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.
Assalamu 'alaikum弯角。白平衡。Alhamdulillahirabbil”可以。经过近一年的漫长等待，穆罕默迪亚帕朗卡拉亚大学药学系的新科学杂志可以出版了。这本科学杂志被命名为分子对接杂志(J Mol对接)，灵感来自计算机辅助药物设计中最流行的计算机方法之一。《分子对接》杂志每6个月出版一次(2期/年)，每年6月和12月出版。该书收录了埃及、印度尼西亚、塞尔维亚、斯洛文尼亚、孟加拉国、越南等6个国家的5篇文章。作者来自几个机构，包括生物搜索研究所、Sekolah Tinggi Farmasi Muhammadiyah Tangerang、开罗大学、benememacriad University Autónoma de Puebla、universverzitet u Prištini、母校Europaea - ECM、universverzitet Privredna akademija u Novom Sadu、universverzitet Odbrane、Vojvode Tankosica卫生中心、BDORT功能补充和综合医学中心、Jagannath大学、Can Tho大学和Universitas 17 Agustus 1945 Jakarta。编委会充分意识到本版仍有改进的余地，因此，我们非常谦虚地愿意接受建设性的建议和反馈，以改进下一版的出版物。编辑委员会在此感谢所有编辑和审稿人，以及为本期科学文章提供重复清单的贡献者。我们希望各方，特别是文章的撰稿人能够再次参与到2022年6月出版的下一版中来。Wassalamu 'alaikum弯角。白平衡。
{"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}
Momir Dunjic, S. Turini, Slaviša Stanišić, N. Sulovic, S. Cvetkovic, Dejan Mihajlovic, M. Dunjic, Dusan Simic, Katarina Dunjić
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.
{"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}
Israa. M. Shamkh, D. Pratiwi, Hanaa S. Omar, N. E. Reyad
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.
被称为COVID-19的严重急性呼吸系统综合征冠状病毒在全球范围内急剧增加。这种疾病于2019年12月左右在中国武汉开始，然后传播到大多数国家。保持社交距离是预防感染的最佳措施。由于计算机辅助药物设计(CADD)方法，筛选包含数百万药物分子或植物化学物质的可用数据库变得快速和直接。本研究通过对接研究筛选了300种植物化学物质和纤维素醚衍生物。对接分析表明，只有4个分子(a-新橙皮苷、槲皮素3- o -葡萄糖糖苷、14-酮苯二醇二乙酸酯和羟丙基甲基纤维素)能够与穗蛋白相互作用。其中槲皮素3- o -葡萄糖糖苷和14-酮戊二醇二醋酸酯可与SARS-CoV-2宿主细胞受体(ACE2)相互作用。这四种化合物的结合亲和力都很高。尽管如此，根据利平斯基的五法则，由于其药代动力学和ADMET特性，只有14-酮苯二醇二乙酸酯被选为药物分子。筛选14-酮苯二醇二乙酸酯的药物类似物检测到五种批准的药物。这些药物与靶蛋白对接分析表明，5种药物与宿主受体蛋白相互作用，3种药物与病毒刺突蛋白相互作用。因此，我们建议分子对接和药物类似物研究可以支持快速药物开发。此外，需要对14-酮苯二醇二乙酸酯的治疗应用进行未来的展望，以便将其用于治疗SARS-CoV-2感染。
{"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}
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.
作者在之前的版本中发现了一个错误(Shamkh, IM， & Pratiwi, D.(2021))。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抑制剂分子对接学报，1(1)，1-14。https://doi.org/10.33084/jmd.v1i1.2212)， Hanaa S. Omar博士是该研究的主管，但并未被列为作者之一。本注中增加了Hanaa S. Omar博士为作者之一，并注明了本研究通讯作者的身份。
{"title":"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]","authors":"Israa. M. Shamkh, D. Pratiwi, Hanaa S. Omar","doi":"10.33084/jmd.v1i2.3063","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.3063","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88299080","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}
G. N. Lopez-Castillo, V. Alatriste, J. Sandoval-Ramírez, F. Luna, A. Carrasco-Carballo
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.
{"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}
Sukumar Bepary, B. Biswas, P. Ghosh, Md. Aminul Haque, Tran Quang De
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.
{"title":"N-acetylation of 2-aminobenzothiazoles with Acetic Acid for Evaluation of Antifungal Activity and In Silico Analysis","authors":"Sukumar Bepary, B. Biswas, P. Ghosh, Md. Aminul Haque, Tran Quang De","doi":"10.33084/jmd.v1i2.3142","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.3142","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85126630","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}
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.
{"title":"In Silico Anti-Inflammation Prediction of Glycyrrhiza Extracts Against Covid-19","authors":"Mansoureh Nazari","doi":"10.33084/jmd.v1i2.3154","DOIUrl":"https://doi.org/10.33084/jmd.v1i2.3154","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"76 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91240376","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}
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.
{"title":"A Comparative Study of Approved Drugs for SARS-CoV-2 by Molecular Docking","authors":"A. Mishra, Radhika Waghela","doi":"10.33084/jmd.v1i1.2148","DOIUrl":"https://doi.org/10.33084/jmd.v1i1.2148","url":null,"abstract":"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.","PeriodicalId":16421,"journal":{"name":"Journal of Molecular Docking","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83597690","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}
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.
新型冠状病毒SARS-CoV-2是在中国武汉市出现的一种急性呼吸道感染。冠状病毒的刺突蛋白是宿主细胞识别的主要驱动力，负责与宿主细胞上的ACE2受体结合，介导宿主与病毒膜的融合。识别可以与刺突蛋白(s蛋白)形成复合物的化合物可以有效地抑制SARS-CoV-2感染。该软件用于调查300种植物天然化合物或衍生物与SARS-CoV-2 s蛋白的结合能力。计算配体与每个蛋白质的对接分数，以估计结合自由能。四种化合物(新橙皮苷、槲皮素3- o -芦丁苷-7- o -葡萄糖苷、14-酮苯二醇二乙酸酯和羟丙基甲基纤维素)与s蛋白具有很强的结合能力，并用于预测s蛋白的对接模型和结合区域。预测配体/蛋白亲和力最高的是槲皮素3- o -芦丁苷-7- o -葡萄糖苷，其次是新橙皮苷。这四种化合物还对其他相关冠状病毒进行了检测，显示出它们与蝙蝠、SARS和中东呼吸综合征冠状病毒株的s蛋白结合能力，表明它们可以结合并阻断刺突活性，从而阻止它们感染不同的冠状病毒。分子对接也显示了四种配体与宿主细胞受体ACE2结合的概率。鉴定了配合物的相互作用残基和结合能。这四种化合物与s蛋白和ACE2蛋白的强结合能力表明，它们可能用于开发针对SARS-CoV-2和密切相关的人类冠状病毒的特异性治疗药物。
{"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}
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.
{"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}
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