{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T17:37:23Z","timestamp":1790185043990,"version":"4.1.0"},"reference-count":58,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,12]],"date-time":"2023-01-12T00:00:00Z","timestamp":1673481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100017485","name":"institutional fund projects","doi-asserted-by":"publisher","award":["IFP-A-2022-2-5-19"],"award-info":[{"award-number":["IFP-A-2022-2-5-19"]}],"id":[{"id":"10.13039\/100017485","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>The Bcl-2 protein has a vital function in controlling the programmed cell doom of mitochondria. If programmed cell death signals are obstructed, an imbalance between cell survival and death will occur, which is a significant reason for cancer. Therefore, the Bcl-2 protein was identified as a possible therapeutic target for carcinoma treatment. Herein, the Natural Products Atlas (NPAtlas) compounds were virtually screened, seeking potent inhibitors towards the Bcl-2 protein. The performance of AutoDock Vina software to predict the docking score and pose of the investigated compounds was first validated according to the available experimental data. Based on the validated AutoDock Vina parameters, the NPAtlas database was filtered against the Bcl-2 protein. The natural compounds with docking scores less than that of the venetoclax (calc. \u221210.6 kcal\/mol) were submitted to MD simulations, followed by MM-GBSA binding energy calculations. According to MM-GBSA\/\/200 ns MD simulations, saquayamycin F (NPA002200) demonstrated promising binding affinity with a \u0394Gbinding value of \u221253.9 kcal\/mol towards the Bcl-2 protein when compared to venetoclax (\u0394Gbinding = \u221250.6 kcal\/mol). The energetical and structural analyses showed a great constancy of the saquayamycin F inside the Bcl-2 protein active site. Moreover, the ADMET and drug-likeness features of the saquayamycin F were anticipated, indicating its good oral bioavailability. According to in silico computations, saquayamycin F is proposed to be used as a therapeutic agent against the wild-type Bcl-2 protein and warrants further experimental assays.<\/jats:p>","DOI":"10.3390\/molecules28020783","type":"journal-article","created":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T02:57:33Z","timestamp":1673578653000},"page":"783","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["In Silico Mining of Natural Products Atlas (NPAtlas) Database for Identifying Effective Bcl-2 Inhibitors: Molecular Docking, Molecular Dynamics, and Pharmacokinetics Characteristics"],"prefix":"10.3390","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3907-7091","authenticated-orcid":false,"given":"Nahlah Makki","family":"Almansour","sequence":"first","affiliation":[{"name":"Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 1803, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6486-9835","authenticated-orcid":false,"given":"Khaled S.","family":"Allemailem","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abeer Abas","family":"Abd El Aty","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 1803, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8422-0737","authenticated-orcid":false,"given":"Ekram Ismail Fagiree","family":"Ismail","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin 1803, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4819-2040","authenticated-orcid":false,"given":"Mahmoud A. A.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt"},{"name":"School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"448","DOI":"10.21037\/jtd.2017.02.75","article-title":"Cancer prevention from the perspective of global cancer burden patterns","volume":"9","author":"Nagai","year":"2017","journal-title":"J. Thorac. Dis."},{"key":"ref_2","first-page":"85","article-title":"Cancer issue: Global burden of cancer","volume":"79","author":"Ma","year":"2006","journal-title":"Yale J. Biol. 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