scholarly journals In Silico Design of Human IMPDH Inhibitors Using Pharmacophore Mapping and Molecular Docking Approaches

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Rui-Juan Li ◽  
Ya-Li Wang ◽  
Qing-He Wang ◽  
Jian Wang ◽  
Mao-Sheng Cheng
Keyword(s):  
Molecular Docking ◽  
De Novo ◽  
Homo Sapiens ◽  
Pharmacophore Mapping ◽  
Scoring Method ◽  
Lead Compounds ◽  
Zinc Database ◽  
Pharmacophore Hypotheses ◽  
Key Residues

Inosine 5′-monophosphate dehydrogenase (IMPDH) is one of the crucial enzymes in thede novobiosynthesis of guanosine nucleotides. It has served as an attractive target in immunosuppressive, anticancer, antiviral, and antiparasitic therapeutic strategies. In this study, pharmacophore mapping and molecular docking approaches were employed to discover novel Homo sapiens IMPDH (hIMPDH) inhibitors. The Güner-Henry (GH) scoring method was used to evaluate the quality of generated pharmacophore hypotheses. One of the generated pharmacophore hypotheses was found to possess a GH score of 0.67. Ten potential compounds were selected from the ZINC database using a pharmacophore mapping approach and docked into the IMPDH active site. We find two hits (i.e., ZINC02090792 and ZINC00048033) that match well the optimal pharmacophore features used in this investigation, and it is found that they form interactions with key residues of IMPDH. We propose that these two hits are lead compounds for the development of novel hIMPDH inhibitors.

scholarly journals Dual Binding Site and Selective Acetylcholinesterase Inhibitors Derived from Integrated Pharmacophore Models and Sequential Virtual Screening

2014 ◽  
Vol 2014 ◽  
pp. 1-21 ◽  
Author(s):  
Shikhar Gupta ◽  
C. Gopi Mohan
Keyword(s):  
Molecular Docking ◽  
Binding Site ◽  
Enzyme Inhibitors ◽  
Acetylcholinesterase Inhibitors ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Test Set ◽  
Zinc Database ◽  
Pharmacophore Hypotheses ◽  
Pharmacophore Models

In this study, we have employedin silicomethodology combining double pharmacophore based screening, molecular docking, and ADME/T filtering to identify dual binding site acetylcholinesterase inhibitors that can preferentially inhibit acetylcholinesterase and simultaneously inhibit the butyrylcholinesterase also but in the lesser extent than acetylcholinesterase. 3D-pharmacophore models of AChE and BuChE enzyme inhibitors have been developed from xanthostigmine derivatives through HypoGen and validated using test set, Fischer’s randomization technique. The best acetylcholinesterase and butyrylcholinesterase inhibitors pharmacophore hypotheses Hypo1_A and Hypo1_B, with high correlation coefficient of 0.96 and 0.94, respectively, were used as 3D query for screening the Zinc database. The screened hits were then subjected to the ADME/T and molecular docking study to prioritise the compounds. Finally, 18 compounds were identified as potential leads against AChE enzyme, showing good predicted activities and promising ADME/T properties.

scholarly journals Molecular docking of Sulfobacillus acidophilus barbiturase with s-triazine compounds

2016 ◽  
Author(s):  
Zarrin Basharat ◽  
Azra Yasmin
Keyword(s):  
Molecular Docking ◽  
Structure Prediction ◽  
De Novo ◽  
Structural Information ◽  
Sequence Data ◽  
Raw Material ◽  
Biological Information ◽  
Docking Analysis ◽  
Herbicide Degradation ◽  
Key Residues

Barbiturases have scarce structural information available and do not fit in the conventional group of proteins. It is contemplated that they play a role in catabolism of s-triazine herbicide compounds. Structure as well as interaction data information of barbiturase with s-triazine compounds is missing. Sequence data is a goldmine of biological information and acts as raw material for structure and docking analysis. De novo structure prediction of the Sulfobacillus acidophilus DSM 10332 barbiturase has been attempted in this data article. Molecular docking analysis was carried out with atrazine, simazine and hexazinone belonging to s-triazine class of herbicides. The analysis revealed key residues necessary for these interactions. The generated data could be used by environmental scientists working on the enzyme assisted herbicide degradation.

scholarly journals Molecular docking of Sulfobacillus acidophilus barbiturase with s-triazine compounds

2016 ◽  
Author(s):  
Zarrin Basharat ◽  
Azra Yasmin
Keyword(s):  
Molecular Docking ◽  
Structure Prediction ◽  
De Novo ◽  
Structural Information ◽  
Sequence Data ◽  
Raw Material ◽  
Biological Information ◽  
Docking Analysis ◽  
Herbicide Degradation ◽  
Key Residues

Barbiturases have scarce structural information available and do not fit in the conventional group of proteins. It is contemplated that they play a role in catabolism of s-triazine herbicide compounds. Structure as well as interaction data information of barbiturase with s-triazine compounds is missing. Sequence data is a goldmine of biological information and acts as raw material for structure and docking analysis. De novo structure prediction of the Sulfobacillus acidophilus DSM 10332 barbiturase has been attempted in this data article. Molecular docking analysis was carried out with atrazine, simazine and hexazinone belonging to s-triazine class of herbicides. The analysis revealed key residues necessary for these interactions. The generated data could be used by environmental scientists working on the enzyme assisted herbicide degradation.

scholarly journals In Silico Prediction, Molecular Docking and Dynamics Studies of Steroidal Alkaloids of Holarrhena pubescens Wall. ex G. Don to Guanylyl Cyclase C: Implications in Designing of Novel Antidiarrheal Therapeutic Strategies

Molecules ◽  
2021 ◽  
Vol 26 (14) ◽  
pp. 4147
Author(s):  
Neha Gupta ◽  
Saurav Kumar Choudhary ◽  
Neeta Bhagat ◽  
Muthusamy Karthikeyan ◽  
Archana Chaturvedi
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Guanylyl Cyclase ◽  
Extracellular Domain ◽  
Enterotoxigenic Escherichia Coli ◽  
Watery Diarrhea ◽  
Guanylyl Cyclase C ◽  
Amino Acid Residues ◽  
Lead Compounds

The binding of heat stable enterotoxin (STa) secreted by enterotoxigenic Escherichia coli (ETEC) to the extracellular domain of guanylyl cyclase c (ECDGC-C) causes activation of a signaling cascade, which ultimately results in watery diarrhea. We carried out this study with the objective of finding ligands that would interfere with the binding of STa on ECDGC-C. With this view in mind, we tested the biological activity of a alkaloid rich fraction of Holarrhena pubescens against ETEC under in vitro conditions. Since this fraction showed significant antibacterial activity against ETEC, we decided to test the screen binding affinity of nine compounds of steroidal alkaloid type from Holarrhena pubescens against extracellular domain (ECD) by molecular docking and identified three compounds with significant binding energy. Molecular dynamics simulations were performed for all the three lead compounds to establish the stability of their interaction with the target protein. Pharmacokinetics and toxicity profiling of these leads demonstrated that they possessed good drug-like properties. Furthermore, the ability of these leads to inhibit the binding of STa to ECD was evaluated. This was first done by identifying amino acid residues of ECDGC-C binding to STa by protein–protein docking. The results were matched with our molecular docking results. We report here that holadysenterine, one of the lead compounds that showed a strong affinity for the amino acid residues on ECDGC-C, also binds to STa. This suggests that holadysenterine has the potential to inhibit binding of STa on ECD and can be considered for future study, involving its validation through in vitro assays and animal model studies.

scholarly journals Prospect into therapeutic potentials of Moringa oleifera phytocompounds against cancer upsurge: de novo synthesis of test compounds, molecular docking, and ADMET studies

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
P. M. Aja ◽  
P. C. Agu ◽  
E. M. Ezeh ◽  
J. N. Awoke ◽  
H. A. Ogwoni ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Drug Discovery ◽  
Cancer Chemotherapy ◽  
Moringa Oleifera ◽  
De Novo ◽  
Gas Chromatography Mass Spectrometry ◽  
Molecular Docking Study ◽  
Cancer Proliferation ◽  
Target Proteins ◽  
Potential Inhibitors

Abstract Background Cancer chemotherapy is difficult because current medications for the treatment of cancer have been linked to a slew of side effects; as a result, researchers are tasked with developing greener cancer chemotherapies. Moringa oleifera has been reported with several bioactive compounds which confirm its application for various ailments by traditional practitioners. In this study, we aim to prospect the therapeutic potentials of M. oleifera phytocompounds against cancer proliferation as a step towards drug discovery using a computational approach. Target proteins: dihydrofolate reductase (DHFR) and B-Cell Lymphoid-2 (BCL-2), were retrieved from the RCSB PDB web server. Sixteen and five phytocompounds previously reported in M. oleifera leaves (ML) and seeds (MS), respectively, by gas chromatography–mass spectrometry were synthesized and used in the molecular docking study. For accurate prediction of binding sites of the target proteins; standard inhibitors, Methotrexate (MTX) for DHFR, and Venetoclax (VTC) for BCL-2, were docked together with the test compounds. We further predicted the ADMET profile of the potential inhibitors for an insight into their chance of success as candidates in drug discovery. Results Results for the binding affinities, docking poses, and the interactions showed that ML2, ML4-6, ML8-15, and MS1-5 are potential inhibitors of DHFR and BCL-2, respectively. In the ADMET profile, ML2 and ML4 showed the best drug-likeness by non-violation of Lipski Rule of Five. ML4-6, ML8, ML11, ML14-15, and MS1, MS3-5 exhibit high GI absorption; ML2, ML4-6, ML8, MS1, and MS5 are blood–brain barrier permeants. ML2, ML4, ML9, ML13, and MS2 do not interfere with any of the CYP450 isoforms. The toxicity profile showed that all the potential inhibitors are non-carcinogenic and non-hERG I (human ether-a-go-go related gene I) inhibitors. ML4, ML11, and MS4 are hepatotoxic and ML7, ML10, and MS4 are hERG II inhibitors. A plethora of insights on the toxic endpoints and lethal concentration values showed that ML5, ML13, and MS2 are comparatively less lethal than other potential inhibitors. Conclusion This study has demonstrated that M. oleifera phytocompounds are potential inhibitors of the disease proteins involved in cancer proliferation, thus, an invaluable step toward the discovery of cancer chemotherapy with lesser limitations.

scholarly journals Evaluation of Environmental Information Disclosure of Listed Companies in China’s Heavy Pollution Industries: A Text Mining-Based Methodology

2021 ◽  
Vol 13 (10) ◽  
pp. 5415
Author(s):  
Rongjiang Cai ◽  
Tao Lv ◽  
Xu Deng
Keyword(s):  
Text Mining ◽  
Information Disclosure ◽  
Listed Companies ◽  
Environmental Information ◽  
Evaluation Framework ◽  
Scoring Method ◽  
Study Results ◽  
Environmental Information Disclosure ◽  
Heavy Pollution

Environmental information disclosure (EID) of listed companies is a significant and essential reference for assessing their environmental protection commitment. However, the content and form of EID are complex, and previous assessment studies involved manual scoring mainly by the experts in this field. It is subjective and has low timeliness. Therefore, this paper proposes an automatic evaluation framework of EID quality based on text mining (TM), including the EID index system’s construction, automatic scoring of environmental information disclosure quality, and EID index calculation. Furthermore, based on the EID of 801 listed companies in China’s heavy pollution industry from 2013 to 2017, case studies are conducted. The case study results show that the overall quality of the EID of listed companies in China’s heavily polluting industries is low, and there is a gap differentiation between the 16 industries. Compared with the subjective manual scoring method, TM evaluation can evaluate the quality of EID more effectively and accurately. It has great potential and can become an essential tool for the sustainable development of society and listed companies.

Arthroscopic International Cartilage Repair Society Classification System Has Only Moderate Reliability in a Porcine Cartilage Repair Model

2021 ◽  
pp. 036354652199800
Author(s):  
Jani Puhakka ◽  
Teemu Paatela ◽  
Eve Salonius ◽  
Virpi Muhonen ◽  
Anna Meller ◽  
...  
Keyword(s):  
Cartilage Repair ◽  
Scoring System ◽  
Femoral Condyle ◽  
Intraclass Correlation ◽  
Type Iii Collagen ◽  
Intrarater Reliability ◽  
Scoring Method ◽  
International Cartilage Repair Society ◽  
Made In

Background: The International Cartilage Repair Society (ICRS) score was designed for arthroscopic use to evaluate the quality of cartilage repair. Purpose: To evaluate the reliability of the ICRS scoring system using an animal cartilage repair model. Study Design: Controlled laboratory study. Methods: A chondral defect with an area of 1.5 cm2 was made in the medial femoral condyle of 18 domestic pigs. Five weeks later, 9 pigs were treated using a novel recombinant human type III collagen/polylactide scaffold, and 9 were left to heal spontaneously. After 4 months, the pigs were sacrificed, then 3 arthroscopic surgeons evaluated the medial femoral condyles via video-recorded simulated arthroscopy using the ICRS scoring system. The surgeons repeated the evaluation twice within a 9-month period using their recorded arthroscopy. Results: The porcine cartilage repair model produced cartilage repair tissue of poor to good quality. The mean ICRS total scores for all observations were 6.6 (SD, 2.6) in arthroscopy, 5.9 (SD, 2.7) in the first reevaluation, and 6.2 (SD, 2.8) in the second reevaluation. The interrater reliability with the intraclass correlation coefficient (ICC) for the ICRS total scores (ICC, 0.46-0.60) and for each individual subscore (ICC, 0.26-0.71) showed poor to moderate reliability. The intrarater reliability with the ICC also showed poor to moderate reliability for ICRS total scores (ICC, 0.52-0.59) and for each individual subscore (ICC, 0.29-0.58). A modified Bland-Altman plot for the initial arthroscopy and for the 2 reevaluations showed an evident disagreement among the observers. Conclusion: In an animal cartilage repair model, the ICRS scoring system seems to have poor to moderate reliability. Clinical Relevance: Arthroscopic assessment of cartilage repair using the ICRS scoring method has limited reliability. We need more objective methods with acceptable reliability to evaluate cartilage repair outcomes.

scholarly journals What Is Known and Unknown About Twice-Weekly Hemodialysis

2015 ◽  
Vol 40 (4) ◽  
pp. 298-305 ◽  
Author(s):  
Yoshitsugu Obi ◽  
Rieko Eriguchi ◽  
Shuo-Ming Ou ◽  
Connie M. Rhee ◽  
Kamyar Kalantar-Zadeh
Keyword(s):  
Quality Of Life ◽  
De Novo ◽  
Urine Volume ◽  
Cost Effective ◽  
Standard Of Care ◽  
Treatment Regimens ◽  
Interdialytic Weight Gain ◽  
Cost Effective Treatment ◽  
Incremental Hemodialysis

Background: The 2006 Kidney Disease Outcomes Quality Initiative guidelines suggest twice-weekly or incremental hemodialysis for patients with substantial residual kidney function (RKF). However, in most affluent nations de novo and abrupt transition to thrice-weekly hemodialysis is routinely prescribed for all dialysis-naïve patients regardless of their RKF. We review historical developments in hemodialysis therapy initiation and revisit twice-weekly hemodialysis as an individualized, incremental treatment especially upon first transitioning to hemodialysis therapy. Summary: In the 1960's, hemodialysis treatment was first offered as a life-sustaining treatment in the form of long sessions (≥10 hours) administered every 5 to 7 days. Twice- and then thrice-weekly treatment regimens were subsequently developed to prevent uremic symptoms on a long-term basis. The thrice-weekly regimen has since become the ‘standard of care' despite a lack of comparative studies. Some clinical studies have shown benefits of high hemodialysis dose by more frequent or longer treatment times mainly among patients with limited or no RKF. Conversely, in selected patients with higher levels of RKF and particularly higher urine volume, incremental or twice-weekly hemodialysis may preserve RKF and vascular access longer without compromising clinical outcomes. Proposed criteria for twice-weekly hemodialysis include urine output >500 ml/day, limited interdialytic weight gain, smaller body size relative to RKF, and favorable nutritional status, quality of life, and comorbidity profile. Key Messages: Incremental hemodialysis including twice-weekly regimens may be safe and cost-effective treatment regimens that provide better quality of life for incident dialysis patients who have substantial RKF. These proposed criteria may guide incremental hemodialysis frequency and warrant future randomized controlled trials.

scholarly journals Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Momchilo Vuyisich ◽  
Ayesha Arefin ◽  
Karen Davenport ◽  
Shihai Feng ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Gc Content ◽  
Library Preparation ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Dna Amount ◽  
High Quality ◽  
Preparation Methods

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing andde novoassembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing andde novoassembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderiaspp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing andde novoassembly is not decreased when only 10 ng of input genomic DNA is used.

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