http://journal.umpalangkaraya.ac.id/index.php/jmd/issue/feed Journal of Molecular Docking 2022-01-20T08:47:50+07:00 Mohammad Rizki Fadhil Pratama mohammadrizkifadhilpratama@gmail.com Open Journal Systems <p style="text-align: justify;"><strong>Title:</strong>&nbsp;Journal of Molecular Docking<strong><br>ISSN:</strong> <a href="https://portal.issn.org/resource/ISSN/2798-138X" target="_blank" rel="noopener">2798-138X</a>&nbsp;(online)<strong><br>Subject:</strong> Pharmacy, Chemistry, Physics, Bioinformatics, and other fields that utilize molecular docking methods<strong><br> Frequency:</strong> Biannual (2 issues per year in June and December) onward June 2021<strong><br>Indexing:</strong> <a href="https://search.crossref.org/?q=2798-138X">Crossref</a>,&nbsp;<a href="https://scholar.google.com/citations?hl=id&amp;user=bbYxnBEAAAAJ">Google Scholar</a>, <a href="https://www.lens.org/lens/search/scholar/list?p=0&amp;n=100&amp;s=_score&amp;d=%2B&amp;f=false&amp;e=false&amp;l=en&amp;authorField=author&amp;dateFilterField=publishedYear&amp;orderBy=%2B_score&amp;presentation=false&amp;preview=true&amp;regex=false&amp;stemmed=true&amp;useAuthorId=false&amp;sourceTitle.must=Journal%20of%20Molecular%20Docking">LENS.ORG</a><strong><br> DOI: </strong><a href="https://doi.org/10.33084/jmd">10.33084/jmd</a><strong><br>Archive preservation:</strong> <a href="https://onesearch.id/Search/Results?filter[]=repoId:IOS15741">Indonesia OneSearch</a><strong><br> Publisher:</strong> <a href="http://lp2m.umpr.ac.id" target="_blank" rel="noopener">Institute for Researches and Community Services</a> <a href="http://umpr.ac.id" target="_blank" rel="noopener">Universitas Muhammadiyah Palangkaraya</a><strong><br> Editor in Chief: </strong><a href="https://orcid.org/0000-0002-0727-4392">Mohammad Rizki Fadhil Pratama</a></p> <p style="text-align: justify;"><strong>Journal of Molecular Docking</strong> (<em>J. Mol. Docking</em>)&nbsp;is an international scientific platinum open-access journal managed by the <a href="https://fik.umpr.ac.id/program-studi/d3-farmasi/"><em>Department of Pharmacy</em></a>, <em><a href="http://umpr.ac.id/">Universitas Muhammadiyah Palangkaraya</a></em>&nbsp;and published two times a year (in June and December) onward <strong>June 2021</strong> by <em><a href="http://lp2m.umpr.ac.id/">Institute for Researches and Community Services Universitas Muhammadiyah Palangkaraya</a></em>, contains articles of original research and literature review in the field of science and health using Molecular Docking Simulation as its main analysis method.</p> http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/3063 Corrigendum to "Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2” [J Mol Docking. 2021;1(2):1-14] 2021-12-30T09:19:56+07:00 Israa Mohamed Shamkh esraa.m.ahmed@std.agr.cu.edu.eg Dina Pratiwi dinapratiwi91@gmail.com Hanaa S. Omar hanaa8324@yahoo.com <p style="text-align: justify;">Authors have found an error in the previous version (Shamkh, IM, &amp; Pratiwi, D. (2021). Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2. Journal of Molecular Docking, 1(1), 1-14. <a href="https://doi.org/10.33084/jmd.v1i1.2212">https://doi.org/10.33084/jmd.v1i1.2212</a>), of which Dr. Hanaa S. Omar as supervisor of the research, is not listed as one of the authors. In this note, Dr. Hanaa S. Omar was added as one of the authors, with the status of the corresponding author in the study.</p> 2021-12-30T09:19:33+07:00 ##submission.copyrightStatement## http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/2213 In Silico Study for Similar FDA Approved Drugs as Inhibitors of SARS-CoV-2 Spike and the Host Receptor Proteins 2022-01-12T20:59:59+07:00 Israa Mohamed Shamkh esraa.m.ahmed@std.agr.cu.edu.eg Dina Pratiwi dinapratiwi91@gmail.com Hanaa S. Omar hanaa8324@yahoo.com Nour El-Houda A. Reyad nourelhoudareyad53@gmail.com <p style="text-align: justify;">The severe acute respiratory syndrome coronavirus 2, known as COVID-19, has been hideously increased worldwide. The disease began in Wuhan, China, around December 2019, then spread to most countries. Social distancing is the best procedure to prevent infection. Screening the available database containing millions of drug molecules or phytochemicals has become rapid and straightforward because of the computer-aided drug design (CADD) methods. In the present study, 300 phytochemicals and cellulose ether derivatives are screened through a docking study. Docking analysis showed that only four molecules (a-neohesperidin, quercetin 3-O-glucosylrutinoside, 14-ketostypodiol diacetate, and hydroxypropyl methylcellulose) were able to interact with the spike protein. However, two among them (quercetin 3-O-glucosylrutinoside and 14-ketostypodiol diacetate) could interact with the host cell receptor (ACE2) of SARS-CoV-2. The binding affinity of the four compounds is high. Still, according to Lipinski's rule of five, only 14-ketostypodiol diacetate was selected as a drug molecule due to its pharmacokinetic and ADMET properties. Screening for drug analogs to the 14-ketostypodiol diacetate detected five approved drugs. Docking analysis of these drugs with the target proteins showed that the five drugs interact with the host receptor protein, and three interact with viral spike protein. Accordingly, we suggest that molecular docking and drug analogs studies could support rapid drug development. In addition, future perspectives on therapeutic applications of 14-ketostypodiol diacetate are required for using it against SARS-CoV-2 infections.</p> 2021-12-30T00:00:00+07:00 ##submission.copyrightStatement## http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/2904 Molecular Docking Studies of Spirostans as MAPK14 (P38α) Inhibitors and Their Potential Use against Cancer 2022-01-14T09:00:41+07:00 Guiee Niza Lopez-Castillo guiee.lopezc@alumno.buap.mx Victorino Alatriste victorino.alatriste@correo.buap.mx Jesus Sandoval-Ramírez jesus.sandoval@correo.buap.mx Felix Luna felix.luna@correo.buap.mx Alan Carrasco-Carballo alan.carrascoc@correo.buap.mx <p style="text-align: justify;">Spirostans (SPs) are chemical products widely distributed in the plant kingdom; currently, they are studied by their medical applications. Cancer has a high incidence in humans; it reaches second place worldwide deaths. In molecular biology, it has been accepted that Mitogen-Activated Protein p38alpha Kinase (MAPK14 (p38α) is implicated in the regulation of cancer. This study aimed to identify SPs as potential MAPK14 (p38α) inhibitors. From a set of 133 modified SPs, SwissTargetPrediction platform, and molecular docking, it was obtained that 129 chemical structures had molecular interaction with the MAPK14 (p38α). From those molecules, 123 were bound to a specific inhibition site of MAPK14 (p38α), and 6 of the structures resulted in inhibitors similarly to minocycline and dasatinib. One SP had binding couple energy (BCE, kcal/mol) as that of fostamatinib. In addition, 115 modified SPs had better BCE than the minocycline but not as that using fostamatinib. The key amino acids (aa) for the protein kinase MAPK14 (p38α) inhibition were Arg 70, Asp 168, Lys 53, His 148, and Ile 145, at a different interaction level. The BCE was enhanced when the H atom was substituted in C-2, C-11, and C-17 SPs positions. Similarly, the αOH group at C-5 and C-6 upgraded BCE. Stereochemistry and substitution at C-3, C-12, and C-25 did not present significant differences (Kruskal-Wallis test, p &lt;0.05). From all this ensemble of results, it is foreseeable that the SPs can be an option for MAPK14 (p38α) inhibition, a key modulator in cancer processes.</p> 2021-12-30T00:00:00+07:00 ##submission.copyrightStatement## http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/3011 New Approach to create an Effective Natural Treatments of Infections caused by Human Papillomavirus 2022-01-14T10:43:51+07:00 Momir Dunjic dr.momirdunjic@gmail.com Stefano Giuseppe Turini turini.stefano@yahoo.it Slavisa Stanisic profstanisic@yahoo.com Nenad Sulovic sulovicnenad@yahoo.com Sasa Cvetkovic sasacvet@yahoo.com Dejan Mihajlovic dejomihajlovic@gmail.com Marija Dunjic marijadunjic@yahoo.com Dusan Simic dusan.m.simic@gmail.com Katarina Dunjic dunjickatarina@gmail.com <p style="text-align: justify;">Human Papillomavirus (HPV) has a double-stranded DNA (dsDNA) genome. Infections, mainly sexually transmitted, usually resolve spontaneously. However, if the infection persists over time, lesions of the skin and mucous membranes tend to appear, notably mucosal lesions in the cervix or the appearance of warts. Some of those slowly progress to cancers such as cervical, oral, anus, esophagus, and larynx carcinoma. Diagnosis of an HPV infection is made by Papanicolaou test (Pap test) or molecular screening such as the HPV DNA Test. Treatment with natural products is based on essential oils. The main point of this work is to identify natural molecules from vegetal derivation capable of inhibiting the proliferation of HPV-16 with the same and/or superior affinity as regular drugs used in pharmacological treatment. Once we have identified the main components in these plants, we have applied molecular docking software 1-Click Docking, for virtual testing of those, on main antigenic determinants of HPV-16 as oncoproteins E6 and E7 as well as major capsid protein L1. The major active component to bind oncoprotein E6, apigenin, has shown an affinity bigger than other molecules. For major capsid protein L1, apigenin has shown one level of affinity similar to conventional drugs. These results have shown how it is possible, with natural products present in our daily lives, to inhibit the proliferation of HPV.</p> 2021-12-30T00:00:00+07:00 ##submission.copyrightStatement## http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/3142 N-acetylation of 2-aminobenzothiazoles with Acetic Acid for Evaluation of Antifungal Activity and In Silico Analysis 2022-01-20T08:45:22+07:00 Sukumar Bepary sukumarsb@yahoo.com Bishyajit Kumar Biswas thichraucantho@yahoo.com.vn Prosenjit Ghosh detran1979@yahoo.com.vn Md. Aminul Haque ngocvytran19072010@yahoo.com Tran Quang De tqde@ctu.edu.vn <p style="text-align: justify;">Acetamides (S30A1 and S30) were synthesized from benzo[d]thiazol 2 amine and 6 nitrobenzo[d]thiazol 2 amine by direct use of acetic acid instead of acetylating agents. The usual acetylating agents, acetic anhydride and acetyl chloride are very unstable especially because of their high sensitivity to environmental moisture. Thus, acetylation by direct use of acetic acid was searched as an alternative approach for synthesizing acetanilides. In this study, acetamides were synthesized with a yield of 88% and 82% respectively. The synthesized compounds were then screened for antifungal activity. At a concentration of 300 µg/disc, S30A1 showed 18 mm, 28 mm, 20 mm, and 16 mm zone of inhibitions against <em>Penicillium notatum</em>, <em>Candida albicans</em>, <em>Aspergillus flavus</em>, and <em>Aspergillus niger</em>, respectively. The standard miconazole was used at 50 µg/disc concentration. An in silico analysis was done for the possible binding modes in the Candida albicans N myristoyltransferase enzyme.</p> 2021-12-30T00:00:00+07:00 ##submission.copyrightStatement## http://journal.umpalangkaraya.ac.id/index.php/jmd/article/view/3154 In silico Anti-Inflammation Prediction of Glycyrrhiza Extracts Against Covid-19 2022-01-20T08:47:50+07:00 Mansoureh Nazari nazarimansoure@gmail.com <p style="text-align: justify;">Due to its anti-inflammation effect, <em>Glycyrrhiza</em> extract is one of the natural extracts that may potentially combat coronavirus disease in 2019 (COVID-19). In the current article, we evaluate <em>in silico</em> (molecular docking) properties of active compounds available in <em>Glycyrrhiza,</em>&nbsp;native to Western Asia, North Africa, and Southern Europe, and compare its anti-inflammation effect with remdesivir as positive compounds based on molecular docking characteristics. The main active compounds were selected based on their significant roles in the pharmacological effects of <em>Glycyrrhiza</em>. The results obtained in this study demonstrated that most of the studied main compounds interacted stronger than selected remdesivir to inhibit the spike protein in COVID-19. The combined scores (binding affinity and drug-likeness properties of the ligand, demonstrated to be the potentially possible covid19 inhibitor compared with positive control. The active site analysis of the interactions also showed that <em>Glycyrrhiza</em> extract containing active compounds might have therapeutic effects against COVID-19.</p> 2021-12-30T00:00:00+07:00 ##submission.copyrightStatement##