Yoshiaki Kiso

Nagahama Institute of Bio-Science and Technology, Нагахама, Shiga Prefecture, Japan

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Publications (377)871.23 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: We describe here the design, synthesis and biological evaluation of a series of molecules toward the development of novel peptidomimetic inhibitors of SARS-CoV 3CL(pro). A docking study involving binding between the initial lead compound 1 and the SARS-CoV 3CL(pro) motivated the replacement of a thiazole with a benzothiazole unit as a warhead moiety at the P1' site. This modification led to the identification of more potent derivatives, including 2i, 2k, 2m, 2o, and 2p, with IC(50) or K(i) values in the submicromolar to nanomolar range. In particular, compounds 2i and 2p exhibited the most potent inhibitory activities, with K(i) values of 4.1 and 3.1nM, respectively. The peptidomimetic compounds identified through this process are attractive leads for the development of potential therapeutic agents against SARS. The structural requirements of the peptidomimetics with potent inhibitory activities against SARS-CoV 3CL(pro) may be summarized as follows: (i) the presence of a benzothiazole warhead at the S1'-position; (ii) hydrogen bonding capabilities at the cyclic lactam of the S1-site; (iii) appropriate stereochemistry and hydrophobic moiety size at the S2-site and (iv) a unique folding conformation assumed by the phenoxyacetyl moiety at the S4-site.
    Bioorganic & medicinal chemistry 11/2012; 21(2). DOI:10.1016/j.bmc.2012.11.017 · 2.82 Impact Factor
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    ABSTRACT: Structure-activity relationships of cyclic peptides mimicking the β-hairpin structure of the 'dimerization arm' at residues 242-259 of the EGF receptor are examined. Cyclic peptides containing the arm head of the β-hairpin loop showed inhibitory activity toward the EGF receptor's dimerization. Cyclic peptides containing a Retro-Inverso sequence of the dimerization arm showed clear inhibitory effects on the dimerization in vitro and efficiently suppressed the proliferation of A431 cells, which abundantly express the EGF receptor on their surface. The effects at a specific hydrophobic site of the loop structure were expected to enhance the interactions with the receptor.
    Bioorganic & medicinal chemistry 08/2012; 20(19):5730-7. DOI:10.1016/j.bmc.2012.08.013 · 2.82 Impact Factor
  • Yoshio Hamada, Yoshiaki Kiso
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    ABSTRACT: Introduction: A bioisostere is a powerful concept for medicinal chemistry. It allows the improvement of the stability; oral absorption; membrane permeability; and absorption, distribution, metabolism and excretion (ADME) of drug candidate, while retaining their biological properties. The term 'bioisostere' is derived from 'isostere', whose physical and chemical properties, such as steric size, hydrophobicity, and electronegativity, are similar to those of a functional or atomic group, and is considered to possess biological properties. Here, the authors highlight the recent applications of bioisosteres in drug design, mainly based on our drug discovery studies. Areas covered: This review discusses the application of bioisosteres for novel drug discovery with focus on the authors' drug discovery studies such as renin, HIV-protease, and β-secretase inhibitors. The authors highlight that some bioisosteres can form the scaffolding for drug candidates, namely substrate transition state, amide/ester, and carboxylic acid bioisosteres. Moreover, the authors propose the new terms 'electron-donor bioisostere' and 'conformational bioisostere' for drug discovery. Expert opinion: The authors discuss the importance of bioisostere's design concept based on specific interaction with the corresponding biomolecule. In addition, some strategies for drug discovery based on the bioisostere concept are introduced. Many bioisosteres, which are recognized by corresponding target biomolecules as exhibiting similar biological properties, have been reported to date; most of the recently developed bioisosteres were designed by cheminformatics approaches. Some molecular design softwares and databases are introduced.
    Expert Opinion on Drug Discovery 08/2012; 7(10):903-22. DOI:10.1517/17460441.2012.712513 · 3.47 Impact Factor
  • ChemInform 06/2012; 43(25). DOI:10.1002/chin.201225259
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    ABSTRACT: KPU-105 (4), a potent anti-microtubule agent that contains a benzophenone was derived from the diketopiperazine-type vascular disrupting agent (VDA) plinabulin 3, which displays colchicine-like tubulin depolymerization activity. To develop derivatives with more potent anti-microtubule and cytotoxic activities, we further modified the benzophenone moiety of 4. Accordingly, we obtained a 4-fluorobenzophenone derivative 16j that inhibited tumor cell growth in vitro with a subnanomolar IC(50) value against HT-29 cells (IC(50)=0.5 nM). Next, the effect of 16j on mitotic spindles was evaluated in HeLa cells. Treatment with 3nM of 16j partially disrupted the interphase microtubule network. By contrast, treatment with the same concentration of CA-4 barely affected the microtubule network, indicating that 16j exhibited more potent anti-mitotic effects than did CA-4.
    Bioorganic & medicinal chemistry 06/2012; 20(14):4279-89. DOI:10.1016/j.bmc.2012.05.059 · 2.82 Impact Factor
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    ABSTRACT: Recently, we reported substrate-based pentapeptidic BACE1 inhibitors possessing a hydroxymethylcarbonyl isostere as a substrate transition-state mimic. These inhibitors showed potent inhibitory activities in enzymatic and cell assays. We also designed and synthesized non-peptidic and small-sized inhibitors possessing a heterocyclic scaffold at the P(2) position. By studying the structure-activity relationship of these inhibitors, we found that the σ-π interaction of an inhibitor with the BACE1-Arg235 side chain played a key role in the inhibition mechanism. Hence, we optimized the inhibitors with a focus on their P(2) regions. In this Letter, a series of novel BACE1 inhibitors possessing a 5-nitroisophthalic scaffold at the P(2) position are described along with the results of the related structure-activity relationship study. These small-sized inhibitors are expected improved membrane permeability and bioavailability.
    Bioorganic & medicinal chemistry letters 06/2012; 22(14):4640-4. DOI:10.1016/j.bmcl.2012.05.089 · 2.65 Impact Factor
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    ABSTRACT: Although it is known that neutrophils infiltrate damaged sites immediately after tissue injury, the endogenous factors that induce their acute transmigration and activation have not been thoroughly investigated. For the candidates of those factors, we recently discovered two novel neutrophil-activating cryptides, mitocryptide-1 (MCT-1) and mitocryptide-2 (MCT-2), hidden in mitochondrial proteins. In addition, many unknown neutrophil-activating peptides other than MCT-1 and MCT-2 were also observed during their purification. Here, we isolated and purified a novel neutrophil-activating peptide from porcine hearts, which we showed by structural analyses to have an identical primary structure to porcine mitochondrial cytochrome c (68-85). We named this novel functional octadecapeptide as mitocryptide-CYC (MCT-CYC). Structure-activity relationships of cytochrome c on β-hexosaminidase (β-HA) release from neutrophilic-differentiated HL- 60 cells demonstrated that peptides derived from the C-terminal part of cytochrome c induced β-HA release and that cytochrome c (70-85) was the most potent cryptide among them. Since cytochrome c is known to be involved in the apoptotic process, our results suggest that cryptides, including MCT-CYC, derived from mitochondrial cytochrome c are possible factors that induce scavenging of toxic debris produced from apoptotic cells by neutrophils.
    Protein and Peptide Letters 04/2012; 19(6):680-7. DOI:10.2174/092986612800494048 · 1.74 Impact Factor
  • Yoshio Hamada, Shoichi Ishiura, Yoshiaki Kiso
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    ABSTRACT: Recently, we reported substrate-based pentapeptidic β-secretase (BACE1) inhibitors with a hydroxymethylcarbonyl isostere as a substrate transition-state mimic. These inhibitors showed potent BACE1 inhibitory activity in enzyme and cell assays, with KMI-429 showing in vivo inhibition of Aβ production. We also designed and synthesized nonpeptidic and small-sized BACE1 inhibitors using "in-silico conformational structure-based design". By studying the structure-activity relationship of these inhibitors, we found that the σ-π interaction of an inhibitor with the BACE1-Arg235 side chain played a key role in the inhibition of BACE1. We speculated that a peptide capable of binding to the BACE1-Arg235 side chain via the σ-π interaction might exhibit BACE1 inhibitory activity. Hence, we designed and synthesized a series of peptides that were modified at the P2 position and found that some of these peptides exhibited a potent BACE1 inhibitory activity despite their structural similarity to the BACE1 substrate.
    ACS Medicinal Chemistry Letters 03/2012; 3(3):193-7. DOI:10.1021/ml2002373 · 3.07 Impact Factor
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    ABSTRACT: A series of (+)-negamycin 1 analogues were synthesized, and their readthrough-promoting activity was evaluated for nonsense mutations in Duchenne muscular dystrophy (DMD). A structure-activity relationship study indicated that 11b was the most potent drug candidate. Immunohistochemical analyses suggested that treatment with 11b restored dystrophin expression in mdx mice, a DMD mouse model. Furthermore, 11b decreased serum creatine kinase (CK) levels, an indicator of muscle fiber destruction. Most importantly, 11b demonstrated lower toxicity than 1, and thus, it could be a useful candidate for long-term treatment of DMD.
    ACS Medicinal Chemistry Letters 02/2012; 3:118-122. DOI:10.1021/ml200245t · 3.07 Impact Factor
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    ABSTRACT: Toward future applications to the discovery of drugs against membrane receptors on pathological cells, an intact-cell-based surface plasmon resonance (SPR) methodology has been developed. The injection of a suspension of epidermal carcinoma A431 cells (5×10(7)cells/ml), as an analyte, generated clear SPR responses to epidermal growth factor (EGF) immobilized on the sensor chip. Because the responses were competitively reduced by the free ligand EGF, added to the analyte cell suspension, they certainly reflect the specific interaction of the immobilized EGF with the extracellular region of its receptor, which is highly expressed on the surface of the A431 cells.
    Analytical Biochemistry 01/2012; 420(2):185-7. DOI:10.1016/j.ab.2011.09.022 · 2.31 Impact Factor
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    ABSTRACT: Plinabulin (11, NPI-2358) is a potent microtubule-targeting agent derived from the natural diketopiperazine "phenylahistin" (1) with a colchicine-like tubulin depolymerization activity. Compound 11 was recently developed as VDA and is now under phase II clinical trials as an anticancer drug. To develop more potent antimicrotubule and cytotoxic derivatives based on the didehydro-DKP skeleton, we performed further modification on the tert-butyl or phenyl groups of 11, and evaluated their cytotoxic and tubulin-binding activities. In the SAR study, we developed more potent derivatives 33 with 2,5-difluorophenyl and 50 with a benzophenone in place of the phenyl group. The anti-HuVEC activity of 33 and 50 exhibited a lowest effective concentration of 2 and 1 nM for microtubule depolymerization, respectively. The values of 33 and 50 were 5 and 10 times more potent than that of CA-4, respectively. These derivatives could be a valuable second-generation derivative with both vascular disrupting and cytotoxic activities.
    Journal of Medicinal Chemistry 12/2011; 55(3):1056-71. DOI:10.1021/jm2009088 · 5.48 Impact Factor
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    ABSTRACT: Previously reported pentapeptidic BACE1 inhibitors, designed using a substrate-based approach, were used as lead compounds for the further design of non-peptidic BACE1 inhibitors. Although these peptidic and non-peptidic inhibitors, with a hydroxymethylcarbonyl isostere as a substrate transition-state mimic, exhibited potent BACE1 inhibitory activities, their molecular-sizes appeared a little too big (molecular weight of >600daltons) for developing practical anti-Alzheimer's disease drugs. To develop lower weight BACE1 inhibitors, a series of tripeptidic BACE1 inhibitors were devised using a design approach based on the conformation of a virtual inhibitor bound to the BACE1 active site, also called 'in-silico conformational structure-based design'. Although these tripeptidic BACE1 inhibitors contained some natural amino acid residues, they are expected to be useful as lead compounds for developing the next generation BACE1 inhibitors, due to their low molecular size and unique structural features compared with previously reported inhibitors.
    Bioorganic & medicinal chemistry letters 12/2011; 22(2):1130-5. DOI:10.1016/j.bmcl.2011.11.102 · 2.65 Impact Factor
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    ABSTRACT: By using dimethylformamide to suppress the O-to-N acyl migration, we efficiently synthesized an O-acyl isopeptide by native chemical ligation of a peptide-thioester and a Cys-O-acyl isopeptide. The reaction mixture was then loaded onto an octadecylsilane reverse-phase HPLC column, and the isopeptide was purified by using a linear gradient of CH3CN in 0.1% aqueous trifluoroacetic acid. The recovery rate of the O-acyl isopeptide was considerably higher than that of the corresponding native polypeptide. Synthesis of O-acyl isopeptides via native chemical ligation, with O-to-N acyl migration as the final step to give the native form, has potential as an efficient method of constructing hydrophobic polypeptides.
    Tetrahedron Letters 12/2011; 52(52). DOI:10.1016/j.tetlet.2011.10.116 · 2.39 Impact Factor
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    ABSTRACT: Histo-aspartic protease (HAP) from Plasmodium falciparum is a promising target for the development of novel antimalarial drugs. The sequence of HAP is highly similar to those of pepsin-like aspartic proteases, but one of the two catalytic aspartates, Asp32, is replaced with histidine. Crystal structures of the truncated zymogen of HAP and of the complex of the mature enzyme with inhibitor KNI-10395 have been determined at 2.1 and 2.5 Å resolution, respectively. As in other proplasmepsins, the propeptide of the zymogen interacts with the C-terminal domain of the enzyme, forcing the N- and C-terminal domains apart, thereby separating His32 and Asp215 and preventing formation of the mature active site. In the inhibitor complex, the enzyme forms a tight domain-swapped dimer, not previously seen in any aspartic proteases. The inhibitor is found in an unprecedented conformation resembling the letter U, stabilized by two intramolecular hydrogen bonds. Surprisingly, the location and conformation of the inhibitor are similar to those of the fragment of helix 2 comprising residues 34p-38p in the prosegments of the zymogens of gastric aspartic proteases; a corresponding helix assumes a vastly different orientation in proplasmepsins. Each inhibitor molecule is in contact with two molecules of HAP, interacting with the carboxylate group of the catalytic Asp215 of one HAP protomer through a water molecule, while also making a direct hydrogen bond to Glu278A' of the other protomer. A comparison of the shifts in the positions of the catalytic residues in the inhibitor complex presented here with those published previously gives further hints regarding the enzymatic mechanism of HAP.
    Biochemistry 09/2011; 50(41):8862-79. DOI:10.1021/bi201118z · 3.38 Impact Factor
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    ABSTRACT: Previously, we reported potent pentapeptidic BACE1 inhibitors with the hydroxymethylcarbonyl isostere as a substrate transition-state mimic. To improve the in vitro potency, we further reported pentapeptidic inhibitors with carboxylic acid bioisosteres at the P(4) and P1' positions. In the current study, we screened new P1' position 1-phenylcycloalkylamine analogs to find non-acidic inhibitors that possess double-digit nanomolar range IC(50) values. An extensive structure-activity relationship study was performed with various amine derivatives at the P1' position. The most potent inhibitor of this pentapeptide series, KMI-1830, possessing 1-phenylcyclopentylamine at the P1' position had an IC(50) value of 11.6 nM against BACE1 in vitro enzymatic assay.
    Bioorganic & medicinal chemistry 09/2011; 19(17):5238-46. DOI:10.1016/j.bmc.2011.07.002 · 2.82 Impact Factor
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    ABSTRACT: Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1Å, respectively. The apoenzyme crystallized in the orthorhombic space group P2(1)2(1)2(1) with two molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4(3) with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.
    Journal of Structural Biology 07/2011; 175(1):73-84. DOI:10.1016/j.jsb.2011.04.009 · 3.37 Impact Factor
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    ABSTRACT: The recently identified E22Δ-type amyloid β peptide (Aβ) mutants are reported to favor oligomerization over fibrillization and to exhibit more-potent synaptotoxicity than does wild-type (WT) Aβ. Aβ(E22Δ) mutants can thus be expected to serve as tools for clarifying the impact of Aβ oligomers in Alzheimer's disease (or Alzheimer's-type dementia). However, the biochemical and biophysical properties of Aβ(E22Δ) have not been conclusively determined. Here, we evaluated the self-assembly pathways of Aβ(E22Δ) mutants generated from water-soluble, non-aggregative O-acyl isopeptide precursors. Circular dichroism spectroscopy, Western blot analysis, and thioflavin-T fluorescence intensity and cellular toxicity assays suggest that the self-assembly pathways of Aβ(E22Δ) differed from those of Aβ(WT). Aβ1-40(E22Δ) underwent a rapid random coil→β-sheet conformational change in its monomeric or low-molecular-weight oligomeric states, whereas Aβ1-40(WT) self-assembled gradually without losing its propensity to form random coil structures. The Aβ1-42(E22Δ) monomer formed β-sheet-rich oligomers more rapidly than did Aβ1-42(WT). Additionally, the Aβ1-42(E22Δ) oligomers appear to differ from Aβ1-42(WT) oligomers in size, shape, or both. These results should provide new insights into the functions of Aβ(E22Δ) mutants.
    Bioorganic & medicinal chemistry 06/2011; 19(12):3787-92. DOI:10.1016/j.bmc.2011.04.056 · 2.82 Impact Factor
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    ABSTRACT: A concise method was developed for quantifying native disulfide-bond formation in proteins using isotopically labeled internal standards, which were easily prepared with proteolytic ¹⁸O-labeling. As the method has much higher throughput to estimate the amounts of fragments possessing native disulfide arrangements by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) than the conventional high performance liquid chromatography (HPLC) analyses, it allows many different experimental conditions to be assessed in a short time. The method was applied to refolding experiments of a recombinant neuregulin 1-β1 EGF-like motif (NRG1-β1), and the optimum conditions for preparing native NRG1-β1 were obtained by quantitative comparisons. Protein disulfide isomerase (PDI) was most effective at the reduced/oxidized glutathione ratio of 2:1 for refolding the denatured sample NRG1-β1 with the native disulfide bonds.
    Protein Science 06/2011; 20(6):1090-6. DOI:10.1002/pro.637 · 2.86 Impact Factor
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    ABSTRACT: The O-acyl isopeptide (1) of islet amyloid polypeptide (IAPP), which contains an ester moiety at both Ala8-Thr9 and Ser19-Ser20, was prepared by sequential segment condensation based on the O-acyl isopeptide method. Isopeptide 1 possessed nonaggregative properties, retaining its random coil structure under the acidic conditions; this suggests that the insertion of the O-acyl isopeptide structures in IAPP suppressed aggregation of the molecule. As a result of the rapid O-to-N acyl shift of 1 under neutral pH, in situ-formed IAPP adopted a random-coil structure at the start of the experiment, and then underwent conformational change to α-helix/β-sheet mixed structures as well as aggregation. The click peptide strategy with the nonaggregative precursor molecule 1 could be a useful experimental tool to identify the functions of IAPP, by overcoming the handling difficulties that arise from IAPP's intense and uncontrollable self-assembling nature.
    ChemBioChem 05/2011; 12(8):1216-22. DOI:10.1002/cbic.201100025 · 3.06 Impact Factor

Publication Stats

6k Citations
871.23 Total Impact Points


  • 2011–2015
    • Nagahama Institute of Bio-Science and Technology
      Нагахама, Shiga Prefecture, Japan
  • 1986–2014
    • Toyohashi University of Technology
      • • Department of Environmental and Life Sciences
      • • Department of Ecological Engineering
      • • Faculty of Engineering
      Toyohasi, Aichi, Japan
  • 1984–2014
    • Kyoto Pharmaceutical University
      • • Laboratory of Medicinal Chemistry
      • • Center for Frontier Research in Medicinal Science
      • • Division of Medicinal Chemical Sciences
      Kioto, Kyōto, Japan
  • 2013
    • Peptide Institute, Inc.
      Ibaragi, Ōsaka, Japan
  • 2011–2013
    • Kobe Gakuin University
      • Faculty of Pharmaceutical Sciences
      Kōbe-shi, Hyogo-ken, Japan
  • 2012
    • University of Queensland
      • School of Chemistry and Molecular Biosciences
      Brisbane, Queensland, Australia
  • 1968–2009
    • Kyoto University
      • • Department of Medical Chemistry
      • • Division of Pharmaceutical Sciences
      • • Research Reactor Institute
      Kioto, Kyōto, Japan
  • 2008
    • Tokyo University of Pharmacy and Life Science
      • Department of Medicinal Chemistry
      Tokyo, Tokyo-to, Japan
    • University of Tsukuba
      • Institute of Applied Biochemistry
      Tsukuba, Ibaraki, Japan
  • 2001–2004
    • Osaka University of Pharmaceutical Sciences
      • Department of Physical Chemistry
      Takatuki, Ōsaka, Japan
  • 2002–2003
    • Johns Hopkins University
      • Department of Biology
      Baltimore, MD, United States
  • 2001–2002
    • Assiut University
      • Faculty of Pharmacy
      Asyūţ, Muhafazat Asyut, Egypt
  • 1999
    • Osaka University
      • Institute for Protein Research
      Suika, Ōsaka, Japan
  • 1996
    • University of Florida
      • Department of Materials Science and Engineering
      Gainesville, FL, United States