Pub Date : 2022-08-21DOI: 10.25135/acg.oc.135.2206.2485
Adnan Dahadha, Mohammad Abunuwar, Mohammad Al-Dhoun, Mohammad Hassan, M. Saadh
{"title":"Optimization of Kumada cross-coupling reactions of tri- and tetra- bromothiophenes and symmetrical di-bromo-2, 2' bithiophene with cyclohexylmagnesium bromide: Synthesis, DFT studies and nonlinear optical analysis","authors":"Adnan Dahadha, Mohammad Abunuwar, Mohammad Al-Dhoun, Mohammad Hassan, M. Saadh","doi":"10.25135/acg.oc.135.2206.2485","DOIUrl":"https://doi.org/10.25135/acg.oc.135.2206.2485","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44199015","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}
Pub Date : 2022-08-14DOI: 10.25135/acg.oc.133.2204.2439
A. Kumer, M. Kobir, Mahbub Alam, Unesco Chakma, Parul Akter, M. H. Bhuiyan
Pyrimido[4,5-d]pyrimidine conveys antimicrobial activity against various micro pathogens having functionalized properties. As a result, this study has designed to illustrate the antibacterial, antifungal, and antiviral properties of pyrimido[4,5-d]pyrimidine. First of all, these structures have been optimized from the characterization of synthesis for calculating chemical descriptors by DFT. Next, the auto docking and target docking against 12 proteins, such as Pseudomonas aeruginosa (2Y0H), Bacillus cereus (1AH7), Escherichia coli (6DR3), Shigella dysenteriae (3FHH) Salmonella typhi (3FHU), Aspergillus niger (1ACZ), Aspergillus flavus (1XY3), Rhizomucor miehei (4WTP), Candida auris (6U8J), three proteins of SARS-CoV-2 (7T9J, 7T9L, and 7TB4) were performed for the determination of binding sites and binding affinity. One FDA approved drug (Ampicillin) has docked against 12 proteins while the Bacillus cereus (Bacteria), Aspergillus flavus (Fungus), and SARS-CoV-2, 7T9L (Omicron) are obtained the best binding affinity after docking. The most common residues are the PHE-66, ARG-176 and VAL-124 for Bacillus cereus, Aspergillus flavus and SARS-CoV-2, Omicron (7T9L), respectively, as they blocked the active sites by the ligands as inhibitors. It is revealed that this study contained both auto docking and target docking whereas the binding affinity of auto docking is that the binding affinity for auto docking is higher than target docking. Finally, among the nine compounds, three compounds show outstanding results against bacteria, fungus and virus. At last, molecular dynamics were performed to check the stability and validation of the docked complex and quantum calculations obtained the molecular properties, as well as ADMET, pharmacokinetics, Lipinski Rule and QSAR data.
{"title":"Antibacterial, antifungal and antiviral activities of pyrimido[4,5-d]pyrimidine derivatives through computational approaches","authors":"A. Kumer, M. Kobir, Mahbub Alam, Unesco Chakma, Parul Akter, M. H. Bhuiyan","doi":"10.25135/acg.oc.133.2204.2439","DOIUrl":"https://doi.org/10.25135/acg.oc.133.2204.2439","url":null,"abstract":"Pyrimido[4,5-d]pyrimidine conveys antimicrobial activity against various micro pathogens having functionalized properties. As a result, this study has designed to illustrate the antibacterial, antifungal, and antiviral properties of pyrimido[4,5-d]pyrimidine. First of all, these structures have been optimized from the characterization of synthesis for calculating chemical descriptors by DFT. Next, the auto docking and target docking against 12 proteins, such as Pseudomonas aeruginosa (2Y0H), Bacillus cereus (1AH7), Escherichia coli (6DR3), Shigella dysenteriae (3FHH) Salmonella typhi (3FHU), Aspergillus niger (1ACZ), Aspergillus flavus (1XY3), Rhizomucor miehei (4WTP), Candida auris (6U8J), three proteins of SARS-CoV-2 (7T9J, 7T9L, and 7TB4) were performed for the determination of binding sites and binding affinity. One FDA approved drug (Ampicillin) has docked against 12 proteins while the Bacillus cereus (Bacteria), Aspergillus flavus (Fungus), and SARS-CoV-2, 7T9L (Omicron) are obtained the best binding affinity after docking. The most common residues are the PHE-66, ARG-176 and VAL-124 for Bacillus cereus, Aspergillus flavus and SARS-CoV-2, Omicron (7T9L), respectively, as they blocked the active sites by the ligands as inhibitors. It is revealed that this study contained both auto docking and target docking whereas the binding affinity of auto docking is that the binding affinity for auto docking is higher than target docking. Finally, among the nine compounds, three compounds show outstanding results against bacteria, fungus and virus. At last, molecular dynamics were performed to check the stability and validation of the docked complex and quantum calculations obtained the molecular properties, as well as ADMET, pharmacokinetics, Lipinski Rule and QSAR data.","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43014708","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}
Pub Date : 2022-07-18DOI: 10.25135/acg.oc.132.2203.2374
O. Oyeneyin, Nureni Ipinloju, C. G. Iwegbulam, A. Oyebamiji, Bambo F. Olajide
{"title":"Prediction of the antiproliferative effects of some benzimidazole-chalcone derivatives against MCF-7 breast cancer cell lines: QSAR and molecular docking studies","authors":"O. Oyeneyin, Nureni Ipinloju, C. G. Iwegbulam, A. Oyebamiji, Bambo F. Olajide","doi":"10.25135/acg.oc.132.2203.2374","DOIUrl":"https://doi.org/10.25135/acg.oc.132.2203.2374","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42614196","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}
Pub Date : 2022-06-28DOI: 10.25135/acg.oc.123.2112.2279
K. Prasada Rao, C. Subramanyam, Meson Haji Basha, Sagurthi Someswara Rao, C. Malar
{"title":"Nano TiO2.SiO2 catalyzed, microwave assisted synthesis of new α-aminophosphonates as potential anti-diabetic agents: In silico ADMET and molecular docking study","authors":"K. Prasada Rao, C. Subramanyam, Meson Haji Basha, Sagurthi Someswara Rao, C. Malar","doi":"10.25135/acg.oc.123.2112.2279","DOIUrl":"https://doi.org/10.25135/acg.oc.123.2112.2279","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45516604","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}
Pub Date : 2022-06-28DOI: 10.25135/acg.oc.122.2203.2397
S. Kawsar, A. Kumer, Nasrin S Munia, Mohammed A. Hosen, Unesco Chakma, S. Akash
: The methyl α-D-glucopyranoside and its derivatives have been estimated as the antimicrobial agents against numerous human pathogens, which is constantly amplifying the attention of medicinal chemists to design new bioactive molecules and their structure-activity relationship (SAR) while the computational tools are the most lucid and trustable avenue to perform their theoretical profile building up. Firstly, the predictionof activity spectra for substances (PASS) value has illustrated initially information about the antifungal, antibacterial, antiviral, and anticancer potential. It was observed that the PASS predicted pathogens supported their score higher in fungal species than bacteria. However, the “Lipinski five rule” has been monitored for drug-likeness properties. After confirming their biological significance, molecular docking has been completed against both the bacteria and fungi and these docked complexes have been optimized for molecular dynamics through the water system. A molecular docking study against nine bacterial and fungal pathogens revealed promising binding affinity and non-bonding interaction mostly for derivatives ( 5-8 ). The chemical descriptors have been obtained using the density functional theory (DFT) and predict their chemical stability and softness in the biological system. The molecular dynamics study was found to be the best stability of all docked complexes. At last, the ADMET properties have been calculated and provide the safe use and non-carcinogenic fact with low toxicity for both aquatic and non-aquatic species. Finally, it is concluded that these selected derivatives ( 5-8 ) are highly antifungal potential molecules than antibacterial potential which has been varied with respect to their structural side chain in the D-glucopyranoside sequence. antibiotic, anticancer antiviral. results reveal that these were more efficient against bacterial and virus pathogens in comparison with fungal pathogens. The attachment of additional aliphatic acyl chainincreased antibacterial activity Pa 0.534) 0.534) of Pa 0.614), whereas the insertion of
{"title":"Chemical descriptors, PASS, molecular docking, molecular dynamics and ADMET predictions of glucopyranoside derivatives as inhibitors to bacteria and fungi growth","authors":"S. Kawsar, A. Kumer, Nasrin S Munia, Mohammed A. Hosen, Unesco Chakma, S. Akash","doi":"10.25135/acg.oc.122.2203.2397","DOIUrl":"https://doi.org/10.25135/acg.oc.122.2203.2397","url":null,"abstract":": The methyl α-D-glucopyranoside and its derivatives have been estimated as the antimicrobial agents against numerous human pathogens, which is constantly amplifying the attention of medicinal chemists to design new bioactive molecules and their structure-activity relationship (SAR) while the computational tools are the most lucid and trustable avenue to perform their theoretical profile building up. Firstly, the predictionof activity spectra for substances (PASS) value has illustrated initially information about the antifungal, antibacterial, antiviral, and anticancer potential. It was observed that the PASS predicted pathogens supported their score higher in fungal species than bacteria. However, the “Lipinski five rule” has been monitored for drug-likeness properties. After confirming their biological significance, molecular docking has been completed against both the bacteria and fungi and these docked complexes have been optimized for molecular dynamics through the water system. A molecular docking study against nine bacterial and fungal pathogens revealed promising binding affinity and non-bonding interaction mostly for derivatives ( 5-8 ). The chemical descriptors have been obtained using the density functional theory (DFT) and predict their chemical stability and softness in the biological system. The molecular dynamics study was found to be the best stability of all docked complexes. At last, the ADMET properties have been calculated and provide the safe use and non-carcinogenic fact with low toxicity for both aquatic and non-aquatic species. Finally, it is concluded that these selected derivatives ( 5-8 ) are highly antifungal potential molecules than antibacterial potential which has been varied with respect to their structural side chain in the D-glucopyranoside sequence. antibiotic, anticancer antiviral. results reveal that these were more efficient against bacterial and virus pathogens in comparison with fungal pathogens. The attachment of additional aliphatic acyl chainincreased antibacterial activity Pa 0.534) 0.534) of Pa 0.614), whereas the insertion of","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46583602","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}
Pub Date : 2022-06-28DOI: 10.25135/acg.oc.133.2203.2388
T. K. Shabeer, Abbas Khaja Mohideen, Kasim Mohammed Mustaque, Ismail Salim Meeran, Annadurai Subramani, V. S. Jamal Ahamed, H. Thajudeen
{"title":"Solvent-free synthesis, molecular simulation and cytotoxicity of 1,4-benzodiazepine-2,5-diones","authors":"T. K. Shabeer, Abbas Khaja Mohideen, Kasim Mohammed Mustaque, Ismail Salim Meeran, Annadurai Subramani, V. S. Jamal Ahamed, H. Thajudeen","doi":"10.25135/acg.oc.133.2203.2388","DOIUrl":"https://doi.org/10.25135/acg.oc.133.2203.2388","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41871463","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}
Pub Date : 2022-06-28DOI: 10.25135/acg.oc.132.2203.2370
J. Soni, Rahul H. Rayani, Deepa R. Parmar, Anand Vala, R. Kusurkar, V. Zunjar, Satyanarayana Battula
{"title":"Design, synthesis, in silico and biological evaluation of biotin-pyrazole derivatives as anti-cancer activity","authors":"J. Soni, Rahul H. Rayani, Deepa R. Parmar, Anand Vala, R. Kusurkar, V. Zunjar, Satyanarayana Battula","doi":"10.25135/acg.oc.132.2203.2370","DOIUrl":"https://doi.org/10.25135/acg.oc.132.2203.2370","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49038112","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}
Pub Date : 2022-06-28DOI: 10.25135/acg.oc.128.2202.2356
Alkesh N Patel, Rushi Shah, Diwyanshi Zinzuvadia, Sagar Mahant, A. Patel
The first incidence of corona virus was reported in China in December of 2019, and the virus quickly spread over the world, eventually being designated a pandemic in March of 2020. It has had a disastrous impact on the global healthcare system. Virus has claimed the lives of 5,298,933 people through December 2021. As a result of the pandemic, there was a boost of research into diagnostic and therapeutic methods to infection. Gradually, the world has discovered new vaccine candidates and medicinal repurposing strategies that have a significant influence on mortality, by which there has been a drop-in death rates over the world since July, 2021. Many patients, particularly those who have been hospitalized due to a viral infection, experience complications beyond discharge that have a significant influence on their lives. Post COVID-19 complications are problems that last longer than 3-4 weeks following a viral infection. There is currently no specific treatment accessible for post COVID-19 problems because whatever medications are available or repurposed are limited to disease prophylaxis and therapeutics. As a result, we're looking for a remedy employing natural substances using the In-Silico technique (molecular docking) and recent research from reputable journals. Allicin, Berberine, Epigallocatechin, Rosmarinic acid and Withaferin-A were docked against ACE (PDB ID: 1O8A), IL-6 (PDB ID: 1ALU), NADPH Oxidase (PDB ID: 2CDU) and TNF-alpha (PDB ID: 2AZ5) using Autodock.
{"title":"Discovering the potential of natural remedies in the post COVID-19 complications based on in silico techniques","authors":"Alkesh N Patel, Rushi Shah, Diwyanshi Zinzuvadia, Sagar Mahant, A. Patel","doi":"10.25135/acg.oc.128.2202.2356","DOIUrl":"https://doi.org/10.25135/acg.oc.128.2202.2356","url":null,"abstract":"The first incidence of corona virus was reported in China in December of 2019, and the virus quickly spread over the world, eventually being designated a pandemic in March of 2020. It has had a disastrous impact on the global healthcare system. Virus has claimed the lives of 5,298,933 people through December 2021. As a result of the pandemic, there was a boost of research into diagnostic and therapeutic methods to infection. Gradually, the world has discovered new vaccine candidates and medicinal repurposing strategies that have a significant influence on mortality, by which there has been a drop-in death rates over the world since July, 2021. Many patients, particularly those who have been hospitalized due to a viral infection, experience complications beyond discharge that have a significant influence on their lives. Post COVID-19 complications are problems that last longer than 3-4 weeks following a viral infection. There is currently no specific treatment accessible for post COVID-19 problems because whatever medications are available or repurposed are limited to disease prophylaxis and therapeutics. As a result, we're looking for a remedy employing natural substances using the In-Silico technique (molecular docking) and recent research from reputable journals. Allicin, Berberine, Epigallocatechin, Rosmarinic acid and Withaferin-A were docked against ACE (PDB ID: 1O8A), IL-6 (PDB ID: 1ALU), NADPH Oxidase (PDB ID: 2CDU) and TNF-alpha (PDB ID: 2AZ5) using Autodock.","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47724067","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}
Pub Date : 2022-05-15DOI: 10.25135/acg.oc.125.2203.2407
N. Kahriman, N. Yaylı, G. KiliÇ, Vildan Serdaroğlu, R. Aliyazicioglu, H. E. Sellitepe, Şengül Alpay Karaoğlu, Gizem Tatar Yılmaz
{"title":"Molecular docking, synthesis and biological evaluation (enzyme inhibition, antimicrobial and antioxidant) of methoxy benzoin/benzil/stilbenoid derivatives","authors":"N. Kahriman, N. Yaylı, G. KiliÇ, Vildan Serdaroğlu, R. Aliyazicioglu, H. E. Sellitepe, Şengül Alpay Karaoğlu, Gizem Tatar Yılmaz","doi":"10.25135/acg.oc.125.2203.2407","DOIUrl":"https://doi.org/10.25135/acg.oc.125.2203.2407","url":null,"abstract":"","PeriodicalId":19553,"journal":{"name":"Organic Communications","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2022-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48574978","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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