cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25093383.v1
title: Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6

description: Transient Receptor Potential Canonical 5 (T RP C5) and T RP C6 channels play critical physiological roles in various cell types. Their involvement in numerous disease progression mechanisms has led to extensive searches for their inhibitors. Although several potent T RP C inhibitors have been developed and the structure of their binding sites were mapped using cryo electron microscopy, a comprehensive understanding of the molecular interactions within the inhibitor binding site of T RP Cs remains elusive. This study aimed to decipher the structural determinants and molecular mechanisms contributing to the differential binding of clemizole to T RP C5 and T RP C6, with a particular focus on the accessibility of binding site residues. This information can help better understand what molecular features allow for selective binding, which is a key characteristic of clinically effective pharmacological agents. Using computational methodologies, we conducted an in-depth molecular docking analysis of clemizole with T RP C5 and T RP C6 channels. The protein structures were retrieved from publicly accessible protein databases. Discovery Studio 2020 Client Visualizer and Chimera software facilitated our in-silico mutation experiments and enabled us to identify the critical structural elements influencing clemizole binding. Our study reveals key molecular determinants at the clemizole binding site, specifically outlining the role of residues' Accessible Surface Area (ASA) and Relative Accessible Surface Area (RASA) in differential binding. We found that lower accessibility of T RP C6 binding site residues, compared to those in T RP C5, could account for the lower affinity binding of clemizole to T RP C6. This work illuminates the pivotal role of binding site residue accessibility in determining the affinity of clemizole to T RP C5 and T RP C6. A nuanced understanding of the distinct binding properties between these homologous proteins may pave the way for the development of more selective inhibitors, promising improved therapeutic efficacy and fewer off-target effects. By demystifying the structural and molecular subtleties of T RP C inhibitors, this research could significantly accelerate the drug discovery process, offering hope to patients afflicted with T RP C-related diseases.
DOI: 10.6084/m9.figshare.25011570
title: Unveiling the potential of recently FDA-approved drugs as quorum sensing inhibitors against <i>P. Aeruginosa</i> using high-performance computational techniques

description: Through cell-to-cell communication, activation of efflux pumps, formation of biofilms, and other mechanisms, <i>pseudomonas aeruginosa’s</i> quorum sensing systems (QSS), notably the lasl/las-r system, contribute a vital role in the development of anti-microbial resistance (AMR). Identifying potential drugs against these targets could have significant implications for combating <i>pseudomonal</i> infections. The current study aims to identify promising recently FDA-approved drugs against lasl/las-r proteins. The ligands were selected from the FDA-approved drug lists of the last 5 years. Out of 202, 78 drugs were checked for interaction with lasl/las-r protein and 4 drugs revealed top binding conformations characterized by favorable energetic profiles within the active site of the las-r protein which were further assigned for 250-ns molecular dynamics (MD) simulation. The MD analysis confirmed the dynamical stability of brexanolone and oteseconazole with las-r protein. The root mean square deviation (RMSD), radius of gyration (Rg) and solvent-accessible surface area (SASA) analysis have indicated less deviation, more compactness of protein and less exposure of protein ligand complex to its surroundings as compared to the reference ligand-protein complex. The hydroxyl group in the oteseconazole whereas hydroxyl and ketone group in the brexanolone were responsible for hydrogen bonds with the active site residue of las r ptotein as indicated by ligand-protein contacts diagram. The binding energies per residue analysis revealed TYR-47 as the most contributing amino acid residue for interaction with oteseconazole and brexanolone. The identified drugs may be potential repurposing candidates against <i>pseudomonal</i> infections through inhibition of las-r protein.
DOI: 10.6084/m9.figshare.25011570.v1
title: Unveiling the potential of recently FDA-approved drugs as quorum sensing inhibitors against <i>P. Aeruginosa</i> using high-performance computational techniques

description: Through cell-to-cell communication, activation of efflux pumps, formation of biofilms, and other mechanisms, <i>pseudomonas aeruginosa’s</i> quorum sensing systems (QSS), notably the lasl/las-r system, contribute a vital role in the development of anti-microbial resistance (AMR). Identifying potential drugs against these targets could have significant implications for combating <i>pseudomonal</i> infections. The current study aims to identify promising recently FDA-approved drugs against lasl/las-r proteins. The ligands were selected from the FDA-approved drug lists of the last 5 years. Out of 202, 78 drugs were checked for interaction with lasl/las-r protein and 4 drugs revealed top binding conformations characterized by favorable energetic profiles within the active site of the las-r protein which were further assigned for 250-ns molecular dynamics (MD) simulation. The MD analysis confirmed the dynamical stability of brexanolone and oteseconazole with las-r protein. The root mean square deviation (RMSD), radius of gyration (Rg) and solvent-accessible surface area (SASA) analysis have indicated less deviation, more compactness of protein and less exposure of protein ligand complex to its surroundings as compared to the reference ligand-protein complex. The hydroxyl group in the oteseconazole whereas hydroxyl and ketone group in the brexanolone were responsible for hydrogen bonds with the active site residue of las r ptotein as indicated by ligand-protein contacts diagram. The binding energies per residue analysis revealed TYR-47 as the most contributing amino acid residue for interaction with oteseconazole and brexanolone. The identified drugs may be potential repurposing candidates against <i>pseudomonal</i> infections through inhibition of las-r protein.
DOI: 10.6084/m9.figshare.25018126
title: Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus

description: Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement to design and develop efficient therapeutic molecules. Here, a comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented to identify the potential molecule from the anti-dengue compound library that can inhibit the function of the VP24 protein of Marburg. Virtual high throughput screening identified five effective binders of VP24 after screening 484 anti-dengue compounds. These compounds were treated in MD simulation at four different temperatures: 300, 340, 380, and 420 K. Higher temperatures showed dissociation of hit compounds from the protein. Further, triplicates of 100 ns MD simulation were conducted which showed that compounds ID = <b>118717693</b>, and ID = <b>5361</b> showed strong stability with the protein molecule. These compounds were further validated using ΔG binding free energies and they showed: −30.38 kcal/mol, and −67.83 kcal/mol binding free energies, respectively. Later, these two compounds were used in steered MD simulation to detect its dissociation. Compound ID = <b>5361</b> showed the maximum pulling force of 199.02 kcal/mol/nm to dissociate the protein-ligand complex while ID = <b>118717693</b> had a pulling force of 101.11 kcal/mol/nm, respectively. This ligand highest number of hydrogen bonds with varying occupancies at 89.93%, 69.80%, 57.93%, 52.33%, and 50.63%. This study showed that ID = <b>5361</b> can bind with the VP24 strongly and has the potential to inhibit its function which can be validated in the in-vitro experiment.
DOI: 10.6084/m9.figshare.25018126.v1
title: Application of temperature-dependent and steered molecular dynamics simulation to screen anti-dengue compounds against Marburg virus

description: Marburg virus infections are extremely fatal with a fatality range of 23% to 90%, therefore there is an urgent requirement to design and develop efficient therapeutic molecules. Here, a comprehensive temperature-dependent molecular dynamics (MD) simulation method was implemented to identify the potential molecule from the anti-dengue compound library that can inhibit the function of the VP24 protein of Marburg. Virtual high throughput screening identified five effective binders of VP24 after screening 484 anti-dengue compounds. These compounds were treated in MD simulation at four different temperatures: 300, 340, 380, and 420 K. Higher temperatures showed dissociation of hit compounds from the protein. Further, triplicates of 100 ns MD simulation were conducted which showed that compounds ID = <b>118717693</b>, and ID = <b>5361</b> showed strong stability with the protein molecule. These compounds were further validated using ΔG binding free energies and they showed: −30.38 kcal/mol, and −67.83 kcal/mol binding free energies, respectively. Later, these two compounds were used in steered MD simulation to detect its dissociation. Compound ID = <b>5361</b> showed the maximum pulling force of 199.02 kcal/mol/nm to dissociate the protein-ligand complex while ID = <b>118717693</b> had a pulling force of 101.11 kcal/mol/nm, respectively. This ligand highest number of hydrogen bonds with varying occupancies at 89.93%, 69.80%, 57.93%, 52.33%, and 50.63%. This study showed that ID = <b>5361</b> can bind with the VP24 strongly and has the potential to inhibit its function which can be validated in the in-vitro experiment.
DOI: 10.6084/m9.figshare.28882419
title: Identifying potent Janus kinase 3 inhibitors using structure-guided virtual screening for inflammatory and neoplastic disease therapy

description: Janus kinases (JAKs) are potential therapeutic targets for anti-inflammatory and anti-cancer agents due to their involvement in cytokine signaling and cell proliferation. One of the major issues in the development of JAK inhibitors is the problem of selectivity for certain isoforms; since the isoforms are highly homologous, selective targeting is difficult. Of the JAKs, Janus kinase 3 (JAK3) which is mainly found in immune cells, is the most suitable isoform to target selectively to enhance the efficacy of treatment. In this study, we used a structure-based virtual screening method to screen PubChem for high-affinity JAK3 inhibitors using known JAK3-inhibitor complex structures. Through stringent filtering criteria, including structural similarity, physicochemical properties, and molecular interactions, we identified two promising compounds, CID:68715657 and CID:68585456, which showed potential JAK3 inhibition activity. These compounds showed better binding affinity than the parent molecules, and the structural modifications also improved the interaction with JAK3, indicating better potency and selectivity. Molecular dynamics (MD) simulations and MM-PBSA confirmed the stability of JAK3 complexes with CID:68715657 and CID:68585456, which further support their prospect as therapeutic targets of JAK3-related diseases. However, this study is limited by its reliance on computational predictions without experimental validation and the constraints of the PubChem database in capturing novel chemical scaffolds. Taken together, the results offer a sound basis for the further optimization of these compounds as highly effective and selective JAK3 inhibitors.
DOI: 10.6084/m9.figshare.28882419.v1
title: Identifying potent Janus kinase 3 inhibitors using structure-guided virtual screening for inflammatory and neoplastic disease therapy

description: Janus kinases (JAKs) are potential therapeutic targets for anti-inflammatory and anti-cancer agents due to their involvement in cytokine signaling and cell proliferation. One of the major issues in the development of JAK inhibitors is the problem of selectivity for certain isoforms; since the isoforms are highly homologous, selective targeting is difficult. Of the JAKs, Janus kinase 3 (JAK3) which is mainly found in immune cells, is the most suitable isoform to target selectively to enhance the efficacy of treatment. In this study, we used a structure-based virtual screening method to screen PubChem for high-affinity JAK3 inhibitors using known JAK3-inhibitor complex structures. Through stringent filtering criteria, including structural similarity, physicochemical properties, and molecular interactions, we identified two promising compounds, CID:68715657 and CID:68585456, which showed potential JAK3 inhibition activity. These compounds showed better binding affinity than the parent molecules, and the structural modifications also improved the interaction with JAK3, indicating better potency and selectivity. Molecular dynamics (MD) simulations and MM-PBSA confirmed the stability of JAK3 complexes with CID:68715657 and CID:68585456, which further support their prospect as therapeutic targets of JAK3-related diseases. However, this study is limited by its reliance on computational predictions without experimental validation and the constraints of the PubChem database in capturing novel chemical scaffolds. Taken together, the results offer a sound basis for the further optimization of these compounds as highly effective and selective JAK3 inhibitors.
DOI: 10.6084/m9.figshare.25027507
title: Identification of ZINC08101049 as a potential IL1β inhibitor through molecular docking and MD simulations for cancer therapeutics

description: Cancer is a significant global health concern that has a major impact on morbidity and mortality worldwide. Research has demonstrated the involvement of Interleukin-1 beta (IL1β) in various aspects of cancer development and progression, including angiogenesis, tumor growth and metastasis. Consequently, targeting IL1β activity represents a promising approach for cancer therapeutics. In this study, we utilized molecular docking and MD simulations to discover potent IL1β inhibitors for the treatment of cancer. Five thousand compounds from ZINC15 database were screened against IL1β target, and the top ten small molecules were selected based on their binding energy. The small molecule named ‘ZINC08101049’ was prioritized based on binding energy (−9.1 kcal/Mol) and residual interaction specifically forming seven hydrogen bonds with amino acid residues namely GLN81, GLY136, LEU134, LYS138, SER84, THR137 and TYR24 of IL1β. Next, IL1β alone and in complex with ZINC08101049 was subjected to MD simulations to determine their behavior at atomic level. The results of molecular docking and MD simulation revealed ZINC08101049 as a potential inhibitor of IL1β, reflecting that ZINC08101049 can emerge as a promising small molecule paving for cancer therapeutics.
DOI: 10.6084/m9.figshare.25027507.v1
title: Identification of ZINC08101049 as a potential IL1β inhibitor through molecular docking and MD simulations for cancer therapeutics

description: Cancer is a significant global health concern that has a major impact on morbidity and mortality worldwide. Research has demonstrated the involvement of Interleukin-1 beta (IL1β) in various aspects of cancer development and progression, including angiogenesis, tumor growth and metastasis. Consequently, targeting IL1β activity represents a promising approach for cancer therapeutics. In this study, we utilized molecular docking and MD simulations to discover potent IL1β inhibitors for the treatment of cancer. Five thousand compounds from ZINC15 database were screened against IL1β target, and the top ten small molecules were selected based on their binding energy. The small molecule named ‘ZINC08101049’ was prioritized based on binding energy (−9.1 kcal/Mol) and residual interaction specifically forming seven hydrogen bonds with amino acid residues namely GLN81, GLY136, LEU134, LYS138, SER84, THR137 and TYR24 of IL1β. Next, IL1β alone and in complex with ZINC08101049 was subjected to MD simulations to determine their behavior at atomic level. The results of molecular docking and MD simulation revealed ZINC08101049 as a potential inhibitor of IL1β, reflecting that ZINC08101049 can emerge as a promising small molecule paving for cancer therapeutics.
DOI: 10.15468/dl.pe2apr
title: Occurrence Download

description: A dataset containing 4350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tribulus cistoides L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4350 records from 183 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014501-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j97d9t
title: Occurrence Download

description: A dataset containing 2754 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-98.49761 19.23007,-98.55923 19.26556,-98.59081 19.21486,-98.53894 19.19651,-98.49761 19.23007))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 2754 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014504-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6mndmy
title: Occurrence Download

description: A dataset containing 29087 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tridax procumbens L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 29087 records from 464 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014503-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufkced
title: Occurrence Download

description: A dataset containing 4684 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Chenopodium quinoa Willd."
 ]
}

 The dataset includes 4684 records from 214 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014505-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvbm6d
title: Occurrence Download

description: A dataset containing 4963 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-52.65539 -28.40316,-52.18971 -28.40316,-52.18971 -28.12093,-52.65539 -28.12093,-52.65539 -28.40316))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 4963 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014509-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nz9tnc
title: Occurrence Download

description: A dataset containing 278538 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "Country is Colombia",
 "Geometry POLYGON((-75.58688 6.45195,-74.65629 6.45195,-74.65629 7.05436,-75.58688 7.05436,-75.58688 6.45195))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 278538 records from 110 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014495-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y662jy
title: Occurrence Download

description: A dataset containing 195309 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is one of (Africa, Asia, Europe)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Scarabaeidae",
 "Year 1995-2025"
 ]
}

 The dataset includes 195309 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014508-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15571645
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250601i Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250601i Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.15571646
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS250601i Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS250601i Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.15468/dl.wmezzq
title: Occurrence Download

description: A dataset listing the 1154 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-52.68199 -28.40603,-52.14876 -28.40603,-52.14876 -28.16444,-52.68199 -28.16444,-52.68199 -28.40603))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1154 records were derived from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014507-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cn2n2s
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Xenodermichthys copei (Gill, 1884)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((8.9648 28.8496,-0.0352 28.8496,-0.0352 19.8496,8.9648 19.8496,8.9648 28.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010490-250525065834625/datasets/export for details.