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Journal of Molecular Docking

jmd
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Published by Universitas Muhammadiyah Palangkaraya

ISSN : - EISSN : 2798138X DOI : https://doi.org/10.33084/jmd

Core Subject : Health,

Medicine & Pharmacology

Journal of Molecular Docking is an international scientific platinum open access journal managed by the Department of Pharmacy, Universitas Muhammadiyah Palangkaraya and published two times a year in June and December by Institute for Researches and Community Services Universitas Muhammadiyah Palangkaraya, contains articles of original research and literature review in the field of science and health using Molecular Docking Simulation as its main analysis method.

Arjuna Subject : Pharmacology, Toxicology and Pharmaceutics - Penemuan Obat

Articles 25 Documents

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A Comparative Study of Approved Drugs for SARS-CoV-2 by Molecular Docking Achal Mishra; Radhika Waghela
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

SARS-CoV-2, a new type of Coronavirus, has affected more millions of people worldwide. From the spread of this infection, many studies related to this virus and drug designing for the treatment have been started. Most of the studies target the SARS-CoV-2 main protease, spike protein of SASR-CoV-2, and some are targeting the human furin protease. In the current work, we chose the clinically used drug molecules remdesivir, favipiravir, lopinavir, hydroxychloroquine, and chloroquine onto the target protein SARS-CoV-2 main protease. Docking studies were performed using Arguslab, while Discovery Studio collected 2D and 3D pose views with the crystal structure of COVID-19 main protease in complex with an inhibitor N3 with PDB ID 6LU7. Computational studies reveal that all ligands provided good binding affinities towards the target protein. Among all the chosen drugs, lopinavir showed the highest docking score of -11.75 kcal/mol. The results from this molecular docking study encourage the use of lopinavir as the first-line treatment drug due to its highest binding affinity.

Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2 Israa Mohamed Shamkh; Dina Pratiwi
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

The novel coronavirus SARS-CoV-2 is an acute respiratory tract infection that emerged in Wuhan city, China. The spike protein of coronaviruses is the main driving force for host cell recognition and is responsible for binding to the ACE2 receptor on the host cell and mediates the fusion of host and viral membranes. Recognizing compounds that could form a complex with the spike protein (S-protein) potently could inhibit SARS-CoV-2 infections. The software was used to survey 300 plant natural compounds or derivatives for their binding ability with the SARS-CoV-2 S-protein. The docking score for ligands towards each protein was calculated to estimate the binding free energy. Four compounds showed a strong ability to bind with the S-protein (neohesperidin, quercetin 3-O-rutinoside-7-O-glucoside, 14-ketostypodiol diacetate, and hydroxypropyl methylcellulose) and used to predict its docking model and binding regions. The highest predicted ligand/protein affinity was with quercetin 3-O-rutinoside-7-O-glucoside followed by neohesperidin. The four compounds were also tested against other related coronavirus and showed their binding ability to S-protein of the bat, SARS, and MERS coronavirus strains, indicating that they could bind and block the spike activities and subsequently prevent them infection of different coronaviruses. Molecular docking also showed the probability of the four ligands binding to the host cell receptor ACE2. The interaction residues and the binding energy for the complexes were identified. The strong binding ability of the four compounds to the S-protein and the ACE2 protein indicates that they might be used to develop therapeutics specific against SARS-CoV-2 and close related human coronaviruses.

In Silico Study for Similar FDA Approved Drugs as Inhibitors of SARS-CoV-2 Spike and the Host Receptor Proteins Israa Mohamed Shamkh; Dina Pratiwi; Hanaa S. Omar; Nour El-Houda A. Reyad
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

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.

Molecular Docking Studies of Phytoconstituents Identified in Traditional Siddha Polyherbal Formulations Against Possible Targets of SARS-CoV-2 Logesh Kumar Selvaraj; Geethanjali Thayumanavan; Srikanth Jeyabalan; Sugin Lal Jabaris
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

The Indian Traditional Medicines System has long used Siddha polyherbal formulations for different viral diseases. The ingredients of these formulas have been proven to be antiviral. The study focuses on in silico computational evaluation of phytoconstituents of the official Siddha formulation Kabasura, Thonthasura, and Vishasura Kudineer, which were widely used in treating viral fever and respiratory infections and may influence the current SARS-CoV-2 coronary virus pandemic. Maestro interface (Schrödinger Suite, LLC, NY) was used for molecular docking studies against MPro (PDB ID 5R82, 6Y2F, and 6LU7), Nsp15 endoribonuclease (6W01), RNA-dependent RNA polymerase (6M71), and spike protein (6VW1) of SARS-CoV-2. In addition, pharmacokinetics (ADME) and safety profile prediction studies were performed to identify the best drug candidates using Qikpro and Toxicity Estimation Software Tool (T.E.S.T). A total of 36 compounds were screened, of which nine displayed strong binding affinity and drug-likeness. Luteolin and chrysoeriol produced stronger results. These nine compounds were free of oral toxicity as evaluated by the Toxicity estimation software. Based on further in vitro, in vivo, and clinical effectiveness trials, these compounds may be used for the prevention or treatment as per the Indian system of traditional medicines.

The Study of Potential Antiviral Compounds from Indonesian Medicinal Plants as Anti-COVID-19 with Molecular Docking Approach Baiq Ressa Puspita Rizma; Agus Dwi Ananto; Anggit Listyacahyani Sunarwidhi
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Corona Virus Disease 2019 (COVID-19) is a new strain of coronavirus called SARS-CoV-2, which was identified in Wuhan, China, in December 2019. The rapid transmission of COVID-19 from human to human forced researchers to find a potent drug by setting aside the time-consuming traditional method in drug development. The molecular docking approach is one a reliable method to screening compound from chemical drug or by finding a compound from Indonesian herbal plants. The present study aimed to assess the potency of compounds from five medicinal plants as potential inhibitors of PLpro and 3CLpro from SARS-CoV-2 using molecular study. The molecular docking was performed using Protein-Ligand Ant System (PLANTS) to analyze the potential compounds by the docking score. Remdesivir triphosphate was used as a standard for the comparison of the test compounds. The docking score obtained from the docking of PLpro with native ligand, remdesivir triphosphate, curcumin, demethoxycurcumin, bisdemethoxycurcumin, luteolin, apigenin, quercetin, kaempferol, formononetin-7-O-glucuronide, andrographolide, and neoandrographolide were -111.441, -103.827, -103.609, -102.363, -100.27, -79.6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452, respectively. Meanwhile, docking score with 3CLpro for the same ligand were -64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345, -70.3368, -71.5539, -68.4321, -72.0154, -75.9777, and -93.7746. The docking score data suggest that curcumin was the most potential as a PLpro inhibitor, while neoandrographolide was the best as a 3CLpro inhibitor.

Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects Emilio Viktorov Mateev; Iva Valkova; Maya Georgieva; Alexander Zlatkov
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possible pairwise correlation. Numerous modifications in the docking settings such as alteration in the scoring functions, size of the grid space, presence of active waters, and side-chain flexibility were conducted. Furthermore, ensemble docking simulations into two superimposed complexes were performed. The model was validated with a test set. A significant Pearson’s correlation coefficient of 0.8217 was obtained for the latter. In the final stage of our work, we observed the major interactions between the top-scored ligands and the active site of 1S3B.

Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 1 June 2021 Chief Editor of J Mol Docking
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Assalamu’alaikum Wr. Wb.Alhamdulillahirabbil ‘alamin. After a long wait for almost 1 year from the first planned, finally, the new scientific journal of the Department of Pharmacy Universitas Muhammadiyah Palangkaraya can be published. This scientific journal was named the Journal of Molecular Docking (J Mol Docking), inspired by one of the most popular in silico methods in computer-aided drug design. Journal of Molecular Docking published every 6 months (2 issues/year) every June and December.This edition contains five articles consisting of writings from four countries including Indonesia, India, Bulgaria, and Egypt. The authors come from several institutions, including Bio Search Research Institution, Sekolah Tinggi Farmasi Muhammadiyah Tangerang, Sri Ramachandra Institute of Higher Education and Research, Siddha Central Research Institute – Central Council for Research in Siddha, Chhattisgarh Swami Vivekanand Technical University, Universitas Mataram, and Medical University – Sofia.Editorial boards are fully aware that there is still room for improvement in this edition, hence with all humility willing to accept constructive suggestions and feedback for improvements to the publication for the next editions. The editorial board would like to thank all editors and reviewers, and contributors of the scientific articles who have provided the repertoire in this issue. We hope that all parties, especially the contributors of the articles, could re-participate for publication in the next edition in December 2021.Wassalamu’alaikum Wr. Wb.

Molecular Docking Studies of Spirostans as MAPK14 (P38α) Inhibitors and Their Potential Use against Cancer Guiee Niza Lopez-Castillo; Victorino Alatriste; Jesus Sandoval-Ramírez; Felix Luna; Alan Carrasco-Carballo
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

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 <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.

New Approach to create an Effective Natural Treatments of Infections caused by Human Papillomavirus Momir Dunjic; Stefano Giuseppe Turini; Slavisa Stanisic; Nenad Sulovic; Sasa Cvetkovic; Dejan Mihajlovic; Marija Dunjic; Dusan Simic; Katarina Dunjic
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

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.

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] Israa Mohamed Shamkh; Dina Pratiwi; Hanaa S. Omar
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Authors have found an error in the previous version (Shamkh, IM, & 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. https://doi.org/10.33084/jmd.v1i1.2212), 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.

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Mohammad Rizki Fadhil Pratama

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mohammadrizkifadhilpratama@gmail.com

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Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya Building B 1st Floor RTA Milono St. Km.1,5 Palangka Raya 73111 INDONESIA

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Kota palangkaraya,

Kalimantan tengah

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Home Page

OAI Link

Editorial Team

Contact

Reviewer

Google Scholar

Contact Name Mohammad Rizki Fadhil Pratama

Contact Email mohammadrizkifadhilpratama@gmail.com

Phone +6287815093560

Journal Mail Official jmd@umpr.ac.id

Editorial Address Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya Building B 1st Floor RTA Milono St. Km.1,5 Palangka Raya 73111 INDONESIA

Location Kota palangkaraya, Kalimantan tengah INDONESIA

Abstract

Abstract

Abstract

Abstract

Abstract

Abstract

Abstract

Abstract

Abstract

Abstract

Contact Name
Mohammad Rizki Fadhil Pratama

Contact Email
mohammadrizkifadhilpratama@gmail.com

Phone
+6287815093560

Journal Mail Official
jmd@umpr.ac.id

Editorial Address
Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya Building B 1st Floor RTA Milono St. Km.1,5 Palangka Raya 73111 INDONESIA

Location
Kota palangkaraya,

Kalimantan tengah

INDONESIA