Journal of Molecular Docking https://journal.umpr.ac.id/index.php/jmd <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> en-US <p style="text-align: justify;">Authors continue to retain the copyright to the article if the article is published in the <em><strong>Journal of Molecular Docking</strong></em>. They will also retain the publishing rights to the article without any restrictions.</p> <p style="text-align: justify;">Authors who publish with this journal agree to the following terms:</p> <ol> <li class="show" style="text-align: justify;">Any article on the copyright is retained by the author(s).</li> <li class="show" style="text-align: justify;">The author grants the journal, right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share work with an acknowledgment of the work authors and initial publications in this journal.</li> <li class="show" style="text-align: justify;">Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of published articles of work (eg, post-institutional repository) or publish it in a book, with acknowledgment of its initial publication in this journal.</li> <li class="show" style="text-align: justify;">Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their websites) prior to and during the submission process, as can lead to productive exchanges, as well as earlier and greater citation of published work.</li> <li class="show" style="text-align: justify;">The article and any associated published material are distributed under the <a href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons Attribution-ShareAlike 4.0 International License</a>.</li> </ol> mohammadrizkifadhilpratama@gmail.com (Mohammad Rizki Fadhil Pratama) jmd@umpr.ac.id (Admin LP2M) Sat, 31 Dec 2022 00:00:00 +0000 OJS 3.2.1.4 http://blogs.law.harvard.edu/tech/rss 60 Identification of Bioactive Molecules from Combretum micranthum as Potential Inhibitors of α-amylase through Computational Investigations https://journal.umpr.ac.id/index.php/jmd/article/view/3673 <p>The rising prevalence of diabetes necessitates continued research into natural antidiabetic medicines that target a key biochemical enzyme involved. The α-amylase enzyme is involved in the digestion of starch, glycogen, and disaccharides in the gastrointestinal tract. Its essential roles and distinct properties make it an effective antidiabetic target. This work aimed to use <em>in silico</em> approaches to find possible α-amylase inhibitors from <em>Combretum micranthum</em> bioactive substances. On the Schrödinger Maestro 12.5, over 50 <em>C. micranthum</em> compounds were screened, followed by MM-GBSA and ADMET (absorption, distribution, metabolism, excretion, and toxicity) studies of the highest affinity compounds. The α-amylase binding affinities were higher for rutin trihydrate and myricetin-3-rutinoside (-12.162 kcal/mol and -10.935 kcal/mol, respectively). They reacted with amino acids that are required for the inhibition of α-amylase. As a result, these compounds have the structural characteristics, binding affinities, and molecular interactions necessary as α-amylase inhibitors and could be turned into antidiabetic medicines through lead optimization and experimental research.</p> Damilola Samuel Bodun, Damilola Alex Omoboyowa, Toheeb Adewale Balogun, Abigail Osinachi Enyinnaya Copyright (c) 2022 Damilola Samuel Bodun, Damilola Alex Omoboyowa, Toheeb Adewale Balogun, Abigail Osinachi Enyinnaya http://creativecommons.org/licenses/by-sa/4.0 https://journal.umpr.ac.id/index.php/jmd/article/view/3673 Sat, 31 Dec 2022 00:00:00 +0000 Alantolactone: A Potential Multitarget Drug candidate for Prevention of SARS-CoV-2 Cell Entry https://journal.umpr.ac.id/index.php/jmd/article/view/3679 <p>The novel strain of coronavirus, SARS-CoV-2, has spread adverse effects on human health with high mortality rates worldwide. SARS-CoV-2 is a severe respiratory disease expressed through positive single stranded RNA enveloped virus. SARS-CoV-2 had affected globally and is influencing the economy as well. The rapidly spreading coronavirus infection has discombobulated the researchers in perpetuate search for different or effective therapeutic drugs. Most of the connatural products are proposed to have significant clinical outcomes but their pathways of action are not clear. This molecular docking study presents alantolactone, a bio-active member of sesquiterpene family as a successful inhibitor of SARS-Cov-2 and human receptor proteins. Alantolactone shows high binding affinity with the SARS-CoV-2 target proteins such as spike glycoprotein (S-protein), nucleocapsid protein (N-protein), main protease (M<sup>Pro</sup>), and papain-like protease (PL<sup>Pro</sup>) with a binding affinity of -7.3 kcal/mol, -7.9 kcal/mol, -6.8 kcal/mol, and -7.1 kcal/mol, respectively as well as human receptor proteins associated with the recognition, binding and biogenesis of SARS-CoV-2 such as angiotensin-converting enzyme 2 (ACE-2), receptor binding domain (S1-RBD) and ACE2 interphase, furin, adaptor-associated protein kinase 1 (AAK1), cyclin G-associated kinase (GAK), and both closed and open configurations of the two-pore channel (TPC2) with binding energies of -6.7 kcal/mol, - 6.9 kcal/mol, -8.1 kcal/mol, -7.3 kcal/mol, and -7.9 kcal/mol, respectively. Molecular docking and ADMET properties and toxicity predictions suggest that alantolactone could effectively binds with various viral target protein and human target proteins and could be developed into a novel SARS-coV-2 inhibitor.</p> Erum Zafar, Zainab Ahsan, Muhammad Faisal Maqbool, Aqsa Zaman, Sameena Gul, Amara Maryam, Muhammad Khan, Hafiz Abdullah Shakir, Muhammad Irfan Copyright (c) 2022 Erum Zafar, Zainab Ahsan, Muhammad Faisal Maqbool, Aqsa Zaman, Sameena Gul, Amara Maryam, Muhammad Khan, Hafiz Abdullah Shakir, Muhammad Irfan http://creativecommons.org/licenses/by-sa/4.0 https://journal.umpr.ac.id/index.php/jmd/article/view/3679 Sat, 31 Dec 2022 00:00:00 +0000 Docking and Dynamics Study of Phytochemicals as Potent Inhibitors against SARS-CoV-2 Main Protease https://journal.umpr.ac.id/index.php/jmd/article/view/3969 <p style="text-align: justify;">Coronavirus Infectious Disease-19 (COVID-19) caused by coronavirus 2 is a global health hazard. The lack of medications against the disease is a major concern of the research community today. Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease (SARS-CoV-2 M<sup>Pro</sup>) is the most extensively studied protein responsible for spreading disease. Several plant-based products are utilized to treat the disease's symptoms. Here, we have attempted to screen 377 phytocompounds against the target computationally. We have sorted eight best-pose compounds based on docking studies for further analysis. Lipinski and Adsorption, Distribution, Metabolism, Elimination/Toxicity (ADME/T) properties were also evaluated to assess the drug-like properties and toxicity of the screened compounds. Finally, we discovered Coruscanone to be the most effective lead compound for the target. The best complex was further undertaken for dynamic simulation. RMSD, RMSF, h-bond, and Rg were analyzed and studied related to the reference compound. The study additionally continues to elucidate its inhibitory action via <em>in vitro</em> studies.</p> Palla Ramprasad, Arunkumar Babu, Suveena Sukumaran Copyright (c) 2022 Palla Ramprasad, Arunkumar Babu, Suveena Sukumaran http://creativecommons.org/licenses/by-sa/4.0 https://journal.umpr.ac.id/index.php/jmd/article/view/3969 Sat, 31 Dec 2022 00:00:00 +0000 De Novo Class of Momordicoside with Potent and Selective Tumor Cell Growth Inhibitory Activity as Pyruvate Kinase Muscle Isozyme 2 and Anti-apoptotic Myeloid Leukemia 1 Inhibitors https://journal.umpr.ac.id/index.php/jmd/article/view/4006 <p style="text-align: justify;">The difficulty in treating cancer resides in targeting abnormal proliferation while protecting normal proliferation, necessitating a thorough comprehension of the normal and malignant mechanisms that promote cell growth and proliferation. Targeting cell death signaling pathways such as glycolytic and mitochondrial apoptosis is the hallmark of many cancers, the aim of which this research is ready to evaluate. Atomistic molecular dynamics simulation of top hits after molecular docking and ADMET profiling of the ligands were performed for main protease-hit complexes. Docking scores of ligands used against PKM2 range from –9.36 to –12.1 kcal/mol, wherein momordicoside-F2 had the highest score (2.1 kcal/mol), performing better than the FDA-approved drug benserazide. Likewise, the scores ranged between –8.51 and –12.05 kcal/mol for Anti-apoptotic Myeloid Leukemia 1 (MCL-1), with momordicoside-F1 being the highest-ranked compound. The RMSD plots depicted stable trajectories with consistent and minor fluctuations implying that the protein (PKM2 and MCL1) backbone underwent minor structural perturbations. In addition, several significant peaks of increased fluctuations were also observed, indicating their increased interaction potential, implying that the ligands could adapt well in the protein's binding pocket. The SASA analysis results show that the ligands retained inside their shallow binding pocket. The phylogenetic tree obtained implies the likelihood of recurring results of the <em>in silico</em> profiling. Conclusively, this research unveils that Mormordicoside F1 shows good stability with MCL-1, likewise, momordicoside-F2 against PKM2. These hits can be a better re-purposing option.</p> Tope Abraham Ibisanmi, ‪Jamiu Olaseni Aribisala, Peace Ifeoma Odjegba, Damilola Ademuyi, Ayomide Akinmusere, Faith I Ajayi Copyright (c) 2022 Tope Abraham Ibisanmi, ‪Jamiu Olaseni Aribisala, Peace Ifeoma Odjegba, Damilola Ademuyi, Ayomide Akinmusere, Faith I Ajayi http://creativecommons.org/licenses/by-sa/4.0 https://journal.umpr.ac.id/index.php/jmd/article/view/4006 Sat, 31 Dec 2022 00:00:00 +0000 Phytochemical Molecules Binding with the Proteins of Mycolic Acid Synthesis Pathway of Mycobacterium tuberculosis https://journal.umpr.ac.id/index.php/jmd/article/view/4074 <p style="text-align: justify;">Resistance against anti-tubercular drugs is a significant problem. This elucidates the need for novel drug targets. Altering and targeting the enzymes involved in cell wall synthesis led to fatal damage to the bacterial cell. Mycolic acids are critically responsible for the virulence of <em>Mycobacterium Tuberculosis</em>. This pathway represents an essential reservoir of novel targets for developing new TB drugs. The study&nbsp;aims to identify phytochemicals with the capacity to bind with enzymes of mycolic acid synthesis pathways. This study shows&nbsp;the interaction between phytochemicals and proteins responsible for mycolic acid synthesis is shown through bioinformatics &amp; molecular docking tools.&nbsp;Docking showed binding affinity between protein molecules of the mycolic acid synthesis pathway and ligand molecules in the study. PKS13 (polyketide synthase) interacts with the ligand beta-amyrin acetate with a vina score of -7.1 Kcal/mol. At the same time, its binding energy with Piperine is -6.8 Kcal/mol. DprE1 (Decaprenylphosphoryl-bet-D-ribose-2-epimerase), the other protein docked with beta-amyrin acetate, showed a vina score of -9.7 Kcal/mol binding energy. Piperine with DprE1 exhibits interaction with a score of -8.3 Kcal/mol. Beta-amyrin acetate is docked with a score of -6.9 Kcal/mol against KasA (Beta-ketoacyl-acyl carrier protein synthase). On the other hand, Piperine with KasA gave a result of -7.0 Kcal/mol. Piperine and Beta-amyrin acetate binds to PKS13, DprE1 &amp; KasA protein/enzymes responsible for mycolic acid biosynthesis.</p> Rishabh Gaur, Praveen Kumar Anand Copyright (c) 2022 Rishabh Gaur, Praveen Kumar Anand http://creativecommons.org/licenses/by-sa/4.0 https://journal.umpr.ac.id/index.php/jmd/article/view/4074 Sat, 31 Dec 2022 00:00:00 +0000