cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.bknyfz
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parribacus antarcticus (Lund, 1793)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 12 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016222-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nemfa4
title: Occurrence Download

description: A dataset containing 2134 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Pycnogonida collection of the Shirshov Institute of Oceanology, Laboratory of Ocean Benthic Fauna"
 ]
}

 The dataset includes 2134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016224-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uyj4d8
title: Occurrence Download

description: A dataset containing 1204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerorhinca monocerata (Pallas, 1811)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1204 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016226-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.27958059
title: Scores of 12 employees for Fuzzy TOPSIS evaluation

description: The scores of 12 employees to be used in the decision matrix for the fuzzy TOPSIS evaluation has been provided.
DOI: 10.15468/dl.jw5pqb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alca monocerata Pallas, 1811",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016228-241126133413365/datasets/export for details.
DOI: 10.15468/dl.2j69yp
title: Occurrence Download

description: A dataset containing 106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spisula sachalinensis (Schrenck, 1862)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 106 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016230-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ycbwe
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudocardium sachalinense",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 31 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016232-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24475135
title: The promising impact of Bemcentinib and Repotrectinib on sleep impairment in Alzheimer’s disease

description: Alzheimer’s disease (AD), the most prevalent neurodegenerative disease, demands effective medication to alleviate symptoms. This study focused on sleep impairment as an overt clinical symptom and tauopathy as a prominent molecular symptom of this disease. Multiple compounds from three biomolecule libraries (719 compounds; ChemDiv:366 – ChEMBL:180 – PubChem:173) were evaluated for potential binding affinity and safety using AutoDock Vina and pkCSM, respectively, resulting in the selection of four candidate compounds (Lestaurtinib, Repotrectinib, Bemcentinib, and Zotiraciclib). Due to the similarity of Repotrectinib and Bemcentinib binding sites to ATP, 300 ns Martini 3 coarse-grained molecular dynamics (MD) was performed on these two molecules and ATP by NAMD. The stability of tau protein in the presence of drugs was assessed using a 200 ns Martini 3 MD simulation. Binding site analysis discloses Bemcentinib and Repotrectinib as two inhibitors occupying most amino acids in binding with ATP. The RMSD and RMS average correlation results revealed protein containing Bemcentinib and Repotrectinib to have a more stable state compared to ATP in the first 220 ns simulation. There was only a single detachment of Bemcentinib, while Repotrictinib detached twice at the end of the simulation. Eventually, adding Bemcentinib and Repotrectinib to the enzyme-tau complex significantly increased the number of tau detachments during the 200 ns simulation. We report Bemcentinib and Repotrectinib, formerly prescribed for cancer, as potential inhibitors of the CK1 δ. Besides their high binding affinity compared to ATP, they can inhibit all ATP-binding sites and alter the tau binding stability. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24475135.v1
title: The promising impact of Bemcentinib and Repotrectinib on sleep impairment in Alzheimer’s disease

description: Alzheimer’s disease (AD), the most prevalent neurodegenerative disease, demands effective medication to alleviate symptoms. This study focused on sleep impairment as an overt clinical symptom and tauopathy as a prominent molecular symptom of this disease. Multiple compounds from three biomolecule libraries (719 compounds; ChemDiv:366 – ChEMBL:180 – PubChem:173) were evaluated for potential binding affinity and safety using AutoDock Vina and pkCSM, respectively, resulting in the selection of four candidate compounds (Lestaurtinib, Repotrectinib, Bemcentinib, and Zotiraciclib). Due to the similarity of Repotrectinib and Bemcentinib binding sites to ATP, 300 ns Martini 3 coarse-grained molecular dynamics (MD) was performed on these two molecules and ATP by NAMD. The stability of tau protein in the presence of drugs was assessed using a 200 ns Martini 3 MD simulation. Binding site analysis discloses Bemcentinib and Repotrectinib as two inhibitors occupying most amino acids in binding with ATP. The RMSD and RMS average correlation results revealed protein containing Bemcentinib and Repotrectinib to have a more stable state compared to ATP in the first 220 ns simulation. There was only a single detachment of Bemcentinib, while Repotrictinib detached twice at the end of the simulation. Eventually, adding Bemcentinib and Repotrectinib to the enzyme-tau complex significantly increased the number of tau detachments during the 200 ns simulation. We report Bemcentinib and Repotrectinib, formerly prescribed for cancer, as potential inhibitors of the CK1 δ. Besides their high binding affinity compared to ATP, they can inhibit all ATP-binding sites and alter the tau binding stability. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24452848
title: Unraveling bioactive metabolites of mangroves as putative inhibitors of SARS-CoV-2 Mpro and RBD proteins: molecular dynamics and ADMET analysis

description: COVID-19 is a deadly pandemic caused by Corona virus leading to millions of deaths worldwide. Till today no medicine was available to cure this disease. This study selected 262 potential bioactive natural products derived from mangroves to inhibit the main protease (Mpro) and receptor-binding domain (RBD) protein of the COVID-19 virus. All the ligands were subjected to Adsorption Digestion Metabolism Excretion and Toxicity (ADMET) predictions and docking studies using AutodockVina. Among all the ligands, NP_143 (Shearinine A) and NP_242 (Amentoflavone), having the highest docking score of 10.2 and 10.1 Kj/mole, respectively, were picked for 100 ns of Molecular Dynamics using GROMACS. The trajectories generated were used to estimate Root mean square deviation (RMSD), Root mean square fluctuations (RMSF), Radius of Gyrations (RG), Solvent accessible surface area (SASA), and Hydrogen bonds. From the data generated, both the ligands have good binding ability at the active site of Mpro protein and do not deviate much. They have strong interactions with the amino acids during the 100 ns of simulations and can thus be considered potential drug candidates. Communicated by Ramaswamy H. Sarma SARS-CoV-2 Mpro plays a pivotal role in viral replication and serves as important drug target. Bioactive compounds of mangroves origin are promising source of antiviral drugs. ADMET and docking study explored two lead compounds from mangroves against Mpro. MD simulation validated ligands of lead compounds had stronger binding affinity with Mpro.
DOI: 10.6084/m9.figshare.24452848.v1
title: Unraveling bioactive metabolites of mangroves as putative inhibitors of SARS-CoV-2 Mpro and RBD proteins: molecular dynamics and ADMET analysis

description: COVID-19 is a deadly pandemic caused by Corona virus leading to millions of deaths worldwide. Till today no medicine was available to cure this disease. This study selected 262 potential bioactive natural products derived from mangroves to inhibit the main protease (Mpro) and receptor-binding domain (RBD) protein of the COVID-19 virus. All the ligands were subjected to Adsorption Digestion Metabolism Excretion and Toxicity (ADMET) predictions and docking studies using AutodockVina. Among all the ligands, NP_143 (Shearinine A) and NP_242 (Amentoflavone), having the highest docking score of 10.2 and 10.1 Kj/mole, respectively, were picked for 100 ns of Molecular Dynamics using GROMACS. The trajectories generated were used to estimate Root mean square deviation (RMSD), Root mean square fluctuations (RMSF), Radius of Gyrations (RG), Solvent accessible surface area (SASA), and Hydrogen bonds. From the data generated, both the ligands have good binding ability at the active site of Mpro protein and do not deviate much. They have strong interactions with the amino acids during the 100 ns of simulations and can thus be considered potential drug candidates. Communicated by Ramaswamy H. Sarma SARS-CoV-2 Mpro plays a pivotal role in viral replication and serves as important drug target. Bioactive compounds of mangroves origin are promising source of antiviral drugs. ADMET and docking study explored two lead compounds from mangroves against Mpro. MD simulation validated ligands of lead compounds had stronger binding affinity with Mpro.
DOI: 10.6084/m9.figshare.24647969
title: Rhamnetin, a nutraceutical flavonoid arrests cell cycle progression of human ovarian cancer (SKOV3) cells by inhibiting the histone deacetylase 2 protein

description: Overexpression of HDAC 2 promotes cell proliferation in ovarian cancer. HDAC 2 is involved in chromatin remodeling, transcriptional repression, and the formation of condensed chromatin structures. Targeting HDAC 2 presents a promising therapeutic approach for correcting cancer-associated epigenetic abnormalities. Consequently, HDAC 2 inhibitors have evolved as an attractive class of anti-cancer agents. This work intended to investigate the anti-cancer abilities and underlying molecular mechanisms of Rhamnetin in human epithelial ovarian carcinoma cells (SKOV3), which remain largely unexplored. We employed various <i>in vitro</i> methods, including MTT, apoptosis study, cell cycle analysis, fluorescence microscopy imaging, and <i>in vitro</i> enzymatic HDAC 2 protein inhibition, to examine the chemotherapeutic sensitivity of Rhamnetin in SKOV3 cells. Additionally, we conducted <i>in silico</i> studies using molecular docking, MD simulation, MM-GBSA, DFT, and pharmacokinetic analysis to investigate the binding interaction mechanism within Rhamnetin and HDAC 2, alongside the compound’s prospective as a lead candidate. The <i>in vitro</i> assay confirmed the cytotoxic effects of Rhamnetin on SKOV3 cells, through its inhibition of HDAC 2 activity. Rhamnetin, a nutraceutical flavonoid, halted at the G1 phase of the cell cycle and triggered apoptosis in SKOV3 cells. Furthermore, computational studies provided additional evidence of its stable binding to the HDAC 2 protein’s binding site cavity. Based on our findings, we conclude that Rhamnetin effectively promotes apoptosis and mitigates the proliferation of SKOV3 cells through HDAC 2 inhibition. These results highlight Rhamnetin as a potential lead compound, opening a new therapeutic strategy for human epithelial ovarian cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24647969.v1
title: Rhamnetin, a nutraceutical flavonoid arrests cell cycle progression of human ovarian cancer (SKOV3) cells by inhibiting the histone deacetylase 2 protein

description: Overexpression of HDAC 2 promotes cell proliferation in ovarian cancer. HDAC 2 is involved in chromatin remodeling, transcriptional repression, and the formation of condensed chromatin structures. Targeting HDAC 2 presents a promising therapeutic approach for correcting cancer-associated epigenetic abnormalities. Consequently, HDAC 2 inhibitors have evolved as an attractive class of anti-cancer agents. This work intended to investigate the anti-cancer abilities and underlying molecular mechanisms of Rhamnetin in human epithelial ovarian carcinoma cells (SKOV3), which remain largely unexplored. We employed various <i>in vitro</i> methods, including MTT, apoptosis study, cell cycle analysis, fluorescence microscopy imaging, and <i>in vitro</i> enzymatic HDAC 2 protein inhibition, to examine the chemotherapeutic sensitivity of Rhamnetin in SKOV3 cells. Additionally, we conducted <i>in silico</i> studies using molecular docking, MD simulation, MM-GBSA, DFT, and pharmacokinetic analysis to investigate the binding interaction mechanism within Rhamnetin and HDAC 2, alongside the compound’s prospective as a lead candidate. The <i>in vitro</i> assay confirmed the cytotoxic effects of Rhamnetin on SKOV3 cells, through its inhibition of HDAC 2 activity. Rhamnetin, a nutraceutical flavonoid, halted at the G1 phase of the cell cycle and triggered apoptosis in SKOV3 cells. Furthermore, computational studies provided additional evidence of its stable binding to the HDAC 2 protein’s binding site cavity. Based on our findings, we conclude that Rhamnetin effectively promotes apoptosis and mitigates the proliferation of SKOV3 cells through HDAC 2 inhibition. These results highlight Rhamnetin as a potential lead compound, opening a new therapeutic strategy for human epithelial ovarian cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24496385
title: <i>In silico</i> guided <i>in vitro</i> study of traditionally used medicinal plants reveal the alleviation of post-menopausal symptoms through ERβ binding and MAO-A inhibition

description: The slumping level of estrogen and serotonin in menopausal women is directly associated with the occurrence of menopausal symptoms where, estrogen receptor-β (ERβ) and monoamine oxidase-A (MAO-A) are directly involved. The present investigation aimed for validation of promising plants traditionally used to alleviate menopausal symptoms with ERβ mediated MAO-A inhibition potential through <i>in silico</i> disease-target network construction using Cytoscape plugins followed by molecular docking of phytomolecules through AutoDock vina. ADMET parameters of identified bioactive phytomolecules were analysed through swissADME and ProTox II. The efficacy of promising plant leads was further established through <i>in vitro</i> ERβ competitive binding, MAO-A inhibition, enzyme kinetics and free radical quenching assays. <i>In silico</i> analysis suggested glabrene (ΔG = −9.7 Kcal/mol) as most promising against ERβ in comparison to 17β-estradiol (ΔG = −11.4 Kcal/mol) whereas liquiritigenin (ΔG = −9.4 Kcal/mol) showed potential binding with MAO-A in comparison to standard harmine (ΔG = −8.8 Kcal/mol). <i>In vitro</i> analysis of promising plants segregated <i>Glycyrrhiza glabra</i> (IC<sub>50 </sub>= 0.052 ± 0.007 μg/ml) as most promising, followed by <i>Hypericum perforatum</i> (IC<sub>50</sub> = 0.084 ± 0.01 μg/ml), <i>Trifolium pratense</i> (IC<sub>50</sub> = 0.514 ± 0.01 μg/ml) and <i>Rumex nepalensis</i> (IC<sub>50</sub> = 2.568 ± 0.11 μg/ml). The enzyme kinetics of promising plant leads showed reversible and competitive nature of inhibition against MAO-A. The potency of plant extracts in quenching free radicals was at par with ascorbic acid. The identified four potent medicinal plants with ERβ selective, MAO-A inhibitory and free radical quenching abilities could be used against menopausal symptoms however, finding needs to be validated further for menopausal symptoms in <i>in vivo</i> conditions for drug development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24496385.v1
title: <i>In silico</i> guided <i>in vitro</i> study of traditionally used medicinal plants reveal the alleviation of post-menopausal symptoms through ERβ binding and MAO-A inhibition

description: The slumping level of estrogen and serotonin in menopausal women is directly associated with the occurrence of menopausal symptoms where, estrogen receptor-β (ERβ) and monoamine oxidase-A (MAO-A) are directly involved. The present investigation aimed for validation of promising plants traditionally used to alleviate menopausal symptoms with ERβ mediated MAO-A inhibition potential through <i>in silico</i> disease-target network construction using Cytoscape plugins followed by molecular docking of phytomolecules through AutoDock vina. ADMET parameters of identified bioactive phytomolecules were analysed through swissADME and ProTox II. The efficacy of promising plant leads was further established through <i>in vitro</i> ERβ competitive binding, MAO-A inhibition, enzyme kinetics and free radical quenching assays. <i>In silico</i> analysis suggested glabrene (ΔG = −9.7 Kcal/mol) as most promising against ERβ in comparison to 17β-estradiol (ΔG = −11.4 Kcal/mol) whereas liquiritigenin (ΔG = −9.4 Kcal/mol) showed potential binding with MAO-A in comparison to standard harmine (ΔG = −8.8 Kcal/mol). <i>In vitro</i> analysis of promising plants segregated <i>Glycyrrhiza glabra</i> (IC<sub>50 </sub>= 0.052 ± 0.007 μg/ml) as most promising, followed by <i>Hypericum perforatum</i> (IC<sub>50</sub> = 0.084 ± 0.01 μg/ml), <i>Trifolium pratense</i> (IC<sub>50</sub> = 0.514 ± 0.01 μg/ml) and <i>Rumex nepalensis</i> (IC<sub>50</sub> = 2.568 ± 0.11 μg/ml). The enzyme kinetics of promising plant leads showed reversible and competitive nature of inhibition against MAO-A. The potency of plant extracts in quenching free radicals was at par with ascorbic acid. The identified four potent medicinal plants with ERβ selective, MAO-A inhibitory and free radical quenching abilities could be used against menopausal symptoms however, finding needs to be validated further for menopausal symptoms in <i>in vivo</i> conditions for drug development. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24560543
title: A novel therapeutic approach to prevent <i>Helicobacter pylori</i> induced gastric cancer using networking biology, molecular docking, and simulation approaches

description: <i>Helicobacter pylori</i> infects 50% of the world population and in 80% of cases, the infection progresses to the point where an ulcer develops leading to gastric cancer (GC). This study aimed to prevent GC by predicting Hub genes that are inducing GC. Furthermore, the study objective was to screen inhibitory molecules that block the function of predicted genes through several biophysical approaches. These proteins, such as Mucin 4 (MUC4) and Baculoviral IAP repeat containing 3 (BIRC3), had LogFC values of 2.28 and 3.39, respectively, and were found to be substantially expressed in those who had <i>H. pylori</i> infection. The MUC4 and BIRC3 inhibit apoptosis of infected cells and promote cancerous cell survival. The proteins were examined for their Physico-chemical characteristics, 3D structure and secondary structure analysis, solvent assessable surface area (SASA), active site identification, and network analysis. The MUC4 and BIRC3 expression was inhibited by docking eighty different compounds collected from the ZINC database. Fifty-seven compounds were successfully docked into the active site resulting in the lowest binding energy scores. The ZINC585267910 and ZINC585268691 compounds showed the lowest binding energy of −8.5 kcal/mol for MUC4 and −7.1 kcal/mol for BIRC3, respectively, and were considered best-docked solutions for molecular dynamics simulations. The mean root mean square deviation (RMSD) value for the ZINC585267910-MUC4 complex was 0.86 Å and the ZINC585268691-BIRC3 complex was 1.01 Å. The net MM/GBSA energy value of the ZINC585267910<b>-</b>MUC4 complex estimated was −46.84 kcal/mol and that of the ZINC585268691-BIRC3 complex was −44.84 kcal/mol. In a nutshell, the compounds might be investigated further as an inhibitor of the said proteins to stop the progress of GC induced by <i>H. pylori</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24560543.v1
title: A novel therapeutic approach to prevent <i>Helicobacter pylori</i> induced gastric cancer using networking biology, molecular docking, and simulation approaches

description: <i>Helicobacter pylori</i> infects 50% of the world population and in 80% of cases, the infection progresses to the point where an ulcer develops leading to gastric cancer (GC). This study aimed to prevent GC by predicting Hub genes that are inducing GC. Furthermore, the study objective was to screen inhibitory molecules that block the function of predicted genes through several biophysical approaches. These proteins, such as Mucin 4 (MUC4) and Baculoviral IAP repeat containing 3 (BIRC3), had LogFC values of 2.28 and 3.39, respectively, and were found to be substantially expressed in those who had <i>H. pylori</i> infection. The MUC4 and BIRC3 inhibit apoptosis of infected cells and promote cancerous cell survival. The proteins were examined for their Physico-chemical characteristics, 3D structure and secondary structure analysis, solvent assessable surface area (SASA), active site identification, and network analysis. The MUC4 and BIRC3 expression was inhibited by docking eighty different compounds collected from the ZINC database. Fifty-seven compounds were successfully docked into the active site resulting in the lowest binding energy scores. The ZINC585267910 and ZINC585268691 compounds showed the lowest binding energy of −8.5 kcal/mol for MUC4 and −7.1 kcal/mol for BIRC3, respectively, and were considered best-docked solutions for molecular dynamics simulations. The mean root mean square deviation (RMSD) value for the ZINC585267910-MUC4 complex was 0.86 Å and the ZINC585268691-BIRC3 complex was 1.01 Å. The net MM/GBSA energy value of the ZINC585267910<b>-</b>MUC4 complex estimated was −46.84 kcal/mol and that of the ZINC585268691-BIRC3 complex was −44.84 kcal/mol. In a nutshell, the compounds might be investigated further as an inhibitor of the said proteins to stop the progress of GC induced by <i>H. pylori</i>. Communicated by Ramaswamy H. Sarma