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Design, synthesis, and biological evaluation of novel dipeptide-type SARS-CoV 3CL protease inhibitors: Structure–activity relationship study

Identifieur interne : 000F91 ( Pmc/Curation ); précédent : 000F90; suivant : 000F92

Design, synthesis, and biological evaluation of novel dipeptide-type SARS-CoV 3CL protease inhibitors: Structure–activity relationship study

Auteurs : Pillaiyar Thanigaimalai [Japon] ; Sho Konno [Japon] ; Takehito Yamamoto [Japon] ; Yuji Koiwai [Japon] ; Akihiro Taguchi [Japon] ; Kentaro Takayama [Japon] ; Fumika Yakushiji [Japon] ; Kenichi Akaji [Japon] ; Yoshiaki Kiso [Japon] ; Yuko Kawasaki [États-Unis] ; Shen-En Chen [États-Unis] ; Aurash Naser-Tavakolian [États-Unis] ; Arne Schön [États-Unis] ; Ernesto Freire [États-Unis] ; Yoshio Hayashi [Japon]

Source :

RBID : PMC:7115367

Abstract

This work describes the design, synthesis, and evaluation of low-molecular weight peptidic SARS-CoV 3CL protease inhibitors. The inhibitors were designed based on the potent tripeptidic Z-Val-Leu-Ala(pyrrolidone-3-yl)-2-benzothiazole (8; Ki = 4.1 nM), in which the P3 valine unit was substituted with a variety of distinct moieties. The resulting series of dipeptide-type inhibitors displayed moderate to good inhibitory activities against 3CLpro. In particular, compounds 26m and 26n exhibited good inhibitory activities with Ki values of 0.39 and 0.33 μM, respectively. These low-molecular weight compounds are attractive leads for the further development of potent peptidomimetic inhibitors with pharmaceutical profiles. Docking studies were performed to model the binding interaction of the compound 26m with the SARS-CoV 3CL protease. The preliminary SAR study of the peptidomimetic compounds with potent inhibitory activities revealed several structural features that boosted the inhibitory activity: (i) a benzothiazole warhead at the S1′ position, (ii) a γ-lactam unit at the S1-position, (iii) an appropriately hydrophobic leucine moiety at the S2-position, and (iv) a hydrogen bond between the N-arylglycine unit and a backbone hydrogen bond donor at the S3-position.


Url:
DOI: 10.1016/j.ejmech.2013.05.005
PubMed: 23747811
PubMed Central: 7115367

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PMC:7115367

Le document en format XML

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<name sortKey="Kiso, Yoshiaki" sort="Kiso, Yoshiaki" uniqKey="Kiso Y" first="Yoshiaki" last="Kiso">Yoshiaki Kiso</name>
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<name sortKey="Kawasaki, Yuko" sort="Kawasaki, Yuko" uniqKey="Kawasaki Y" first="Yuko" last="Kawasaki">Yuko Kawasaki</name>
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<name sortKey="Chen, Shen En" sort="Chen, Shen En" uniqKey="Chen S" first="Shen-En" last="Chen">Shen-En Chen</name>
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<name sortKey="Naser Tavakolian, Aurash" sort="Naser Tavakolian, Aurash" uniqKey="Naser Tavakolian A" first="Aurash" last="Naser-Tavakolian">Aurash Naser-Tavakolian</name>
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<wicri:regionArea>Department of Biology, Johns Hopkins University, Baltimore, MD</wicri:regionArea>
</affiliation>
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<name sortKey="Schon, Arne" sort="Schon, Arne" uniqKey="Schon A" first="Arne" last="Schön">Arne Schön</name>
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<nlm:aff id="aff3">Department of Biology, Johns Hopkins University, Baltimore, MD, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biology, Johns Hopkins University, Baltimore, MD</wicri:regionArea>
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<div type="abstract" xml:lang="en">
<p>This work describes the design, synthesis, and evaluation of low-molecular weight peptidic SARS-CoV 3CL protease inhibitors. The inhibitors were designed based on the potent tripeptidic Z-Val-Leu-Ala(pyrrolidone-3-yl)-2-benzothiazole (
<bold>8</bold>
;
<italic>K</italic>
<sub>
<italic>i</italic>
</sub>
 = 4.1 nM), in which the P3 valine unit was substituted with a variety of distinct moieties. The resulting series of dipeptide-type inhibitors displayed moderate to good inhibitory activities against 3CL
<sup>pro</sup>
. In particular, compounds
<bold>26m</bold>
and
<bold>26n</bold>
exhibited good inhibitory activities with
<italic>K</italic>
<sub>
<italic>i</italic>
</sub>
values of 0.39 and 0.33 μM, respectively. These low-molecular weight compounds are attractive leads for the further development of potent peptidomimetic inhibitors with pharmaceutical profiles. Docking studies were performed to model the binding interaction of the compound
<bold>26m</bold>
with the SARS-CoV 3CL protease. The preliminary SAR study of the peptidomimetic compounds with potent inhibitory activities revealed several structural features that boosted the inhibitory activity: (i) a benzothiazole warhead at the S1′ position, (ii) a γ-lactam unit at the S1-position, (iii) an appropriately hydrophobic leucine moiety at the S2-position, and (iv) a hydrogen bond between the
<italic>N</italic>
-arylglycine unit and a backbone hydrogen bond donor at the S3-position.</p>
</div>
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<journal-id journal-id-type="nlm-ta">Eur J Med Chem</journal-id>
<journal-id journal-id-type="iso-abbrev">Eur J Med Chem</journal-id>
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<article-id pub-id-type="pmc">7115367</article-id>
<article-id pub-id-type="publisher-id">S0223-5234(13)00305-X</article-id>
<article-id pub-id-type="doi">10.1016/j.ejmech.2013.05.005</article-id>
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<contrib contrib-type="author" id="au4">
<name>
<surname>Koiwai</surname>
<given-names>Yuji</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author" id="au5">
<name>
<surname>Taguchi</surname>
<given-names>Akihiro</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author" id="au6">
<name>
<surname>Takayama</surname>
<given-names>Kentaro</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author" id="au7">
<name>
<surname>Yakushiji</surname>
<given-names>Fumika</given-names>
</name>
<xref rid="aff1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author" id="au8">
<name>
<surname>Akaji</surname>
<given-names>Kenichi</given-names>
</name>
<xref rid="aff2" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author" id="au9">
<name>
<surname>Kiso</surname>
<given-names>Yoshiaki</given-names>
</name>
<xref rid="aff2" ref-type="aff">b</xref>
</contrib>
<contrib contrib-type="author" id="au10">
<name>
<surname>Kawasaki</surname>
<given-names>Yuko</given-names>
</name>
<xref rid="aff3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author" id="au11">
<name>
<surname>Chen</surname>
<given-names>Shen-En</given-names>
</name>
<xref rid="aff3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author" id="au12">
<name>
<surname>Naser-Tavakolian</surname>
<given-names>Aurash</given-names>
</name>
<xref rid="aff3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author" id="au13">
<name>
<surname>Schön</surname>
<given-names>Arne</given-names>
</name>
<xref rid="aff3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author" id="au14">
<name>
<surname>Freire</surname>
<given-names>Ernesto</given-names>
</name>
<xref rid="aff3" ref-type="aff">c</xref>
</contrib>
<contrib contrib-type="author" id="au15">
<name>
<surname>Hayashi</surname>
<given-names>Yoshio</given-names>
</name>
<email>yhayashi@toyaku.ac.jp</email>
<xref rid="aff1" ref-type="aff">a</xref>
<xref rid="cor1" ref-type="corresp"></xref>
</contrib>
</contrib-group>
<aff id="aff1">
<label>a</label>
Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan</aff>
<aff id="aff2">
<label>b</label>
Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan</aff>
<aff id="aff3">
<label>c</label>
Department of Biology, Johns Hopkins University, Baltimore, MD, USA</aff>
<author-notes>
<corresp id="cor1">
<label></label>
Corresponding author. Tel./fax: +81 42 676 3275.
<email>yhayashi@toyaku.ac.jp</email>
</corresp>
</author-notes>
<pub-date pub-type="pmc-release">
<day>20</day>
<month>5</month>
<year>2013</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub">
<month>7</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="epub">
<day>20</day>
<month>5</month>
<year>2013</year>
</pub-date>
<volume>65</volume>
<fpage>436</fpage>
<lpage>447</lpage>
<history>
<date date-type="received">
<day>11</day>
<month>3</month>
<year>2013</year>
</date>
<date date-type="rev-recd">
<day>20</day>
<month>4</month>
<year>2013</year>
</date>
<date date-type="accepted">
<day>7</day>
<month>5</month>
<year>2013</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright © 2013 Elsevier Masson SAS. All rights reserved.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Elsevier Masson SAS</copyright-holder>
<license>
<license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p>
</license>
</permissions>
<abstract id="abs0010">
<p>This work describes the design, synthesis, and evaluation of low-molecular weight peptidic SARS-CoV 3CL protease inhibitors. The inhibitors were designed based on the potent tripeptidic Z-Val-Leu-Ala(pyrrolidone-3-yl)-2-benzothiazole (
<bold>8</bold>
;
<italic>K</italic>
<sub>
<italic>i</italic>
</sub>
 = 4.1 nM), in which the P3 valine unit was substituted with a variety of distinct moieties. The resulting series of dipeptide-type inhibitors displayed moderate to good inhibitory activities against 3CL
<sup>pro</sup>
. In particular, compounds
<bold>26m</bold>
and
<bold>26n</bold>
exhibited good inhibitory activities with
<italic>K</italic>
<sub>
<italic>i</italic>
</sub>
values of 0.39 and 0.33 μM, respectively. These low-molecular weight compounds are attractive leads for the further development of potent peptidomimetic inhibitors with pharmaceutical profiles. Docking studies were performed to model the binding interaction of the compound
<bold>26m</bold>
with the SARS-CoV 3CL protease. The preliminary SAR study of the peptidomimetic compounds with potent inhibitory activities revealed several structural features that boosted the inhibitory activity: (i) a benzothiazole warhead at the S1′ position, (ii) a γ-lactam unit at the S1-position, (iii) an appropriately hydrophobic leucine moiety at the S2-position, and (iv) a hydrogen bond between the
<italic>N</italic>
-arylglycine unit and a backbone hydrogen bond donor at the S3-position.</p>
</abstract>
<abstract abstract-type="graphical" id="abs0015">
<title>Graphical abstract</title>
<fig id="undfig1" position="anchor">
<graphic xlink:href="fx1"></graphic>
</fig>
</abstract>
<abstract abstract-type="author-highlights" id="abs0020">
<title>Highlights</title>
<p>
<list list-type="simple" id="ulist0010">
<list-item id="u0010">
<label></label>
<p id="p0010">A series of dipeptide-type SARS CoV 3CL
<sup>pro</sup>
inhibitors were synthesized.</p>
</list-item>
<list-item id="u0015">
<label></label>
<p id="p0015">Compounds have shown significant inhibitory activity.</p>
</list-item>
<list-item id="u0020">
<label></label>
<p id="p0020">A potent compound was discovered by changing the P3 position.</p>
</list-item>
<list-item id="u0025">
<label></label>
<p id="p0025">Compounds
<bold>26m</bold>
and
<bold>26n</bold>
displayed potent inhibitory activities.</p>
</list-item>
</list>
</p>
</abstract>
<kwd-group id="kwrds0010">
<title>Keywords</title>
<kwd>SARS</kwd>
<kwd>SARS-CoV 3CL protease</kwd>
<kwd>Peptidomimetics</kwd>
<kwd>Dipeptide</kwd>
<kwd>Cysteine protease inhibitors</kwd>
<kwd>Docking study</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>

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