cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25145998.v1
title: Discovery of thiazolidinedione-based pancreatic lipase inhibitors as anti-obesity agents: synthesis, <i>in silico</i> studies and pharmacological investigations

description: A series of new 2,5-disubstituted arylidene derivatives of thiazolidinedione (<b>16a-e, 17a-d, 18a-c</b>) designed using molecular hybridization approach were synthesized, structurally characterized, and explored for their anti-obesity potential <i>via</i> inhibition of Pancreatic Lipase (PL). Compound <b>18a</b> presented the most potent PL inhibitory activity with IC<sub>50</sub> = 2.71 ± 0.31 µM, as compared to the standard drug, Orlistat (IC<sub>50</sub> = 0.99 µM). Kinetic study revealed reversible competitive mode of enzyme inhibition by compound <b>18a</b> with an inhibitory constant value of 1.19 µM. The most promising compound <b>18a</b> revealed satisfactory binding mode within the active site of the target protein (human PL, PDB ID: 1LPB). Also, MM/PBSA binding free energy and molecular dynamics (MD) simulation analysis were performed for the most promising compound <b>18a</b>, which showed potent inhibition according to the results of <i>in vitro</i> studies. Furthermore, a stable conformation of the 1LPB-ligand suggested the stability of this compound in the dynamic environment. The ADME and toxicity analysis of the compounds were examined using web-based online platforms. Results of <i>in vivo</i> studies confirmed the anti-obesity efficacy of compound <b>18a</b>, wherein oral treatment with compound <b>18a</b> (30 mg/kg) resulted in a significant reduction in the body weight, BMI, Lee index, feed intake (in Kcal), body fat depots and serum triglycerides. Compound <b>18a</b> significantly decreased the levels of serum total cholesterol (TC) to 128.6 ± 0.59 mg/dl and serum total triglycerides (TG) to 95.73 ± 0.67 mg/dl as compared to the HFD control group. The present study identified disubstituted TZD derivatives as a new promising class of anti-obesity agents.
DOI: 10.6084/m9.figshare.28554532
title: Deciphering the binding mechanism of gingerol molecules with plasma proteins: implications for drug delivery and therapeutic potential

description: Ginger is a highly valued herb, renowned globally for its rich content of phenolic compounds. It has been traditionally used to treat various health conditions such as cardiovascular diseases, digestive issues, migraines, Alzheimer’s disease, tumor reduction and chronic inflammation. Despite its potential medicinal applications, the therapeutic effectiveness of ginger is hindered by its limited availability and low plasma concentration levels. In this study, we explored the interaction of ginger’s primary phenolic compounds, specifically 6-gingerol (6 G), 8-gingerol (8 G) and 10-gingerol (10 G), with plasma proteins which are human serum albumin (HSA) and α-1-acid glycoprotein (AGP). These two plasma proteins significantly influence drug distribution and disposition as they are key binding sites for most drugs. Fluorescence emission spectra indicated strong binding of 6, 8 and 10 G with HSA, with binding constants of 2.03 ± 0.01 × 10<sup>4</sup> M<sup>−1</sup>, 4.20 ± 0.01 × 10<sup>4</sup> M<sup>−1</sup> and 6.03 ± 0.01 × 10<sup>6</sup> M<sup>−1</sup>, respectively. However, the binding of gingerols with AGP was found to be negligible. Molecular displacement by site-specific probes and molecular docking analyses revealed that gingerols bind at the IIA domain, with stability provided by hydrogen bonds, van der Waals forces, conventional hydrogen bonds, carbon-hydrogen bonds, alkyl and Pi–alkyl interactions. Further, the partial unfolding of the protein was observed upon binding the gingerol compound with HSA. In addition, molecular dynamic simulations demonstrated that gingerols remained stable in the subdomain IIA over 100 ns. This stability, coupled with Molecular Mechanics Generalized Born Surface Area indicating free energies of −43.765, −57.504 and −66.69 kcal/mol for 6, 8 and 10 G, respectively, reinforces the robust binding potential of these compounds. Circular dichroism studies suggested that the interaction of gingerols leads to the minimal transformation of HSA secondary structure, with the pattern being 10 <i>G</i> &gt; 8 <i>G</i> &gt; 6 G, a finding further substantiated by root mean square deviation and root mean square fluctuation fluctuations. These results propose that HSA has a stronger affinity to gingerols than AGP, which could have significant implications on the therapeutic circulating levels of gingerols.
DOI: 10.6084/m9.figshare.28554532.v1
title: Deciphering the binding mechanism of gingerol molecules with plasma proteins: implications for drug delivery and therapeutic potential

description: Ginger is a highly valued herb, renowned globally for its rich content of phenolic compounds. It has been traditionally used to treat various health conditions such as cardiovascular diseases, digestive issues, migraines, Alzheimer’s disease, tumor reduction and chronic inflammation. Despite its potential medicinal applications, the therapeutic effectiveness of ginger is hindered by its limited availability and low plasma concentration levels. In this study, we explored the interaction of ginger’s primary phenolic compounds, specifically 6-gingerol (6 G), 8-gingerol (8 G) and 10-gingerol (10 G), with plasma proteins which are human serum albumin (HSA) and α-1-acid glycoprotein (AGP). These two plasma proteins significantly influence drug distribution and disposition as they are key binding sites for most drugs. Fluorescence emission spectra indicated strong binding of 6, 8 and 10 G with HSA, with binding constants of 2.03 ± 0.01 × 10<sup>4</sup> M<sup>−1</sup>, 4.20 ± 0.01 × 10<sup>4</sup> M<sup>−1</sup> and 6.03 ± 0.01 × 10<sup>6</sup> M<sup>−1</sup>, respectively. However, the binding of gingerols with AGP was found to be negligible. Molecular displacement by site-specific probes and molecular docking analyses revealed that gingerols bind at the IIA domain, with stability provided by hydrogen bonds, van der Waals forces, conventional hydrogen bonds, carbon-hydrogen bonds, alkyl and Pi–alkyl interactions. Further, the partial unfolding of the protein was observed upon binding the gingerol compound with HSA. In addition, molecular dynamic simulations demonstrated that gingerols remained stable in the subdomain IIA over 100 ns. This stability, coupled with Molecular Mechanics Generalized Born Surface Area indicating free energies of −43.765, −57.504 and −66.69 kcal/mol for 6, 8 and 10 G, respectively, reinforces the robust binding potential of these compounds. Circular dichroism studies suggested that the interaction of gingerols leads to the minimal transformation of HSA secondary structure, with the pattern being 10 <i>G</i> &gt; 8 <i>G</i> &gt; 6 G, a finding further substantiated by root mean square deviation and root mean square fluctuation fluctuations. These results propose that HSA has a stronger affinity to gingerols than AGP, which could have significant implications on the therapeutic circulating levels of gingerols.
DOI: 10.6084/m9.figshare.25146072
title: Design of human ACE2 mimic miniprotein binders that interact with RBD of SARS-CoV-2 variants of concerns

description: The world of medicine demands from the research community solutions to the emerging problem of SARS-CoV-2 variants and other such potential global pandemics. With advantages of specificity over small molecule drugs and designability over antibodies, miniprotein therapeutics offers a unique solution to the threats of rapidly emerging SARS-CoV-2 variants. Unfortunately, most of the promising miniprotein binders are <i>de novo</i> designed and it is not viable to generate molecules for each new variant. Therefore in this study, we demonstrate a method for design of miniprotein mimics from the interaction interphase of human angiotensin converting enzyme 2 (ACE2). ACE2 is the natural interacting partner for the SARS-CoV-2 spike receptor binding domain (RBD) and acts as a recognition molecule for viral entry into the host cells. Starting with ACE2 N-terminal triple helix interaction interphase, we generated more than 70 miniprotein sequences. Employing Rosetta folding and docking scores we selected 10 promising miniprotein candidates amongst which 3 were found to be soluble in lab studies. Further, using molecular mechanics (MM) calculations on molecular dynamics (MD) trajectories we test interaction of miniproteins with RBD from various variants of concern (VOC). Presently, we report two key findings; miniproteins in this study are generated using less than 10 lab testing experiments, yet when tested through <i>in-vitro</i> experiments, they show submicro to nanomolar affinities towards SARS-CoV-2 RBD. Also in simulation studies, when compared with previously developed therapeutics, our miniproteins display remarkable ability to mimic ACE2 interphase; making them an ideal solution to the ever evolving problem of VOCs.
DOI: 10.6084/m9.figshare.25146072.v1
title: Design of human ACE2 mimic miniprotein binders that interact with RBD of SARS-CoV-2 variants of concerns

description: The world of medicine demands from the research community solutions to the emerging problem of SARS-CoV-2 variants and other such potential global pandemics. With advantages of specificity over small molecule drugs and designability over antibodies, miniprotein therapeutics offers a unique solution to the threats of rapidly emerging SARS-CoV-2 variants. Unfortunately, most of the promising miniprotein binders are <i>de novo</i> designed and it is not viable to generate molecules for each new variant. Therefore in this study, we demonstrate a method for design of miniprotein mimics from the interaction interphase of human angiotensin converting enzyme 2 (ACE2). ACE2 is the natural interacting partner for the SARS-CoV-2 spike receptor binding domain (RBD) and acts as a recognition molecule for viral entry into the host cells. Starting with ACE2 N-terminal triple helix interaction interphase, we generated more than 70 miniprotein sequences. Employing Rosetta folding and docking scores we selected 10 promising miniprotein candidates amongst which 3 were found to be soluble in lab studies. Further, using molecular mechanics (MM) calculations on molecular dynamics (MD) trajectories we test interaction of miniproteins with RBD from various variants of concern (VOC). Presently, we report two key findings; miniproteins in this study are generated using less than 10 lab testing experiments, yet when tested through <i>in-vitro</i> experiments, they show submicro to nanomolar affinities towards SARS-CoV-2 RBD. Also in simulation studies, when compared with previously developed therapeutics, our miniproteins display remarkable ability to mimic ACE2 interphase; making them an ideal solution to the ever evolving problem of VOCs.
DOI: 10.6084/m9.figshare.25429338
title: Unraveling the ligand specificity and promiscuity of the <i>Staphylococcus aureus</i> NorA efflux pump: a computational study

description: <i>Staphylococcus aureus</i>, a gram-positive bacterial pathogen, develops antibiotic resistance partly through enhanced activity of transmembrane multi-drug efflux pump proteins like NorA. Being a prominent member of the Major Facilitator Superfamily (MFS), NorA transports various small molecules including hydrophilic fluoroquinolone antibiotics across the cell membrane. Intriguingly, NorA is inhibited by a structurally diverse set of small molecule inhibitors as well, indicating a highly promiscuous ligand/inhibitor recognition. Our study aims to elucidate the structural facets of this promiscuity. Known NorA inhibitors were grouped into five clusters based on chemical class and docked into ligand binding pockets on NorA conformations generated <i>via</i> molecular dynamics simulations. We discovered that several key residues, such as I23, E222, and F303, are involved in inhibitor binding. Additionally, residues I244, T223, F303, and F140 were identified as prominent in interactions with specific ligand clusters. Our findings suggest that NorA's substrate binding site, encompassing residues aiding ligand recognition based on chemical nature, facilitates the recognition of chemically diverse ligands. This insight into NorA's structural promiscuity in ligand recognition not only enhances understanding of antibiotic resistance mechanisms in <i>S. aureus</i> but also sets the stage for the development of more effective efflux pump inhibitors, vital for combating multidrug resistance.
DOI: 10.6084/m9.figshare.25429338.v1
title: Unraveling the ligand specificity and promiscuity of the <i>Staphylococcus aureus</i> NorA efflux pump: a computational study

description: <i>Staphylococcus aureus</i>, a gram-positive bacterial pathogen, develops antibiotic resistance partly through enhanced activity of transmembrane multi-drug efflux pump proteins like NorA. Being a prominent member of the Major Facilitator Superfamily (MFS), NorA transports various small molecules including hydrophilic fluoroquinolone antibiotics across the cell membrane. Intriguingly, NorA is inhibited by a structurally diverse set of small molecule inhibitors as well, indicating a highly promiscuous ligand/inhibitor recognition. Our study aims to elucidate the structural facets of this promiscuity. Known NorA inhibitors were grouped into five clusters based on chemical class and docked into ligand binding pockets on NorA conformations generated <i>via</i> molecular dynamics simulations. We discovered that several key residues, such as I23, E222, and F303, are involved in inhibitor binding. Additionally, residues I244, T223, F303, and F140 were identified as prominent in interactions with specific ligand clusters. Our findings suggest that NorA's substrate binding site, encompassing residues aiding ligand recognition based on chemical nature, facilitates the recognition of chemically diverse ligands. This insight into NorA's structural promiscuity in ligand recognition not only enhances understanding of antibiotic resistance mechanisms in <i>S. aureus</i> but also sets the stage for the development of more effective efflux pump inhibitors, vital for combating multidrug resistance.
DOI: 10.15468/dl.j8s8ab
title: Occurrence Download

description: A dataset containing 97 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Otopharynx speciosus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 97 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016029-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8e2qn9
title: Occurrence Download

description: A dataset listing the 32 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.5493 43.3389,-7.54987 43.32402,-7.52334 43.32213,-7.52362 43.34364,-7.52817 43.34449,-7.52808 43.33994,-7.5493 43.3389))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 32 records were derived from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016012-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bst56
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saururus cernuus",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016032-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7fpzj9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saururus cernuus",
 "Country is Georgia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016030-250914085247600/datasets/export for details.
DOI: 10.15468/dl.nhg93y
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saururus cernuus",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016031-250914085247600/datasets/export for details.
DOI: 10.15468/dl.h77xc4
title: Occurrence Download

description: A dataset containing 804 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scribneria bolanderi"
 ]
}

 The dataset includes 804 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016033-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17155341
title: Introduction to Ancient Metagenomics Textbook (Edition 2025): Ancient Metagenomic Pipelines

description: Data and conda software environment file for the chapter 'Ancient Metagenomic Pipelines' of the SPAAM Community's textbook: Introduction to Ancient Metagenomics (https://www.spaam-community.org/intro-to-ancient-metagenomics-book).
DOI: 10.5281/zenodo.8413239
title: Introduction to Ancient Metagenomics Textbook (Edition 2025): Ancient Metagenomic Pipelines

description: Data and conda software environment file for the chapter 'Ancient Metagenomic Pipelines' of the SPAAM Community's textbook: Introduction to Ancient Metagenomics (https://www.spaam-community.org/intro-to-ancient-metagenomics-book).
DOI: 10.25345/c5707x21w
title: MassIVE MSV000099225 - Bacterial Proteomics_Bacillus velezensis P45
title: Untargeted proteomics of full protein extract of Bacillus velezensis P45 in prebiotics and mucin cultures
DOI: 10.15468/dl.gerqre
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Senilia senilis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 78 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016034-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17148430
title: United Arab Emirates T20I Tri-Series 2025 Cricket Dataset

description: Comprehensive T20 cricket statistics for tri-series between Pakistan, Afghanistan, and UAE
DOI: 10.5281/zenodo.17148431
title: United Arab Emirates T20I Tri-Series 2025 Cricket Dataset

description: Comprehensive T20 cricket statistics for tri-series between Pakistan, Afghanistan, and UAE
DOI: 10.15468/dl.kjwzcc
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pseudophoxinus firati)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 34 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016036-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxqjcn
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Platanus hispanica",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 81 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016035-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.92gff7
title: Occurrence Download

description: A dataset containing 552355 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Sciurus carolinensis"
 ]
}

 The dataset includes 552355 records from 304 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015944-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17155402
title: Introduction to Ancient Metagenomics Textbook (Edition 2025): Phylogenomics

description: Data and conda software environment file for the chapter 'Phylogenomics' of the SPAAM Community's textbook: Introduction to Ancient Metagenomics (https://www.spaam-community.org/intro-to-ancient-metagenomics-book).
DOI: 10.5281/zenodo.8413215
title: Introduction to Ancient Metagenomics Textbook (Edition 2025): Phylogenomics

description: Data and conda software environment file for the chapter 'Phylogenomics' of the SPAAM Community's textbook: Introduction to Ancient Metagenomics (https://www.spaam-community.org/intro-to-ancient-metagenomics-book).
DOI: 10.15468/dl.ptcuy9
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Hyalinobatrachium"
 ]
}

 The dataset includes 625 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016038-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tkhn63
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tegillarca rhombea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016039-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uf4veb
title: Occurrence Download

description: A dataset containing 81682 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tamias striatus"
 ]
}

 The dataset includes 81682 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015958-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yzbstt
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyrilia aurantiocephala"
 ]
}

 The dataset includes 710 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016040-250914085247600/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26275/qcoa-ckbg
title: Generic human dorsal root ganglion scaffold

description: Annotated human dorsal root ganglion scaffold available for registration of experimental data.