1 Ocak 2024 Dergi makalesi Açık Erişim

Yuce, Merve; Ates, Beril; Yasar, Nesrin Isil; Sungur, Fethiye Aylin; Kurkcuoglu, Ozge

MARC21 XML

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nam##2200000uu#4500</leader>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">user-tubitak-destekli-proje-yayinlari</subfield>
    <subfield code="o">oai:aperta.ulakbim.gov.tr:282493</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;The global antibiotic resistance problem necessitates fast and effective approaches to finding novel inhibitors to treat bacterial infections. In this study, we propose a computational workflow to identify plausible high-affinity compounds from FDA-approved, investigational, and experimental libraries for the decoding center on the small subunit 30S of the E. coli ribosome. The workflow basically consists of two molecular docking calculations on the intact 30S, followed by molecular dynamics (MD) simulations coupled with MM-GBSA calculations on a truncated ribosome structure. The parameters used in the molecular docking suits, Glide and AutoDock Vina, as well as in the MD simulations with Desmond were carefully adjusted to obtain expected interactions for the ligandrRNA complexes. A filtering procedure was followed, considering a fingerprint based on aminoglycoside's binding site on the 30S to obtain seven hit compounds either with different clinical usages or aminoglycoside derivatives under investigation, suggested for in vitro studies. The detailed workflow developed in this study promises an effective and fast approach for the estimation of binding free energies of large protein-RNA and ligand complexes.&lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">publication</subfield>
    <subfield code="b">article</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="a">Creative Commons Attribution</subfield>
    <subfield code="u">http://www.opendefinition.org/licenses/cc-by</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">Yuce, Merve</subfield>
    <subfield code="u">Istanbul Tech Univ, Dept Chem Engn, TR-34469 Istanbul, Turkiye</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="z">md5:dd1672062d5181e3aa0056173a044fdb</subfield>
    <subfield code="s">273</subfield>
    <subfield code="u">https://aperta.ulakbim.gov.trrecord/282493/files/bib-eaacde3e-9476-4c89-bf4c-0270a4b95d63.txt</subfield>
  </datafield>
  <controlfield tag="005">20250417233947.0</controlfield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2024-01-01</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.1016/j.jmgm.2024.108817</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of &lt;i&gt;E. coli&lt;/i&gt; ribosome</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="4">
    <subfield code="v">131</subfield>
    <subfield code="c">12</subfield>
    <subfield code="p">JOURNAL OF MOLECULAR GRAPHICS &amp; MODELLING</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Ates, Beril</subfield>
    <subfield code="u">Istanbul Tech Univ, Dept Chem Engn, TR-34469 Istanbul, Turkiye</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Yasar, Nesrin Isil</subfield>
    <subfield code="u">Istanbul Tech Univ, Informat Inst, Computat Sci &amp; Engn Div, Istanbul, Turkiye</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Sungur, Fethiye Aylin</subfield>
    <subfield code="u">Istanbul Tech Univ, Informat Inst, Computat Sci &amp; Engn Div, Istanbul, Turkiye</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Kurkcuoglu, Ozge</subfield>
    <subfield code="u">Istanbul Tech Univ, Dept Chem Engn, TR-34469 Istanbul, Turkiye</subfield>
  </datafield>
  <controlfield tag="001">282493</controlfield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-tubitak-destekli-proje-yayinlari</subfield>
  </datafield>
</record>