cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23616713.v1
title: Naringenin-4'-glucuronide as a new drug candidate against the COVID-19 Omicron variant: a study based on molecular docking, molecular dynamics, MM/PBSA and MM/GBSA

description: This study aimed to identify natural bioactive compounds (NBCs) as potential inhibitors of the spike (S1) receptor binding domain (RBD) of the COVID-19 Omicron variant using computer simulations (<i>in silico)</i>. NBCs with previously proven biological <i>in vitro</i> activity were obtained from the ZINC database and analyzed through virtual screening, molecular docking, molecular dynamics (MD), molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA), and molecular mechanics/generalized Born surface area (MM/GBSA). Remdesivir was used as a reference drug in docking and MD calculations. A total of 170,906 compounds were analyzed. Molecular docking screening revealed the top four NBCs with a high affinity with the spike (affinity energy &lt;-7 kcal/mol) to be ZINC000045789238, ZINC000004098448, ZINC000008662732, and ZINC000003995616. In the MD analysis, the four ligands formed a complex with the highest dynamic equilibrium S1 (mean RMSD &lt;0.3 nm), lowest fluctuation of the complex amino acid residues (RMSF &lt;1.3), and solvent accessibility stability. However, the ZINC000045789238-spike complex (naringenin-4'-O glucuronide) was the only one that simultaneously had minus signal (-) MM/PBSA and MM/GBSA binding free energy values (-3.74 kcal/mol and −15.65 kcal/mol, respectively), indicating favorable binding. This ligand (naringenin-4'-O glucuronide) was also the one that produced the highest number of hydrogen bonds in the entire dynamic period (average = 4601 bonds per nanosecond). Six mutant amino acid residues formed these hydrogen bonds from the RBD region of S1 in the Omicron variant: Asn417, Ser494, Ser496, Arg403, Arg408, and His505. Naringenin-4'-O-glucuronide showed promising results as a potential drug candidate against COVID-19. <i>In vitro</i> and preclinical studies are needed to confirm these findings. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23616715
title: <i>In-silico</i> screening and identification of potential drug-like compounds for dengue-associated thrombocytopenia from <i>Carica papaya</i> leaf extracts

description: Dengue virus is a mosquito-borne pathogen that causes a variety of illnesses ranging from mild fever to severe and fatal dengue haemorrhagic fever or dengue shock syndrome. One of the major clinical manifestations of severe dengue infection is thrombocytopenia. The dengue non-structural protein 1 (NS1) is the primary protein that stimulates immune cells via toll-like receptor 4 (TLR4), induces platelets, and promotes aggregation, which could result in thrombocytopenia. The leaf extracts of <i>Carica papaya</i> seem to have therapeutic benefits in managing thrombocytopenia associated with dengue. The present study focuses on understanding the underlying mechanism of the use of papaya leaf extracts in treating thrombocytopenia. We have identified 124 phytocompounds that are present in the papaya leaf extract. The pharmacokinetics, molecular docking, binding free energy calculations, and molecular dynamic simulations were performed to investigate the drug-like properties, binding affinities, and interaction of phytocompounds with NS1 protein as well as the interactions of NS1 with TLR4. Three phytocompounds were found to bind with the ASN130, a crucial amino acid residue in the active site of the NS1 protein. Thus, we conclude that Rutin, Myricetin 3-rhamnoside, or Kaempferol 3-(2''-rhamnosylrutinoside) may serve as promising molecules by ameliorating thrombocytopenia in dengue-infected patients by interfering the interaction of NS1 with TLR4. These molecules can serve as drugs in the management of dengue-associated thrombocytopenia after verifying their effectiveness and assessing the drug potency, through additional in-vitro assays. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23616713
title: Naringenin-4'-glucuronide as a new drug candidate against the COVID-19 Omicron variant: a study based on molecular docking, molecular dynamics, MM/PBSA and MM/GBSA

description: This study aimed to identify natural bioactive compounds (NBCs) as potential inhibitors of the spike (S1) receptor binding domain (RBD) of the COVID-19 Omicron variant using computer simulations (<i>in silico)</i>. NBCs with previously proven biological <i>in vitro</i> activity were obtained from the ZINC database and analyzed through virtual screening, molecular docking, molecular dynamics (MD), molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA), and molecular mechanics/generalized Born surface area (MM/GBSA). Remdesivir was used as a reference drug in docking and MD calculations. A total of 170,906 compounds were analyzed. Molecular docking screening revealed the top four NBCs with a high affinity with the spike (affinity energy &lt;-7 kcal/mol) to be ZINC000045789238, ZINC000004098448, ZINC000008662732, and ZINC000003995616. In the MD analysis, the four ligands formed a complex with the highest dynamic equilibrium S1 (mean RMSD &lt;0.3 nm), lowest fluctuation of the complex amino acid residues (RMSF &lt;1.3), and solvent accessibility stability. However, the ZINC000045789238-spike complex (naringenin-4'-O glucuronide) was the only one that simultaneously had minus signal (-) MM/PBSA and MM/GBSA binding free energy values (-3.74 kcal/mol and −15.65 kcal/mol, respectively), indicating favorable binding. This ligand (naringenin-4'-O glucuronide) was also the one that produced the highest number of hydrogen bonds in the entire dynamic period (average = 4601 bonds per nanosecond). Six mutant amino acid residues formed these hydrogen bonds from the RBD region of S1 in the Omicron variant: Asn417, Ser494, Ser496, Arg403, Arg408, and His505. Naringenin-4'-O-glucuronide showed promising results as a potential drug candidate against COVID-19. <i>In vitro</i> and preclinical studies are needed to confirm these findings. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23559868.v1
title: Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations

description: Breast cancer is the leading cause of cancer-related deaths in women. Previous studies have indicated that disrupting the interaction between Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) can inhibit breast cancer development. Understanding the binding mode of small molecule inhibitors with SND1 is of great significance for designing drugs targeting the MTDH-SND1 complex. In this study, we conducted all-atom molecular dynamics (MD) simulations in solution and performed binding energy calculations to gain insights into the binding mechanism of small molecules to SND1. The binding site of SND1 for small molecules is relatively rigid, and the binding of the small molecule and the mutation of key residues have little effect on the conformation of the binding site. SND1 binds more tightly to C26-A6 than to C26-A2, as C26-A2 undergoes a 180° directional change during the simulation process. The key residue mutations have a direct effect on the position and orientation of small molecule in the binding site. The key residues make primary contributions to the binding energy through van der Waals interaction and nonpolar solvation energy, although the contribution from nonpolar solvation is relatively minor. The key residue mutations also affect the formation of hydrogen bonds and ultimately the stability of the small molecule-SND1 complex. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23616715.v1
title: <i>In-silico</i> screening and identification of potential drug-like compounds for dengue-associated thrombocytopenia from <i>Carica papaya</i> leaf extracts

description: Dengue virus is a mosquito-borne pathogen that causes a variety of illnesses ranging from mild fever to severe and fatal dengue haemorrhagic fever or dengue shock syndrome. One of the major clinical manifestations of severe dengue infection is thrombocytopenia. The dengue non-structural protein 1 (NS1) is the primary protein that stimulates immune cells via toll-like receptor 4 (TLR4), induces platelets, and promotes aggregation, which could result in thrombocytopenia. The leaf extracts of <i>Carica papaya</i> seem to have therapeutic benefits in managing thrombocytopenia associated with dengue. The present study focuses on understanding the underlying mechanism of the use of papaya leaf extracts in treating thrombocytopenia. We have identified 124 phytocompounds that are present in the papaya leaf extract. The pharmacokinetics, molecular docking, binding free energy calculations, and molecular dynamic simulations were performed to investigate the drug-like properties, binding affinities, and interaction of phytocompounds with NS1 protein as well as the interactions of NS1 with TLR4. Three phytocompounds were found to bind with the ASN130, a crucial amino acid residue in the active site of the NS1 protein. Thus, we conclude that Rutin, Myricetin 3-rhamnoside, or Kaempferol 3-(2''-rhamnosylrutinoside) may serve as promising molecules by ameliorating thrombocytopenia in dengue-infected patients by interfering the interaction of NS1 with TLR4. These molecules can serve as drugs in the management of dengue-associated thrombocytopenia after verifying their effectiveness and assessing the drug potency, through additional in-vitro assays. Communicated by Ramaswamy H. Sarma
DOI: 10.15468/dl.chfktd
title: Occurrence Download

description: A dataset containing 143796565 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Magnoliopsida, Liliopsida, Gnetopsida, Ginkgoopsida, Pinopsida, Cycadopsida, Cycadopsis Debey, 1848)",
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 143796565 records from 4253 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0190759-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wnhmbv
title: Occurrence Download

description: A dataset containing 1312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anoplophora chinensis (Forster, 1771)",
 "Year 2010-2025"
 ]
}

 The dataset includes 1312 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004535-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q3wzf6
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000299-150211104439307/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oeflgy
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000299-150215220751508/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wm6u8t
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000298-150306150734599/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qrvbrf
title: Occurrence Download

description: A dataset listing the 6461 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "Geometry POLYGON((2.54367 48.69929,2.90424 48.69929,2.90424 49.03259,2.54367 49.03259,2.54367 48.69929))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset's 6461 records were derived from 1241 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074815-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d1yclz
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000301-150306150734599/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jpfidl
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000301-150721130643939/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eqwt4n
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000301-150523225239109/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnqiyn
title: Occurrence Download

description: A dataset containing 120803740 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnoliophyta"
 ]
}

 The dataset includes 120803740 records from 2230 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000301-150311145101897/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4qf472
title: Occurrence Download

description: A dataset containing 2885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trifolium alexandrinum L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2885 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074827-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/7d5-50e-zfv
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/da7-sf1-llm
title: †Anthracosia planitumida (Trueman, 1929)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ppd-r7g-4s8
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8wj-21n-lbh
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/txj-c1w-575
title: †Anthracosia beaniana W. King, 1856

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8hy-z0e-saq
title: Salix myrsinifolia subsp. myrsinifolia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/txc-nfv-qje
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rjc-4cq-ay0
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xr8-mab-syf
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/an5-t4p-ak7
title: Quercus L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q2m-4av-zjc
title: Voacanga Thouars

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w52-a8l-h97
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2nd-sae-5cw
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6sc-4xw-dxw
title: Fraxinus Tourn. ex L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cxn-wlr-rga
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5ce-ha4-5pe
title: Voacanga Thouars

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nq8-1se-k57
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9l1-vjv-vad
title: Salix L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/age-rlq-6gz
title: †Rotalia Lamarck, 1804

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1ms-l8d-qxp
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9j5-pw7-w9y
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/feg-qr9-z89
title: Zelkova Spach

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g4q-h5x-yxv
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/466-4wq-4nc
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cy3-qsj-x1c
title: Laurus L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pzt-9n8-jym
title: Fagus L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kkj-njd-2f4
title: Planorbulina d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eh3-qvp-9x8
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q6w-bbt-jk7
title: †Naiadites Dawson, 1860

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0nm-k6p-0xy
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a4n-hwc-p13
title: †Anthracosia regularis (Trueman, 1929)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0v5-th5-gwk
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/p1e-vby-210
title: Zelkova Spach

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6ns-a3e-xy6
title: Zelkova Spach

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gzq-rdv-vm5
title: Globothalamea Pawlowski, Holzmann & Tyszka, 2013

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5s8-svv-0l3
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cyq-tza-lbf
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vde-apv-k8r
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r1g-zgt-sj0
title: Voacanga Thouars

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.qaek2s
title: Occurrence Download

description: A dataset containing 11898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Juncus articulatus L.",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11898 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012412-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pdffqs
title: Occurrence Download

description: A dataset containing 14906100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is New Zealand",
 "Geometry POLYGON((119.67576 -62.42031,229.32424 -62.42031,229.32424 -18.57969,119.67576 -18.57969,119.67576 -62.42031))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 14906100 records from 1046 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012396-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wuhb6s
title: Occurrence Download

description: A dataset containing 5051 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "OccurrenceStatus is Present",
 "TaxonKey is Crassostrea gigas (Thunberg, 1793)"
 ]
}

 The dataset includes 5051 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012414-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.