4 ligands based on known lead compounds including the 14‐mer peptide T140, the cyclic pentapeptide FC131, peptide mimetics, and dipicolylamine‐containing compounds were designed and synthesized. Three types of aromatic spacers, 1,4‐phenylenedimethanamine, naphthalene‐2,6‐diyldimethanamine, and [1,1′‐biphenyl]‐4,4′‐diyldimethanamine, were used to build four pharmacophore groups. As pharmacophore groups, 2‐pyridylmethyl and 1‐naphthylmethyl are present in all of the compounds, and several aromatic groups and a cationic group from 1‐propylguanidine and 1,1,3,3‐tetramethyl‐2‐propylguanidine were also used. Several compounds showed significant CXCR4 binding affinity, and zinc(II) complexation of bis(pyridin‐2‐ylmethyl)amine moieties resulted in a remarkable increase in CXCR4 binding affinity.

Synthesis and Evaluation of Dimeric Derivatives of Diacylglycerol–Lactones as Protein Kinase C Ligands

Protein kinase C (PKC) mediates a central cellular signal transduction pathway involved in disorders such as cancer and Alzheimers disease. PKC is regulated by binding of the second messenger sn-1,2-diacylglycerol (DAG) to its tandem C1 domains, designated C1a and C1b, leading both to PKC activation and to its translocation to the plasma membrane and to internal organelles. Depending on the isoform, there may be differences in the ligand selectivity of the C1a and C1b domains, and there is different spacing between the C1 domains of the conventional and novel PKCs. Bivalent ligands have the potential to exploit these differences between isoforms, yielding isoform selectivity. In the present study, we describe the synthesis of a series of dimeric derivatives of conformationally constrained diacylglycerol (DAG) analogs (DAG-lactones). We characterize the derivatives in vitro for their binding affinities, both to a single C1 domain (the C1b domain of PKCδ) as well as to the conventional PKCα isoform and the novel PKCδ isoform, and we measure their abilities to cause translocation of PKCδ and PKCε in intact cells. The dimeric compound with the 10-carbon linker was modestly more effective for the isolated PKCδ C1b domain than was the monomeric compound. For the intact PKCα and PKCδ, the shortest DAG-lactone dimer had similar affinity to the monomer and affinity decreased progressively up to the 16-carbon linker. The dimeric derivatives did not cause the Golgi accumulation of PKCδ. The present results provide important insights into the development of new chemical tools for biological studies on PKC.

Conformational-Restricted Cyclic Peptides

Peptides are important biological molecules and have various physiological actions. Thus, these might be great candidates for drugs. Cyclic peptides are useful to find biologically active molecules because structural conformation of these compounds might be determined relatively easily, and especially cyclic pentapeptides are applicable as conformationally restricted templates. To date, several antihuman immunodeficiency virus (HIV) drugs such as reverse transcriptase inhibitors, protease inhibitors, and integrase inhibitors have been developed, and the use in combination of these drugs has brought great success in the treatment of HIV-infected and acquired immunodeficiency syndrome (AIDS) patients. We have developed several anti-HIV agents including CXCR4 antagonists, allosteric type integrase inhibitors, fusion inhibitors, vaccines, CD4 mimics, and matrix/capsid fragment peptides. These have been developed based on the corresponding peptides and proteins, and might be useful for an expansion of the drug repertoire. This chapter describes the development of CXCR4 antagonists based on conformational-restricted cyclic peptides. Bivalent CXCR4 ligands linked with two molecules of an FC131 derivative, [cyclo(–d–Tyr–Arg–Arg–Nal–d–Cys–)], connected by poly(l-proline) or PEGylated poly(l-proline) linkers having 5.5–6.5 nm lengths show maximum binding affinity for CXCR4, suggesting that the native state of the CXCR4 dimer has the distance between the ligand binding sites (5.5–6.5 nm). Fluorescent-labeled bivalent ligands are useful tools for the detection of cancer cells that overexpress CXCR4 on the surface. In addition, bivalent CXCR4 ligands linked with two molecules of a T140 derivative are expected as the therapeutic potential for cancer/leukemia.

Peptidomimetics That Mimic the Tertiary Structures of Peptides

In the previous chapter, peptidomimetics of secondary structures involving stapled peptides are described. This chapter introduces peptidomimetics of tertiary structures of peptides, which are also useful for the development of inhibitors of protein–protein interactions. The HIV-1 gp41 ectodomain contains N-terminal heptad repeat (NHR) (heptad repeat 1; HR1) and C-terminal heptad repeat (CHR) (heptad repeat 2; HR2) domains, both of which have helical structures. N36 or C34 is an NHR- or CHR-derived helical peptide, respectively. A three-helical bundle mimetic corresponding to the equivalent trimeric form of N36 was designed and synthesized. As a result, mice immunized with this N36 trimer mimetic induced neutralizing antibodies with higher binding affinity for the N36 trimer than that for the corresponding monomer. Furthermore, a three-helical bundle mimicking the equivalent trimeric form of C34 and the C34 dimer mimetic was designed and synthesized. As a result, the HIV-1 inhibitory potencies of the C34 trimer and dimer mimetics are one hundred times higher than that of the corresponding monomer. The NHR region is more suitable as a vaccine target than the CHR region while the CHR region is more suitable as an inhibitor target. In each case, the assembly of triple (or double)-helical peptides using a C 3-symmetric template is effective to remodel and mimic the natural tertiary structures of the proteins.

Introduction to Mid-size Drugs and Peptidomimetics

In the middle-size region, between small and macromolecules, there is an indispensable drug-like chemical space. These drugs with middle-size molecules are designated as mid-size drugs, which have the advantages that small and macromolecules possess and reduce the drawbacks. Peptide and peptide derivatives are mainly located in the above-mentioned middle-size region, and target not only the active centers of enzymes and pockets of receptors but also the protein–protein interactions because the mid-size drugs can cover target molecules broadly. Thus, the mid-size drugs might be expected as the next generation drugs. However, in therapeutical use of peptides, there is some limitation that involves several factors: low metabolic stability toward proteolysis, undesired activity resulting from interactions with several receptors, etc. Therefore, modifications of their structures for maintenance of biological activity have been considered and tried to develop peptidomimetics. Generally, peptidomimetics point peptide bond isosteres that mimic primary structures of peptides, such as transition-state mimics and ground-state mimics. As ground-state mimics, we have focused on the development of several alkene-type dipeptide isosteres (ADIs) such as chloroalkene dipeptide isosteres (CADIs). In the broad sense, peptidomimetics include mimetics of secondary and tertiary structures of peptides, which are useful for the development of inhibitors of protein–protein interactions.

Mid-size Drugs Based on Peptides and Peptidomimetics

In the middle-size region, between small and macromolecules, there is an indispensable drug-like chemical space. These drugs with middle-size molecules are designated as mid-size drugs, which have the advantages that small and macromolecules possess and reduce the drawbacks. Peptide and peptide derivatives are mainly located in the above-mentioned middle-size region, and target not only the active centers of enzymes and pockets of receptors but also the protein–protein interactions because the mid-size drugs can cover target molecules broadly. Thus, the mid-size drugs might be expected as the next generation drugs. However, in therapeutical use of peptides, there is some limitation that involves several factors: low metabolic stability toward proteolysis, undesired activity resulting from interactions with several receptors, etc. Therefore, modifications of their structures for maintenance of biological activity have been considered and tried to develop peptidomimetics. Generally, peptidomimetics point peptide bond isosteres that mimic primary structures of peptides, such as transition-state mimics and ground-state mimics. As ground-state mimics, we have focused on the development of several alkene-type dipeptide isosteres (ADIs) such as chloroalkene dipeptide isosteres (CADIs). In the broad sense, peptidomimetics include mimetics of secondary and tertiary structures of peptides, which are useful for the development of inhibitors of protein–protein interactions.

Chloroalkene Dipeptide Isosteres as Peptidomimetics

In drug discovery, the development of “isosteres”, in which a part of molecules is changed to their mimetic, is required to enhance the activity of seed or lead compounds. Alkene-type dipeptide isosteres (ADIs), which have been designed based on the ground-state mimics of amide bonds, are expected as useful “peptide bond isosteres” because of their high structural homology with natural dipeptides. Recently, our group has focused on the chloroalkene structure as a chemical equivalent of amide bond, and developed chloroalkene dipeptide isosteres (CADIs). Treatment of a γ,γ-dichloro-α,β-unsaturated ester, which was synthesized from a chiral sulfonamide and an aldehyde corresponding to the alkyl side chain of an amino acid, with higher order organocuprates has led to l-Xaa-Gly type isosteres. Treatment of allylic gem-dichlorides with lower order organocuprates provided the allylic alkylated compound in high yield and excellent diastereoselectivity. In addition, we have succeeded in the synthesis of several (l,d)- and (l,l)-type CADIs by switching olefin geometry of the substrate. Furthermore, we have succeeded in the application of a CADI. Utilizing this methodology, a CADI was incorporated into a cyclic RGD peptide. In addition, this cyclic RGD peptide mimic has shown higher activity than the parent cyclic peptide.

Conjugated Compounds Involving Peptides

Conjugated compounds, based on linking of some peptides and other peptides or small molecules, are important candidates for mid-size drugs. In this chapter, hybrid molecules of small CD4 mimics and peptidic coreceptor antagonists were designed and synthesized, and then evaluated as HIV entry inhibitors. In addition, overlapping libraries of fragment peptides of matrix (MA) and capsid (CA) proteins, which were conjugated with a cell membrane permeable signal, were prepared to discover potent lead compounds which express HIV inhibitory activity inside infectious cells.