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N-acetylation of 2-aminobenzothiazoles with Acetic Acid for Evaluation of Antifungal Activity and In Silico Analysis Sukumar Bepary; Bishyajit Kumar Biswas; Prosenjit Ghosh; Md. Aminul Haque; Tran Quang De
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

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 Penicillium notatum, Candida albicans, Aspergillus flavus, and Aspergillus niger, respectively. The standard miconazole was used at 50 µg/disc concentration. An in silico analysis was done for the possible binding modes in the C. albicans N-myristoyltransferase enzyme.

In Silico Anti-Inflammation Prediction of Glycyrrhiza Extracts Against Covid-19 Mansoureh Nazari
Journal of Molecular Docking Vol 1 No 2 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Due to its anti-inflammation effect, Glycyrrhiza extract is one of the natural extracts that may potentially combat coronavirus disease in 2019 (COVID-19). In the current article, we evaluate in silico (molecular docking) properties of active compounds available in Glycyrrhiza, 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 Glycyrrhiza. 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 COVID-19 inhibitor compared with positive control. The active site analysis of the interactions also showed that Glycyrrhiza extract containing active compounds might have therapeutic effects against COVID-19.

Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 2 December 2021 Chief Editor of J Mol Docking
Journal of Molecular Docking Vol 1 No 2 (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 one year from the first planned, the new scientific journal of the Department of Pharmacy Universitas Muhammadiyah Palangkaraya can be published. This scientifc journal was named 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 six countries including Egypt, Indonesia, Serbia, Slovenia, Bangladesh, and Vietnam. The authors come from several institutions, including Bio Search Research Institution, Sekolah Tinggi Farmasi Muhammadiyah Tangerang, Cairo University, Benemérita Universidad Autónoma de Puebla, Univerzitet u Prištini, Alma Mater Europaea – ECM, Univerzitet Privredna akademija u Novom Sadu, Univerzitet Odbrane, Vojvode Tankosica Health Center, BDORT Center for Functional Supplementation and Integrative Medicine, Jagannath University, Can Tho University, and Universitas 17 Agustus 1945 Jakarta. Editorial boards are fully aware that there are 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 repetoire in this issue. We hope that all parties, especially the contributors of the articles, could re-participate for the the publication in the next edition on June 2022. Wassalamu’alaikum Wr. Wb.

Pharmacophore Based Virtual Screening and Docking of Different Aryl Sulfonamide Derivatives of 5HT7R Antagonist Nahid Fatema; Vijjulatha Manga; Lingala Yamini; Salman Ahmad Khan; Qasim Ullah
Journal of Molecular Docking Vol 2 No 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3165

The selective blockade of 5HT7R (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. Structural information of 5HT7 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 R2 and Q2 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 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.

Homology Modeling and Molecular Docking Studies of Selected Substituted Tetradecane on vlsE Borrelia spielmanii Venu Paritala; Harsha Thummala; Talluri Naga Santosh Mohith
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3407

VlsE is the key enzyme in antibacterial and suicide antigenic variation. While the vlsE of Borrelia burgdorferi 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.

Molecular Docking Screening and Pharmacokinetic Studies of Some Boron-Pleuromutilin Analogues against Possible Targets of Wolbachia pipientis Fabian Audu Ugbe; Gideon Adamu Shallangwa; Adamu Uzairu; Ibrahim Abdulkadir
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3450

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 Wolbachia. 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 Wolbachia 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: 17_6W9O (-117.31 kcal/mol) > 28_6EEZ (-104.43 kcal/mol) > 17_7ESX (-102.56 kcal/mol) > 41_7ESX (-101.51 kcal/mol), greater than that of the reference drug doxycycline_7ESX (-92.15 kcal/mol). These molecules (17, 28, and 41) 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 17_6W9O interactions was confirmed by the MD simulation. Therefore, the selected molecules could be developed as potential drug candidates for treating filarial diseases.

In Silico Approach: Effect of the Oxidation Iron State (Heme-Group) in Steroidogenesis Pathways David Mora-Martinez; Jorge Organista-Nava; Jesús Sandoval-Ramirez; Berenice Illades-Aguiar; Alan Carrasco-Carballo
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3548

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.

Pharmacophore Based Virtual Screening and Docking of Different Aryl Sulfonamide Derivatives of 5HT7R Antagonist Nahid Fatema; Vijjulatha Manga; Lingala Yamini; Salman Ahmad Khan; Qasim Ullah
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3165

The selective blockade of 5HT7R (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. Structural information of 5HT7 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 R2 and Q2 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 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.

Comparative In-Silico Molecular Docking of Silymarin for SARS-CoV-2 Receptor Michael Antony Samy Amutha Gnana Arasi; Sapthasri Ravichandran; Irudayam Iayaraman
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.3270

The COVID-19 pandemic has spread worldwide in over 185 countries, with millions of infections and hundreds of thousands of deaths. The current pandemic has made the situation worse, forcing the development of better treatment. In this work, the binding ability of COVID-19 receptors with silymarin has been analyzed using AutoDock 1.4.6. Further, it is compared with the standard drug remdesivir. Silymarin, a potential phytochemical compound obtained from the seeds of the Silybum marianum (milk thistle) plant, has been documented as an antiviral agent against several viruses. So silymarin can also be an effective compound in the treatment of COVID-19. This study aims to determine the binding ability of COVID-19 receptors towards silymarin and further comparative analysis by remdesivir. Drug Discovery Studio version 2021 software was used to analyze ligands and targets. AutoDock 1.4.6 software was used to perform the docking study. Among the various receptors, 5N11 (Human beta1-coronavirus (β1CoV) OC43), 7MJP (SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39), 7JMO (SARS-CoV-2 receptor-binding domain in complex with neutralizing antibody COVA2-04) receptors showed the highest binding ability of -8.09, -7.23, -6.96 kcal/mol towards silymarin compared to the standard remdesivir having the docking score of -5.21, -3.76, -2.97 kcal/mol, respectively. By the comparative analysis, silymarin has a better and highest binding ability.

Cover, Content, and Editorial Note from J Mol Docking Vol. 2 No. 1 June 2022 Chief Editor of J Mol Docking
Journal of Molecular Docking Vol. 2 No. 1 (2022): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/jmd.v2i1.4601

Assalamu’alaikum Wr. Wb. Alhamdulillahirabbil ‘alamin. After a long wait of 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 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 is published every 6 months (2 issues/year) every June and December. This edition contains five articles consisting of writings from three countries, including India, Mexico, and Nigeria. The authors come from several institutions, including Maulana Azad National Urdu University, Osmania University, Osmania University College for Women, Vignan's Foundation for Science, Technology & Research, Ahmadu Bello University, Benemérita Universidad Autónoma de Puebla, Universidad Autónoma de Guerrero, The Tamil Nadu Dr. M.G.R. Medical University, and Anna University. Editorial boards are fully aware that this edition has room for improvement. 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, can re-participate for publication in the next edition on December 2022. Wassalamu’alaikum Wr. Wb.

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

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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