Journal of Molecular Docking最新文献_第2页

Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 2 December 2021 封面、内容和编辑说明来自jmol对接卷1第2期，2021年12月

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.3238

Chief Editor Of J Mol Docking

{"title":"Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 2 December 2021","authors":"Chief Editor Of J Mol Docking","doi":"10.33084/jmd.v1i2.3238","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.3238","url":null,"abstract":"Assalamu’alaikum Wr. Wb. \u0000Alhamdulillahirabbil ‘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. \u0000This 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. \u0000Editorial 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. \u0000Wassalamu’alaikum Wr. Wb.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86560965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New Approach to create an Effective Natural Treatments of Infections caused by Human Papillomavirus 人类乳头瘤病毒感染的有效自然治疗新方法

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.3011

Momir Dunjic, S. Turini, Slaviša Stanišić, N. Sulovic, S. Cvetkovic, Dejan Mihajlovic, M. Dunjic, Dusan Simic, Katarina Dunjić

{"title":"New Approach to create an Effective Natural Treatments of Infections caused by Human Papillomavirus","authors":"Momir Dunjic, S. Turini, Slaviša Stanišić, N. Sulovic, S. Cvetkovic, Dejan Mihajlovic, M. Dunjic, Dusan Simic, Katarina Dunjić","doi":"10.33084/jmd.v1i2.3011","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.3011","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82280315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In Silico Study for Similar FDA Approved Drugs as Inhibitors of SARS-CoV-2 Spike and the Host Receptor Proteins FDA批准的类似药物作为SARS-CoV-2刺突和宿主受体蛋白抑制剂的计算机研究

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.2213

Israa. M. Shamkh, D. Pratiwi, Hanaa S. Omar, N. E. Reyad

{"title":"In Silico Study for Similar FDA Approved Drugs as Inhibitors of SARS-CoV-2 Spike and the Host Receptor Proteins","authors":"Israa. M. Shamkh, D. Pratiwi, Hanaa S. Omar, N. E. Reyad","doi":"10.33084/jmd.v1i2.2213","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.2213","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90953730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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] “基于不同冠状病毒刺突蛋白和ACE2分子对接研究开发SARS-CoV-2抑制剂”的勘误[J] . Mol对接，2021;1(2):1-14]

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.3063

Israa. M. Shamkh, D. Pratiwi, Hanaa S. Omar

引用次数: 1

Molecular Docking Studies of Spirostans as MAPK14 (P38α) Inhibitors and Their Potential Use against Cancer Spirostans作为MAPK14 (P38α)抑制剂的分子对接研究及其抗癌潜力

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.2904

G. N. Lopez-Castillo, V. Alatriste, J. Sandoval-Ramírez, F. Luna, A. Carrasco-Carballo

{"title":"Molecular Docking Studies of Spirostans as MAPK14 (P38α) Inhibitors and Their Potential Use against Cancer","authors":"G. N. Lopez-Castillo, V. Alatriste, J. Sandoval-Ramírez, F. Luna, A. Carrasco-Carballo","doi":"10.33084/jmd.v1i2.2904","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.2904","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83687388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

N-acetylation of 2-aminobenzothiazoles with Acetic Acid for Evaluation of Antifungal Activity and In Silico Analysis 2-氨基苯并噻唑与乙酸的n -乙酰化及其抑菌活性评价及硅分析

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.3142

Sukumar Bepary, B. Biswas, P. Ghosh, Md. Aminul Haque, Tran Quang De

引用次数: 1

In Silico Anti-Inflammation Prediction of Glycyrrhiza Extracts Against Covid-19 甘草提取物抗新型冠状病毒肺炎的体外抗炎预测

Journal of Molecular Docking Pub Date : 2021-12-30 DOI: 10.33084/jmd.v1i2.3154

Mansoureh Nazari

引用次数: 0

A Comparative Study of Approved Drugs for SARS-CoV-2 by Molecular Docking SARS-CoV-2获批药物的分子对接比较研究

Journal of Molecular Docking Pub Date : 2021-06-30 DOI: 10.33084/jmd.v1i1.2148

A. Mishra, Radhika Waghela

引用次数: 0

Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2 利用不同冠状病毒刺突蛋白和ACE2分子对接研究开发SARS-CoV-2抑制剂

Journal of Molecular Docking Pub Date : 2021-06-30 DOI: 10.33084/jmd.v1i1.2212

Israa. M. Shamkh, D. Pratiwi

{"title":"Development of SARS-CoV-2 Inhibitors Using Molecular Docking Study with Different Coronavirus Spike Protein and ACE2","authors":"Israa. M. Shamkh, D. Pratiwi","doi":"10.33084/jmd.v1i1.2212","DOIUrl":"https://doi.org/10.33084/jmd.v1i1.2212","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86177591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 1 June 2021 封面，内容和编辑说明来自jmol对接卷1第1期2021年6月

Journal of Molecular Docking Pub Date : 2021-06-30 DOI: 10.33084/jmd.v1i1.2382

Chief Editor Of J Mol Docking

{"title":"Cover, Content, and Editorial Note from J Mol Docking Vol. 1 No. 1 June 2021","authors":"Chief Editor Of J Mol Docking","doi":"10.33084/jmd.v1i1.2382","DOIUrl":"https://doi.org/10.33084/jmd.v1i1.2382","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86516654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0