https://journal.umpr.ac.id/index.php/jmd/issue/feed Journal of Molecular Docking 2022-10-07T14:49:51+00:00 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://doaj.org/toc/2798-138X">DOAJ</a>,&nbsp;<a href="https://app.dimensions.ai/discover/publication?search_mode=content&amp;or_facet_source_title=jour.1410537">Dimensions</a>, <a href="https://search.crossref.org/?q=2798-138X">Crossref</a>,&nbsp;<a href="https://journals.indexcopernicus.com/search/details?id=69488">Index Copernicus International</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>, <a href="https://garuda.kemdikbud.go.id/journal/view/23297">GARUDA</a>, and more<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>&nbsp;</strong><a href="https://garuda.kemdikbud.go.id/journal/view/23297">GARUDA</a><strong><br> Publisher:</strong> <a href="https://lp2m.umpr.ac.id/" target="_blank" rel="noopener">Institute For Research 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, ISSN: <a href="https://portal.issn.org/resource/ISSN/2798-138X">2798-138X</a> (online)</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 Research 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. <strong>Journal of Molecular Docking</strong>&nbsp;accepts scientific articles in the form of <strong>original research articles</strong>, <strong>short communication</strong>, <strong>literature review,</strong> and <strong>expert opinion</strong>&nbsp;from anyone without any discrimination, as long as they submit articles that meet scientific principles.</p> https://journal.umpr.ac.id/index.php/jmd/article/view/3165 Pharmacophore Based Virtual Screening and Docking of Different Aryl Sulfonamide Derivatives of 5HT7R Antagonist 2022-07-04T14:29:18+00:00 Nahid Fatema nahid.fatema.smile@gmail.com Vijjulatha Manga vijjulathamanga@gmail.com Lingala Yamini lingalayamini@gmail.com Salman Ahmad Khan sahmad_phd@yahoo.co.in Qasim Ullah drqasimullah@gmail.com <p style="text-align: justify;">The selective blockade of 5HT<sub>7</sub>R (5-hydroxytryptamine 7 receptor) displays an antidepressant-like activity. It is a Gs-coupled receptor, which inactivates the adenyl cyclase enzyme or activates the potassium ion channel<strong>.</strong> Structural information of 5HT<sub>7</sub> was obtained by homology modeling using MODELLER v.9.13. In the present study, pharmacophore-based virtual screening, molecular docking, and binding free energy calculations were performed on a series of antagonist aryl sulphonamide derivatives. A five-point pharmacophore hypothesis with two hydrogen bond acceptor (A), one hydrogen bond donor (D), one positive group (p), and one ring (R) was developed with acceptable R<sup>2 </sup>and Q<sup>2</sup> values of 0.90 and 0.602, respectively. Eventually, common pharmacophore hypothesis-based screening was conducted against Asinex databases. Finally, binding free energy and dock score analysis was carried out for the top hits obtained from the docking process. All 14 hits from the database in this study had a satisfactory dock score and binding energy values within the best active compound range. H bond&nbsp;interaction with amino acid residues Ser212 and π-π stacking with Tyr249 were investigated for the best active molecule. Both are present in the top hits, including other interactions as well.</p> 2022-06-30T00:00:00+00:00 Copyright (c) 2022 Nahid Fatema, Vijjulatha Manga, Lingala Yamini, Salman Ahmad Khan, Qasim Ullah https://journal.umpr.ac.id/index.php/jmd/article/view/3407 Homology Modeling and Molecular Docking Studies of Selected Substituted Tetradecane on vlsE Borrelia spielmanii 2022-10-07T14:49:51+00:00 Venu Paritala vvenuparitala@gmail.com Harsha Thummala hthummala99@gmail.com Talluri Naga Santosh Mohith mohitsantosh2112@gmail.com <p style="text-align: justify;">VlsE is the key enzyme in antibacterial and suicide antigenic variation. While the vlsE of <em>Borrelia burgdorferi</em> sensu lato complex causes Lyme disease. Therefore, vlsE is considered a significant drug target for Lyme disease. In this paper, we report the model of the three-dimensional structure of vlsE resulting from a homology modeling study. Homology modeling was developed using three different software and evaluating the best model. Subsequent docking studies of the natural substrate tetradecane and known antibacterial drugs were performed with SwissDock and shed new light on the binding characteristics of the enzyme. Binding energies ranged from -2024.12 to -2032.17 kcal/mol. As a result, they might be synthesized further and developed into active commercial antibacterial drugs.</p> 2022-06-30T00:00:00+00:00 Copyright (c) 2022 Venu Paritala, Harsha Thummala, Talluri Naga Santosh Mohith https://journal.umpr.ac.id/index.php/jmd/article/view/3450 Molecular Docking Screening and Pharmacokinetic Studies of Some Boron-Pleuromutilin Analogues against Possible Targets of Wolbachia pipientis 2022-10-07T14:49:45+00:00 Fabian Audu Ugbe ugbefabianaudu@gmail.com Gideon Adamu Shallangwa gashallangwa@gmail.com Adamu Uzairu adamuuzairu@gmail.com Ibrahim Abdulkadir ibrahim.abdulkadir@gmail.com <p style="text-align: justify;">Lymphatic filariasis and onchocerciasis are two common filarial diseases caused by a group of parasitic nematodes called filarial worms, which co-habit with the bacteria organism <em>Wolbachia.</em> One good treatment approach seeks Wolbachia as a drug target. Here, a computer-aided molecular docking screening was conducted on a series of 52 pleuromutilin analogs against four&nbsp;<em>Wolbachia</em> enzymes: α-DsbA1 (PDB: 3F4R), α-DsbA2 (6EEZ), OTU deubiquitinase (6W9O), and cytoplasmic incompatibility factor CidA (7ESX) to find a more potent drug candidate(s) for the treatment of filarial diseases. The docking investigation was performed using the iGEMDOCK tool, while NAMD was utilized for the Molecular Dynamic (MD) simulation. The results of the virtual screening identified four ligand-protein interaction pairs with the highest binding affinities in the order: <strong>17</strong>_6W9O (-117.31 kcal/mol) &gt; <strong>28</strong>_6EEZ (-104.43 kcal/mol) &gt; <strong>17</strong>_7ESX (-102.56 kcal/mol) &gt; <strong>41</strong>_7ESX (-101.51 kcal/mol), greater than that of the reference drug doxycycline_7ESX (-92.15 kcal/mol). These molecules (<strong>17</strong>, <strong>28</strong>, and <strong>41</strong>) showed excellent binding interactions, making very close contact with the receptors’ amino acid residues. They also showed better pharmacokinetic properties than doxycycline because they showed high intestinal absorption, were orally bioavailable and showed no AMES toxicity. Also, the stability of <strong>17</strong>_6W9O interactions was confirmed by the MD simulation. Therefore, the selected molecules could be developed as potential drug candidates for treating filarial diseases.</p> 2022-10-07T00:00:00+00:00 Copyright (c) 2022 Fabian Audu Ugbe, Gideon Adamu Shallangwa, Adamu Uzairu, Ibrahim Abdulkadir https://journal.umpr.ac.id/index.php/jmd/article/view/3548 In Silico Approach: Effect of the Oxidation Iron State (Heme-Group) in Steroidogenesis Pathways 2022-10-07T14:49:48+00:00 David Mora-Martinez david.morama@alumno.buap.mx Jorge Organista-Nava jorgeorganista@uagro.mx Jesús Sandoval-Ramirez jesus.sandoval@correo.buap.mx Berenice Illades-Aguiar b.illadesaguiar@gmail.com Alan Carrasco-Carballo alan.carrascoc@correo.buap.mx <p style="text-align: justify;">One of the main design features of enzyme regulators for the CYPs is the presence of a heme-group and different oxidation states in iron atoms. The selective inhibition of a CYP-enzyme can help to reduce the formation of steroidal molecules that causes undesirable disorders and is, therefore a topic of great biochemical-pharmaceutical interest. The present work carried out an analysis of effect on the coupling-energy of the iron core according to its changes from oxidation Fe(II) to Fe(III) state, over inhibitors and substrates, in a particular enzyme. Two crystals from CYP21A2, CYP11A1, CYP17A1 and CYP19A1 enzymes were selected, assigning the oxidation states separately in each case. It was highlighted that for CYP11A1 and CYP19A1 enzymes, no significant difference was observed in coupling energies between Fe oxidation state and crystal stereo-disposition. This last can be used to analyze their congruence towards the reported biological data. For CYP17A1, the ideal crystal for inhibitors design is 6CHI since the crystal with 4NKV presented differences in all the molecules analyzed since the oxidation state of the iron atom changes the molecule's orientation in the enzyme coupling. In contrast, in CYP21A2, no changes were observed. A greater biological congruence with 5BVU was observed because the coupling energies concur with the selectivity of the enzyme towards its endogenous substrates and reported inhibitors. It was concluded that the effect of the oxidation state of iron on the Binding Coupling Energy (BCE) depends directly on the functional groups attached to the steroidal molecule and their stereo-disposition.</p> 2022-06-30T00:00:00+00:00 Copyright (c) 2022 David Mora-Martinez, Jorge Organista-Nava, Jesús Sandoval-Ramirez, Berenice Illades-Aguiar, Alan Carrasco-Carballo