In Silico Pharmacology最新文献

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Quercetin attenuates viral infections by interacting with target proteins and linked genes in chemicobiological models. 槲皮素在化学生物学模型中通过与靶蛋白和相关基因相互作用来减弱病毒感染。
In Silico Pharmacology Pub Date : 2022-09-16 eCollection Date: 2022-01-01 DOI: 10.1007/s40203-022-00132-2
Md Atiar Rahman, Fauzia Mahanaz Shorobi, Md Nazim Uddin, Srabonti Saha, Md Amjad Hossain
{"title":"Quercetin attenuates viral infections by interacting with target proteins and linked genes in chemicobiological models.","authors":"Md Atiar Rahman, Fauzia Mahanaz Shorobi, Md Nazim Uddin, Srabonti Saha, Md Amjad Hossain","doi":"10.1007/s40203-022-00132-2","DOIUrl":"10.1007/s40203-022-00132-2","url":null,"abstract":"<p><p>Medicinally active compounds in the flavonoid class of phytochemicals are being studied for antiviral action against various DNA and RNA viruses. Quercetin is a flavonoid present in a wide range of foods, including fruits and vegetables. It is said to be efficient against a wide range of viruses. This research investigated the usefulness of Quercetin against Hepatitis C virus, Dengue type 2 virus, Ebola virus, and Influenza A using computational models. A molecular docking study using the online tool PockDrug was accomplished to identify the best binding sites between Quercetin and PubChem-based receptors. Network-pharmacological assay to opt to verify function-specific gene-compound interactions using STITCH, STRING, GSEA, Cytoscape plugin cytoHubba. Quercetin explored tremendous binding affinity against NS5A protein for HCV with a docking score of - 6.268 kcal/mol, NS5 for DENV-2 with a docking score of - 5.393 kcal/mol, VP35 protein for EBOV with a docking score of - 4.524 kcal/mol, and NP protein for IAV with a docking score of - 6.954 kcal/mol. In the network-pharmacology study, out of 39 hub genes, 38 genes have been found to interact with Quercetin and the top interconnected nodes in the protein-protein network were (based on the degree of interaction with other nodes) <i>AKT1, EGFR, SRC, MMP9, MMP2, KDR, IGF1R, PTK2, ABCG2,</i> and <i>MET.</i> Negative binding energies were noticed in Quercetin-receptor interaction. Results demonstrate that Quercetin could be a potential antiviral agent against these viral diseases with further study in <i>in-vivo</i> models.</p><p><strong>Graphical abstract: </strong></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-022-00132-2.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10587360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of vaccine candidate against Omicron variant of SARS-CoV-2 using immunoinformatic approaches. 使用免疫信息学方法鉴定针对严重急性呼吸系统综合征冠状病毒2型奥密克戎变异株的候选疫苗。
In Silico Pharmacology Pub Date : 2022-07-26 eCollection Date: 2022-01-01 DOI: 10.1007/s40203-022-00128-y
Aasim, Ruchika Sharma, C R Patil, Anoop Kumar, Kalicharan Sharma
{"title":"Identification of vaccine candidate against Omicron variant of SARS-CoV-2 using immunoinformatic approaches.","authors":"Aasim,&nbsp;Ruchika Sharma,&nbsp;C R Patil,&nbsp;Anoop Kumar,&nbsp;Kalicharan Sharma","doi":"10.1007/s40203-022-00128-y","DOIUrl":"https://doi.org/10.1007/s40203-022-00128-y","url":null,"abstract":"<p><p>Despite the availability of COVID-19 vaccines, additional more potent vaccines are still required against the emerging variations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the present investigation, we have identified a promising vaccine candidate against the Omicron (B.1.1.529) using immunoinformatics approaches. Various available tools like, the Immune Epitope Database server resource, and NetCTL-1.2, have been used for the identification of the promising T-cell and B-cell epitopes. The molecular docking was performed to check the interaction of TLR-3 receptors and validated 3D model of vaccine candidate. The codon optimization was done followed by cloning using SnapGene. Finally, In-silico immune simulation profile was also checked. The identified T-cell and B-cell epitopes have been selected based on their antigenicity (VaxiJen v2.0) and, allergenicity (AllerTOP v2.0). The identified epitopes with antigenic and non-allergenic properties were fused with the specific peptide linkers. In addition, the 3D model was constructed by the PHYRE2 server and validated using ProSA-web. The validated 3D model was further docked with the Toll-like receptor 3 (TLR3) and showed good interaction with the amino acids which indicate a promising vaccine candidate against the Omicron variant of SARS-CoV-2. Finally, the codon optimization, <i>In-silico</i> cloning and immune simulation profile was found to be satisfactory. Overall, the designed vaccine candidate has a potential against variant of SARS-Cov-2. However, further experimental studies are required to confirm.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":" ","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2022-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9315333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40568226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Computational approaches for the design of novel dopamine D2 and serotonin 5-HT2A receptor dual antagonist towards schizophrenia 设计新型多巴胺D2和5-羟色胺5-HT2A受体双拮抗剂治疗精神分裂症的计算方法
In Silico Pharmacology Pub Date : 2022-04-08 DOI: 10.1007/s40203-022-00121-5
Akash Rathore, Vivek Asati, Mitali Mishra, R. Das, Varsha Kashaw, S. Kashaw
{"title":"Computational approaches for the design of novel dopamine D2 and serotonin 5-HT2A receptor dual antagonist towards schizophrenia","authors":"Akash Rathore, Vivek Asati, Mitali Mishra, R. Das, Varsha Kashaw, S. Kashaw","doi":"10.1007/s40203-022-00121-5","DOIUrl":"https://doi.org/10.1007/s40203-022-00121-5","url":null,"abstract":"","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83958039","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: 5
Inhibitory effects of selected isoquinoline alkaloids against main protease (Mpro) of SARS-CoV-2, in silico study. 选定的异喹啉生物碱对 SARS-CoV-2 主要蛋白酶(Mpro)的抑制作用硅学研究。
In Silico Pharmacology Pub Date : 2022-03-14 eCollection Date: 2022-01-01 DOI: 10.1007/s40203-022-00122-4
Morteza Sadeghi, Mehran Miroliaei
{"title":"Inhibitory effects of selected isoquinoline alkaloids against main protease (M<sup>pro</sup>) of SARS-CoV-2, in silico study.","authors":"Morteza Sadeghi, Mehran Miroliaei","doi":"10.1007/s40203-022-00122-4","DOIUrl":"10.1007/s40203-022-00122-4","url":null,"abstract":"<p><p>The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite the production of various vaccines and different treatments, finding natural compounds to control COVID-19 is still a challenging task. Isoquinoline alkaloids are naturally occurring compounds known to have some potential antiviral activity. In this study, ten abundant isoquinoline alkaloids with antiviral activity were selected to analyze the preventive effect on COVID-19. A scrutinized evaluation based on Lipinski's rule showed that one out of ten compounds was toxic. Based on molecular docking analysis using Autodock software one of the best molecules with maximum negative binding energy was selected for further analysis. The Gromacs simulation analysis revealed that Coptisine has more action against active site M<sup>pro</sup> of COVID-19. Overall, to make a rational design of various preventive analogues that inhibit the COVID-19, associated in vitro and in vivo analyses are needed to confirm this claim.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":" ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8918422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40309461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Docking simulation and ADMET prediction based investigation on the phytochemical constituents of Noni (Morinda citrifolia) fruit as a potential anticancer drug. 基于对接模拟和ADMET预测的诺丽果潜在抗癌药物的植物化学成分研究
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00130-4
Kaliraj Chandran, Drose Ignatious Shane, Azar Zochedh, Asath Bahadur Sultan, Thandavarayan Kathiresan
{"title":"Docking simulation and ADMET prediction based investigation on the phytochemical constituents of Noni (<i>Morinda citrifolia</i>) fruit as a potential anticancer drug.","authors":"Kaliraj Chandran,&nbsp;Drose Ignatious Shane,&nbsp;Azar Zochedh,&nbsp;Asath Bahadur Sultan,&nbsp;Thandavarayan Kathiresan","doi":"10.1007/s40203-022-00130-4","DOIUrl":"https://doi.org/10.1007/s40203-022-00130-4","url":null,"abstract":"<p><p><i>Morinda citrifolia</i> is a traditional plant used in Asian and African countries for its wide nutraceutical and therapeutic effects for the treatment of various ailments. The fruit of <i>M. citrifolia</i> has various biological properties such as anti-bacterial, anti-oxidant, anti-cancer. Using the molecular docking based investigation; we explored around twenty three bioactive phytochemicals in <i>M. citrifolia</i> fruit against human cancer. MAPK6 (mitogen-activated protein kinase 6) was selected as target protein and these twenty three phytochemicals along with a known MAPK6 inhibitor were docked against the target protein. The docking scores of the bioactive phytochemicals against MAPK6 protein range between - 4.5 kcal/mol to - 7.9 kcal/mol and the docking score of the standard drug (CID: 447077) was - 7.3 kcal/mol. Based on the binding affinity five phytochemicals asperuloside (- 6.7 kcal/mol), asperulosidic acid (- 7.2 kcal/mol), deacetylasperulosidic acid (- 7.0 kcal/mol), eugenol (- 6.8 kcal/mol) and rutin (- 7.9 kcal/mol) were chosen for further evaluation. These five compounds were further investigated through RC plot analysis, density function theory and ADMET properties. Stable linkage of protein-ligand interaction was observed through RC plot, density function theory showed the structural stability and reactivity of bioactive compounds through the energy gap between HOMO and LUMO and the ADMET (adsorption, distribution, metabolism, excretion and toxicity) studies showed the safety profile of the bioactive compounds. These in silico results support the utilization of <i>M. citrifolia</i> fruit in the traditional medication and the initiation for the development of new drug against human cancer through in vivo and in vitro evaluation.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-022-00130-4.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9411403/pdf/40203_2022_Article_130.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10073007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 17
Ofatumumab and Granzyme B as immunotoxin against CD20 antigen. Ofatumumab和颗粒酶B作为CD20抗原的免疫毒素。
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00120-6
Fateme Sefid, Armina Alagheband Bahrami, Zahra Payandeh, Saeed Khalili, Ghasem Azamirad, Seyed Mehdy Kalantar, Maryam Touhidinia
{"title":"Ofatumumab and Granzyme B as immunotoxin against CD20 antigen.","authors":"Fateme Sefid,&nbsp;Armina Alagheband Bahrami,&nbsp;Zahra Payandeh,&nbsp;Saeed Khalili,&nbsp;Ghasem Azamirad,&nbsp;Seyed Mehdy Kalantar,&nbsp;Maryam Touhidinia","doi":"10.1007/s40203-022-00120-6","DOIUrl":"https://doi.org/10.1007/s40203-022-00120-6","url":null,"abstract":"<p><p>Anti-CD20 antibodies such as ofatumumab has demonstrated efficacy in relapsed/refractory chronic lymphocytic leukemia, are among the most successful therapies to date. In this study, we have designed an immunotoxin composed of Granzyme B and the high affinity variant of Ofatumumab. Different simulation software applied to explore the structure of Granzyme B, a serine protease in cytotoxic lymphocytes granules as an apoptosis mediator was attached to its specific antibody structure (Ofatumumab) via an adaptor sequence. The accuracy, energy minimization and characterization of biological properties of the final structure were evaluated. Our computational outcomes indicated that the employed method for structure prediction has been successfully managed to design the immunotoxin structure. The precise and accurate design of the immune-therapeutic agents against cancer cells can be confirmed by employment of in-silico approaches. Consequently, based on this approach we could introduce a capable immunotoxin which specifically targeting CD20 in an accurate orientation and initiates cancer cell destruction by its toxin domain.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-022-00120-6.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8933591/pdf/40203_2022_Article_120.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9188466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Khaya grandifoliola active fraction as a source of therapeutic compounds for Alzheimer's disease treatment: In silico validation of identified compounds. 桔梗有效成分作为阿尔茨海默病治疗化合物的来源:已鉴定化合物的硅验证。
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00126-0
Brice Ayissi Owona, Frederic N Njayou, Pierre Mkounga, Paul F Moundipa
{"title":"<i>Khaya grandifoliola</i> active fraction as a source of therapeutic compounds for Alzheimer's disease treatment: In silico validation of identified compounds.","authors":"Brice Ayissi Owona,&nbsp;Frederic N Njayou,&nbsp;Pierre Mkounga,&nbsp;Paul F Moundipa","doi":"10.1007/s40203-022-00126-0","DOIUrl":"https://doi.org/10.1007/s40203-022-00126-0","url":null,"abstract":"<p><p>Overproduction of Nitric oxide (NO) and many other pro-inflammatory mediators are responsible for many pathological disorders in humans, including Alzheimer's disease (AD). In this study, active fractions isolated from <i>Khaya grandifoliola</i> (Kg) were screened for their inhibitory activities against NO production in lipopolysaccharide (LPS)-activated microglia. Among the 5 fractions tested, Kg25 was the most active and showed potent inhibitory activity towards NO production. The fraction further showed inhibitory effect on iNOS'<sup>s</sup> mRNA expression and other major pro-inflammatory cytokines including TNFα and IL1-β. Study of the effect of Kg25 on p38MAPKinase and JNK3 showed that the fraction inhibits these signaling pathways known to be involved in cell inflammatory pathways. These observations were confirmed at the protein level with Kg25 inhibiting iNOS and p38MAPK protein expressions in N9 cells. Analysis of Kg25 composition by HPLC identified 3 main compounds, namely: 6 phenyl, 4-(1`oxyehylphenyl) hexane, Carbamic acid, (4-methly-1-phenyl)-1, phenyl, and Benzene, 1 1`-(oxydiethylidene) bis. The above mentionned compounds were further analyzed for their bioactivity against the p38MAPKinase and iNOS receptors using molecular docking. MolDock results showed that 1-phenylethyl <i>N</i>-(4-methylphenyl)carbamate (compound 2) possesses the highest binding affinity (for iNOS); and 1-(1-phenylethoxy)ethylbenzene (compound 3) (for pMAPK) respectively and both compounds interact well with the active site residues. Hence, these compounds could be considered as scaffolds for further development of lead- drugs targeting neuroinflammation in AD.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9253233/pdf/40203_2022_Article_126.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10124784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approach. 建模和靶向线粒体蛋白酪氨酸磷酸酶1:计算方法。
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00119-z
Venkataraghavan Ragunathan, K Chithra, C Shivanika, Meenambiga Setti Sudharsan
{"title":"Modelling and targeting mitochondrial protein tyrosine phosphatase 1: a computational approach.","authors":"Venkataraghavan Ragunathan,&nbsp;K Chithra,&nbsp;C Shivanika,&nbsp;Meenambiga Setti Sudharsan","doi":"10.1007/s40203-022-00119-z","DOIUrl":"https://doi.org/10.1007/s40203-022-00119-z","url":null,"abstract":"<p><p>The present research scintillates on the homology modelling of rat mitochondrial protein tyrosine phosphatase 1 (PTPMT1) and targeting its activity using flavonoids through a computational docking approach. PTPMT1 is a dual-specificity phosphatase responsible for protein phosphorylation and plays a vital role in the metabolism of cardiolipin biosynthesis, insulin regulation, etc. The inhibition of PTPMT1 has also shown enhanced insulin levels. The three-dimensional structure of the protein is not yet known. The homology modelling was performed using SWISS-MODEL and Geno3D webservers to compare the efficiencies. The PROCHECK for protein modelled using SWISS-MODEL showed 91.6% of amino acids in the most favoured region, 0.7% residues in the disallowed region that was found to be significant compared to the model built using Geno3D. 210 common flavonoids were docked in the modelled protein using the AutoDock 4.2.6 along with a control drug alexidine dihydrochloride. Our results show promising candidates that bind protein tyrosine phosphatase 1, including, prunin (- 8.66 kcal/mol); oroxindin (- 8.56 kcal/mol); luteolin 7-rutinoside (- 8.47 kcal/mol); 3(2H)-isoflavenes (- 8.36 kcal/mol); nicotiflorin (- 8.29 kcal/mol), ranked top in the docking experiments. We predicted the pharmacokinetic and Lipinski properties of the top ten compounds with the lowest binding energies. To further validate the stability of the modelled protein and docked complexes molecular dynamics simulations were performed using Desmond, Schrodinger for 150 ns in conjunction with MM-GBSA. Thus, flavonoids could act as potential inhibitors of PTPMT1, and further, in-vitro and in-vivo studies are essential to complete the drug development process.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8762535/pdf/40203_2022_Article_119.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10535474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Theoretical modeling and design of some pyrazolopyrimidine derivatives as Wolbachia inhibitors, targeting lymphatic filariasis and onchocerciasis. 针对淋巴丝虫病和盘尾丝虫病的一些吡唑嘧啶衍生物沃尔巴克氏体抑制剂的理论建模和设计。
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00123-3
Fabian Audu Ugbe, Gideon Adamu Shallangwa, Adamu Uzairu, Ibrahim Abdulkadir
{"title":"Theoretical modeling and design of some pyrazolopyrimidine derivatives as <i>Wolbachia</i> inhibitors, targeting lymphatic filariasis and onchocerciasis.","authors":"Fabian Audu Ugbe,&nbsp;Gideon Adamu Shallangwa,&nbsp;Adamu Uzairu,&nbsp;Ibrahim Abdulkadir","doi":"10.1007/s40203-022-00123-3","DOIUrl":"https://doi.org/10.1007/s40203-022-00123-3","url":null,"abstract":"<p><p>Lymphatic filariasis and onchocerciasis are two common filarial diseases caused by a group of parasitic nematodes called filarial worms, which play host to the bacteria organism <i>Wolbachia</i>. One good treatment approach seeks <i>Wolbachia</i> as drug target. Here, a QSAR study was conducted to investigate the anti-<i>wolbachia</i> activities (pEC<sub>50</sub>) of 52 pyrazolopyrimidine analogues, while using the built model to predict the pEC<sub>50</sub> values of the newly designed analogues. Density Functional Theory was used for the structural optimization, while the model building was based on Genetic Function Algorithm approach. The built QSAR model was validated thus: R<sup>2</sup> = 0.8104, R<sup>2</sup> <sub>adj</sub> = 0.7629, Q<sup>2</sup> <sub>cv</sub> = 0.6981, R<sup>2</sup> <sub>test</sub> = 0.7501 and cRp<sup>2</sup> = 0.7476. The predicted pEC<sub>50</sub> of all newly designed compounds were higher than that of the template (<b>43</b>). The new compounds were; observed to pass the drug-likeness criteria, uniformly distributed to the brain, and found to be non-mutagenic. Also, the new compounds and the reference drug (doxycycline), were docked onto Ovarian Tumor (OTU) deubiquitinase receptor (PDB ID: 6W9O) using iGEMDOCK tool. This protein is known to help <i>Wolbachia</i> subvert host ubiquitin signaling. The resulting binding scores of the newly designed compounds except <b>A5</b> were higher than that of doxycycline, while the protein-ligand interactions were majorly characterized by Hydrogen-bonding and hydrophobic interaction types. Therefore, the newly designed molecules could be developed as potential drug candidates for the treatment of lymphatic filariasis and onchocerciasis.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9079205/pdf/40203_2022_Article_123.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9417893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Optimizing the Sunitinib for cardio-toxicity and thyro-toxicity by scaffold hopping approach. 支架跳跃法优化舒尼替尼的心脏毒性和甲状腺毒性。
In Silico Pharmacology Pub Date : 2022-01-01 DOI: 10.1007/s40203-022-00125-1
Bhagyashri Chaudhari, Harun Patel, Snehal Thakar, Iqrar Ahmad, Deepali Bansode
{"title":"Optimizing the Sunitinib for cardio-toxicity and thyro-toxicity by scaffold hopping approach.","authors":"Bhagyashri Chaudhari,&nbsp;Harun Patel,&nbsp;Snehal Thakar,&nbsp;Iqrar Ahmad,&nbsp;Deepali Bansode","doi":"10.1007/s40203-022-00125-1","DOIUrl":"https://doi.org/10.1007/s40203-022-00125-1","url":null,"abstract":"<p><p>Sunitinib is a potent anti-cancer scaffold that acts as a VEGFR-2 inhibitor. Although the scaffold exhibits potent anti-cancer activity, it is cardiotoxic and also induces hypothyroidism. The current research aims to optimize the Sunitinib for cardio-toxicity and thyro-toxicity by scaffold hopping approach using the admetSAR server. The server has optimized the physico-chemical properties of Sunitinib, which were contributing to the cardiotoxicity and thyro-toxicity. The library of the optimized compounds was further screened by the molecular docking studies and results were validated by the MD simulation and DFT analysis for VEGFR-2 inhibition. Compounds <b>163</b> and <b>432</b> exhibited the highest affinity to VEGFR-2 receptor with minimal cardiotoxicity and thyro-toxicity. These two compounds could be the starting point for the further discovery of angiogenic inhibitors.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s40203-022-00125-1.</p>","PeriodicalId":13380,"journal":{"name":"In Silico Pharmacology","volume":"10 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250587/pdf/40203_2022_Article_125.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9732213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 24
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