{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:35:44Z","timestamp":1793320544848,"version":"4.5.0"},"reference-count":58,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,1,24]],"date-time":"2022-01-24T00:00:00Z","timestamp":1642982400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"This research was supported by the Bio &amp; Medical Technology Development Program of the National Research Foundation (NRF) and funded by the Korean Government (MSIT)","award":["NRF-2018M3A9A7057263"],"award-info":[{"award-number":["NRF-2018M3A9A7057263"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Owing to several mutations, the oncogene Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) is activated in the majority of cancers, and targeting it has been pharmacologically challenging. In this study, using an in silico approach comprised of pharmacophore modeling, molecular docking, and molecular dynamics simulations, potential KRAS G12D inhibitors were investigated. A ligand-based common feature pharmacophore model was generated to identify the framework necessary for effective KRAS inhibition. The chemical features in the selected pharmacophore model comprised two hydrogen bond donors, one hydrogen bond acceptor, two aromatic rings and one hydrophobic feature. This model was used for screening in excess of 214,000 compounds from InterBioScreen (IBS) and ZINC databases. Eighteen compounds from the IBS and ten from the ZINC database mapped onto the pharmacophore model and were subjected to molecular docking. Molecular docking results highlighted a higher affinity of four hit compounds towards KRAS G12D in comparison to the reference inhibitor, BI-2852. Sequential molecular dynamics (MD) simulation studies revealed all four hit compounds them possess higher KRAS G12D binding free energy and demonstrate stable polar interaction with key residues. Further, Principal Component Analysis (PCA) analysis of the hit compounds in complex with KRAS G12D also indicated stability. Overall, the research undertaken provides strong support for further in vitro testing of these newly identified KRAS G12D inhibitors, particularly Hit1 and Hit2.<\/jats:p>","DOI":"10.3390\/ijms23031309","type":"journal-article","created":{"date-parts":[[2022,1,25]],"date-time":"2022-01-25T20:38:58Z","timestamp":1643143138000},"page":"1309","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Identification of New KRAS G12D Inhibitors through Computer-Aided Drug Discovery Methods"],"prefix":"10.3390","volume":"23","author":[{"given":"Apoorva M.","family":"Kulkarni","sequence":"first","affiliation":[{"name":"Department of Bio and Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4468-3459","authenticated-orcid":false,"given":"Vikas","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Bio and Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6566-7496","authenticated-orcid":false,"given":"Shraddha","family":"Parate","sequence":"additional","affiliation":[{"name":"Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gihwan","family":"Lee","sequence":"additional","affiliation":[{"name":"Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanghwa","family":"Yoon","sequence":"additional","affiliation":[{"name":"Department of Bio and Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keun Woo","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Bio and Medical Big Data (BK4 Program), Division of Life Science, Research Institute of Natural Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1126\/science.1062023","article-title":"The Guanine Nucleotide-Binding Switch in Three Dimensions","volume":"294","author":"Vetter","year":"2001","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"6389","DOI":"10.1038\/onc.2016.169","article-title":"Sos1 disruption impairs cellular proliferation and viability through an increase in mitochondrial oxidative stress in primary MEFs","volume":"35","author":"Anta","year":"2016","journal-title":"Oncogene"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"15823","DOI":"10.1073\/pnas.1904529116","article-title":"Drugging an undruggable pocket on KRAS","volume":"116","author":"Kessler","year":"2019","journal-title":"Proc. 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