cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28006400
title: Assessment of binding affinity of major bioactive compounds from <i>Momordica charantia</i>, <i>Azadirachta indica</i>, <i>Nelumbo nucifera</i>, <i>Caesalpinia crista</i>, <i>Martynia annua</i> and <i>Erythrina variegate</i> to COX-2 receptor: an <i>in silico</i> study

description: In traditional medicine, potential anti-inflammatory and pain-relieving activity of <i>Momordica charantia, Azadirachta indica, Nelumbo nucifera, Caesalpinia crista, Martynia annua</i> and <i>Erythrina variegate</i> has been emphasized. In this study, we explored binding affinity of 36 bioactive compounds from these plants to cyclooxygenase-2 (COX-2) receptor using docking method. Six compounds namely, beta carotene, lycopene, lutein, momordicoside, rutin and azadirachtin showed excellent binding affinities (−10.29, −10.22, −10.03, −7.9, −8.81 and −7.88 kcal/mol, respectively) and stable interactions with COX-2 (greater than those of aspirin and diclofenac) and they were chosen for the molecular dynamics (MD) assessments done throughout a 100-ns time period. Based on the computed RMSD, RMSF, Rg, SASA and PCA, all ligands were found to form stable and adequate interactions with COX-2 protein; these findings were comparable to those of aspirin and diclofenac, indicating the potential inhibitory properties of these ligands on COX-2 protein. In addition, the toxicity of compounds was evaluated using Pred-hERG, Pred-Skin and ProTox-II. Since COX-2 inhibitors have been reported to activate the Nrf2 pathway, it is hypothesized that they may confer other health-promoting effects through triggering Nrf2 signaling.
DOI: 10.6084/m9.figshare.28006400.v1
title: Assessment of binding affinity of major bioactive compounds from <i>Momordica charantia</i>, <i>Azadirachta indica</i>, <i>Nelumbo nucifera</i>, <i>Caesalpinia crista</i>, <i>Martynia annua</i> and <i>Erythrina variegate</i> to COX-2 receptor: an <i>in silico</i> study

description: In traditional medicine, potential anti-inflammatory and pain-relieving activity of <i>Momordica charantia, Azadirachta indica, Nelumbo nucifera, Caesalpinia crista, Martynia annua</i> and <i>Erythrina variegate</i> has been emphasized. In this study, we explored binding affinity of 36 bioactive compounds from these plants to cyclooxygenase-2 (COX-2) receptor using docking method. Six compounds namely, beta carotene, lycopene, lutein, momordicoside, rutin and azadirachtin showed excellent binding affinities (−10.29, −10.22, −10.03, −7.9, −8.81 and −7.88 kcal/mol, respectively) and stable interactions with COX-2 (greater than those of aspirin and diclofenac) and they were chosen for the molecular dynamics (MD) assessments done throughout a 100-ns time period. Based on the computed RMSD, RMSF, Rg, SASA and PCA, all ligands were found to form stable and adequate interactions with COX-2 protein; these findings were comparable to those of aspirin and diclofenac, indicating the potential inhibitory properties of these ligands on COX-2 protein. In addition, the toxicity of compounds was evaluated using Pred-hERG, Pred-Skin and ProTox-II. Since COX-2 inhibitors have been reported to activate the Nrf2 pathway, it is hypothesized that they may confer other health-promoting effects through triggering Nrf2 signaling.
DOI: 10.3535/2lr-flt-xce
title: Sympistis Hübner, 1823

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/z4c-epj-zb9
title: Amphipoea Billberg, 1820

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/2zr-l2g-sjz
title: Autographa pulchrina (Haworth, 1809)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/319-86l-7rw
title: Agonopterix ocellana Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/k9t-6sc-bv8
title: Xanthia (Cirrhia) Hübner, 1816

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ylh-4ya-52b
title: Brachionycha nubeculosa Esper, 1785

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.27928831
title: From nature’s pharmacy: harnessing bioactive phytoconstituents as fibroblast growth factor receptor 3 inhibitors for anti-cancer therapeutics

description: Fibroblast growth factor receptor 3 (FGFR3) is a key protein involved in regulating cell growth and development. Aberrant activation of FGFR3 has been linked to several diseases, including cancer and skeletal disorders. Therefore, identifying potential inhibitors of FGFR3 is of great interest in developing targeted therapies. In this study, we employed a combined docking and molecular dynamics simulation (MDS) approach to investigate the inhibitory potential of plant-based compounds against FGFR3. Here, we utilized structure-based virtual screening to identify potential phytoconstituents from the IMPPAT library with the ability to inhibit FGFR3 activity. The initial screening process involved molecular docking to assess the binding potential of the compounds towards FGFR3. Afterward, we employed various filters to determine physicochemical properties, ADMET, and PASS evaluation to identify potential hits against FGFR3. This process discovered two phytoconstituents, Cycloartobiloxanthone and Desoxylimonin, as promising candidates against FGFR3. These compounds exhibited favorable binding affinity, efficiency, and specific interaction towards the FGFR3 binding pocket. They preferred binding to the active site of FGFR3 and possessed desirable drug-like properties. To gain a deeper understanding of their interaction mechanism, conformational dynamics, and stability, we conducted all-atom MDS lasting 200 nanoseconds (ns) on the FGFR3-Cycloartobiloxanthone and FGFR3-Desoxylimonin complexes. The MDS consistently demonstrated the formation of stable protein-ligand complexes between FGFR3 and Cycloartobiloxanthone/Desoxylimonin throughout the trajectory. Based on these results, it can be inferred that Cycloartobiloxanthone and Desoxylimonin can potentially serve as valuable scaffolds in developing drugs targeting FGFR3 for cancer therapeutic after required validation.
DOI: 10.6084/m9.figshare.27928831.v1
title: From nature’s pharmacy: harnessing bioactive phytoconstituents as fibroblast growth factor receptor 3 inhibitors for anti-cancer therapeutics

description: Fibroblast growth factor receptor 3 (FGFR3) is a key protein involved in regulating cell growth and development. Aberrant activation of FGFR3 has been linked to several diseases, including cancer and skeletal disorders. Therefore, identifying potential inhibitors of FGFR3 is of great interest in developing targeted therapies. In this study, we employed a combined docking and molecular dynamics simulation (MDS) approach to investigate the inhibitory potential of plant-based compounds against FGFR3. Here, we utilized structure-based virtual screening to identify potential phytoconstituents from the IMPPAT library with the ability to inhibit FGFR3 activity. The initial screening process involved molecular docking to assess the binding potential of the compounds towards FGFR3. Afterward, we employed various filters to determine physicochemical properties, ADMET, and PASS evaluation to identify potential hits against FGFR3. This process discovered two phytoconstituents, Cycloartobiloxanthone and Desoxylimonin, as promising candidates against FGFR3. These compounds exhibited favorable binding affinity, efficiency, and specific interaction towards the FGFR3 binding pocket. They preferred binding to the active site of FGFR3 and possessed desirable drug-like properties. To gain a deeper understanding of their interaction mechanism, conformational dynamics, and stability, we conducted all-atom MDS lasting 200 nanoseconds (ns) on the FGFR3-Cycloartobiloxanthone and FGFR3-Desoxylimonin complexes. The MDS consistently demonstrated the formation of stable protein-ligand complexes between FGFR3 and Cycloartobiloxanthone/Desoxylimonin throughout the trajectory. Based on these results, it can be inferred that Cycloartobiloxanthone and Desoxylimonin can potentially serve as valuable scaffolds in developing drugs targeting FGFR3 for cancer therapeutic after required validation.
DOI: 10.15468/dl.gjqe3c
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is one of (Salmoniformes)",
 "Geometry POLYGON((19.0 42.0, 19.0 34.5, 29.7 34.5, 29.7 42.0, 19.0 42.0))"
 ]
}

 The dataset includes 297 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028719-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/72y-fgr-d4k
title: Rhizedra lutosa Hübner, 1803

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/gzy-ler-d63
title: Agonopterix ocellana Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.25712771
title: Predictive insights into plant-based compounds as fibroblast growth factor receptor 1 inhibitors: a combined molecular docking and dynamics simulation study

description: The discovery of novel therapeutic agents with potent anticancer activity remains a critical challenge in drug development. Natural products, particularly bioactive phytoconstituents derived from plants, have emerged as promising sources for anticancer drug discovery. In this study, we used virtual screening techniques to explore the potential of bioactive phytoconstituents as inhibitors of fibroblast growth factor receptor 1 (FGFR1), a key signaling protein implicated in cancer progression. We used virtual screening techniques to analyze phytoconstituents extracted from the IMPPAT 2.0 database. Our primary objective was to discover promising inhibitors of FGFR1. To ensure the selection of promising candidates, we initially filtered the molecules based on their physicochemical properties. Subsequently, we performed binding affinity calculations, PAINS, ADMET, and PASS filters to identify nontoxic and highly effective hits. Through this screening process, one phytocompound, namely Mundulone, emerged as a potential lead. This compound demonstrated an appreciable affinity for FGFR1 and exhibited specific interactions with the ATP-binding site residues. To gain further insights into the conformational dynamics of Mundulone and the reference FGFR1 inhibitor, Lenvatinib, we conducted time-evolution analyses employing 200 ns molecular dynamics simulations (MDS) and essential dynamics. These analyses provided valuable information regarding the dynamic behavior and stability of the compounds in complexes with FGFR1. Overall, the findings indicate that Mundulone exhibits promising binding affinity, specific interactions, and favorable drug profiles, making it a promising lead candidate. Further experimental analysis will be necessary to confirm its effectiveness and safety profiles for therapeutic advancement in the cancer field.
DOI: 10.6084/m9.figshare.25712771.v1
title: Predictive insights into plant-based compounds as fibroblast growth factor receptor 1 inhibitors: a combined molecular docking and dynamics simulation study

description: The discovery of novel therapeutic agents with potent anticancer activity remains a critical challenge in drug development. Natural products, particularly bioactive phytoconstituents derived from plants, have emerged as promising sources for anticancer drug discovery. In this study, we used virtual screening techniques to explore the potential of bioactive phytoconstituents as inhibitors of fibroblast growth factor receptor 1 (FGFR1), a key signaling protein implicated in cancer progression. We used virtual screening techniques to analyze phytoconstituents extracted from the IMPPAT 2.0 database. Our primary objective was to discover promising inhibitors of FGFR1. To ensure the selection of promising candidates, we initially filtered the molecules based on their physicochemical properties. Subsequently, we performed binding affinity calculations, PAINS, ADMET, and PASS filters to identify nontoxic and highly effective hits. Through this screening process, one phytocompound, namely Mundulone, emerged as a potential lead. This compound demonstrated an appreciable affinity for FGFR1 and exhibited specific interactions with the ATP-binding site residues. To gain further insights into the conformational dynamics of Mundulone and the reference FGFR1 inhibitor, Lenvatinib, we conducted time-evolution analyses employing 200 ns molecular dynamics simulations (MDS) and essential dynamics. These analyses provided valuable information regarding the dynamic behavior and stability of the compounds in complexes with FGFR1. Overall, the findings indicate that Mundulone exhibits promising binding affinity, specific interactions, and favorable drug profiles, making it a promising lead candidate. Further experimental analysis will be necessary to confirm its effectiveness and safety profiles for therapeutic advancement in the cancer field.
DOI: 10.6084/m9.figshare.28596163
title: Molecular genomic insights into melanoma associated proteins PRAME and BAP1

description: Melanoma, a globally prevalent skin cancer with over 325,000 new cases annually, necessitates a comprehensive under- standing of its molecular components. This study looks at the PRAME (cutaneous melanoma-associated antigen) and BAP1 (gene controlling gene-environment interactions) proteins. Both PRAME and BAP1 are associated with critical genomic alterations that significantly influence melanoma progression and patient outcomes. PRAME is overexpressed in various cancers, especially uveal melanoma (UM), where high levels correlate with poor prognosis and genomic instability linked to chromosome 8q12 alterations. Meanwhile, mutations in BAP1 contribute to increased genomic instability and a higher risk of metastasis in UM, highlighting its importance as a key prognostic marker in tumorigenesis. Established approaches along with features proposed in this work are used to investigate sequence conservation, polyglutamic acid presence, intrinsic disorder of proteins, polar-nonpolar residues arrangement PRAME and BAP1 conserved residues highlight their critical roles in protein function and interaction. Sequence invariance indicates the possibility of functional relevance and evolutionary conservation. PRAME has enhanced intrinsic disorder and flexibility, whereas BAP1 has changed disorder-promoting residue sequences. Polyglutamic acid strings are found in both proteins, emphasizing their modulatory involvement in protein interactions. The ratios and spatial arrangement of amino acids have a profound influence on interactions and gene dysregulation. This work contributes to a better knowledge of the two melanoma-associated proteins viz. PRAME and BAP1 by unraveling their structural and functional complexities.
DOI: 10.6084/m9.figshare.28596163.v1
title: Molecular genomic insights into melanoma associated proteins PRAME and BAP1

description: Melanoma, a globally prevalent skin cancer with over 325,000 new cases annually, necessitates a comprehensive under- standing of its molecular components. This study looks at the PRAME (cutaneous melanoma-associated antigen) and BAP1 (gene controlling gene-environment interactions) proteins. Both PRAME and BAP1 are associated with critical genomic alterations that significantly influence melanoma progression and patient outcomes. PRAME is overexpressed in various cancers, especially uveal melanoma (UM), where high levels correlate with poor prognosis and genomic instability linked to chromosome 8q12 alterations. Meanwhile, mutations in BAP1 contribute to increased genomic instability and a higher risk of metastasis in UM, highlighting its importance as a key prognostic marker in tumorigenesis. Established approaches along with features proposed in this work are used to investigate sequence conservation, polyglutamic acid presence, intrinsic disorder of proteins, polar-nonpolar residues arrangement PRAME and BAP1 conserved residues highlight their critical roles in protein function and interaction. Sequence invariance indicates the possibility of functional relevance and evolutionary conservation. PRAME has enhanced intrinsic disorder and flexibility, whereas BAP1 has changed disorder-promoting residue sequences. Polyglutamic acid strings are found in both proteins, emphasizing their modulatory involvement in protein interactions. The ratios and spatial arrangement of amino acids have a profound influence on interactions and gene dysregulation. This work contributes to a better knowledge of the two melanoma-associated proteins viz. PRAME and BAP1 by unraveling their structural and functional complexities.
DOI: 10.3535/5kx-9w7-831
title: Scoparia cembrella Linnaeus, 1761

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/d99-cy5-stj
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/zxa-w6x-9mm
title: Noctuidae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kz8-7xt-j4z
title: Oligia Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/mv5-mtc-hda
title: Oligia Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.25689737
title: Fungal alkaloid malbrancheamide reorients the lipid binding domain of GRK5

description: G protein-coupled receptors (GPCRs) are the largest group of receptors involved in various types of signaling. GPCR signaling is regulated <i>via</i> receptor phosphorylation by G protein-coupled receptor kinases 5 (GRK5). Calmodulin (CaM), a universal Ca<sup>2+</sup> sensor, inhibits receptor phosphorylation by binding to GRK5. However, the inhibitor malbrancheamide (MBC), which binds at CaM C-lobe, allows for receptor phosphorylation. To understand the phosphorylation mechanism by GRK5, we carried out a MD simulation of the CaM/GRK5 complex in the presence and absence of the MBC inhibitor. The lipid binding domain (LBD) of GRK5 adopted different positions in the presence and absence of inhibitor. Furthermore, the inhibitor MBC restricted the movement of the N-lobe tether (NLT) loop, probably blocking the autophosphorylation of GRK5.
DOI: 10.6084/m9.figshare.25689737.v1
title: Fungal alkaloid malbrancheamide reorients the lipid binding domain of GRK5

description: G protein-coupled receptors (GPCRs) are the largest group of receptors involved in various types of signaling. GPCR signaling is regulated <i>via</i> receptor phosphorylation by G protein-coupled receptor kinases 5 (GRK5). Calmodulin (CaM), a universal Ca<sup>2+</sup> sensor, inhibits receptor phosphorylation by binding to GRK5. However, the inhibitor malbrancheamide (MBC), which binds at CaM C-lobe, allows for receptor phosphorylation. To understand the phosphorylation mechanism by GRK5, we carried out a MD simulation of the CaM/GRK5 complex in the presence and absence of the MBC inhibitor. The lipid binding domain (LBD) of GRK5 adopted different positions in the presence and absence of inhibitor. Furthermore, the inhibitor MBC restricted the movement of the N-lobe tether (NLT) loop, probably blocking the autophosphorylation of GRK5.
DOI: 10.3535/g4j-t9q-168
title: Agonopterix ocellana Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rfx-cn3-wdx
title: Falcaria lacertinaria (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/7k5-904-kyw
title: Lymantria (Lymantria) monacha (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/jfc-71k-c02
title: Amphipyra (Amphipyra) perflua (Fabricius, 1787)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/mg2-0t3-jjm
title: Cucullia gnaphalii (Hübner, 1813)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28039564
title: In silico design, modelling and molecular mechanisms of Axl receptor tyrosine kinase inhibitors

description: A kinase domain from receptor tyrosine kinases (RTKs) regulate intracellular communications to control cellular metabolic activities. Some of the malignant cells have upregulated and overexpressed RTKs which are responsible for angiogenesis in many metastatic cancers. Axl RTK is present in most of the eukaryotic cells and all metastatic cancer cells have overexpressed Axl tyrosine kinase to trigger uncontrolled growth and angiogenesis in the malignant cells. The upregulated kinases can be inhibited in its active and inactive states in the presence of small organic molecule inhibitors. Kinase inhibitors have been discovered to arrest the signal transduction pathways in the malignant cells as a therapy and cure for cancer. In this work, small molecule databases were screened using the pharmacophore features of a macrocyclic inhibitor (7YS) taken as reference from the crystal structure of Axl kinase domain. Pharmacophore based virtual screening of small molecule libraries (CHEMBL32, ChemDiv, Chemspace, Mcule, MolProt, PubChem and Zinc), followed by molecular docking, molecular dynamics simulations, binding energies from MM-PBSA calculations and trajectory analysis as principal component analysis were studied. The molecular basis for the binding of macrocyclic inhibitor, ATP and seven screened hit molecules bound at Axl kinase domain in two different modes at catalytic and regulatory sites was analyzed.
DOI: 10.6084/m9.figshare.28039564.v1
title: In silico design, modelling and molecular mechanisms of Axl receptor tyrosine kinase inhibitors

description: A kinase domain from receptor tyrosine kinases (RTKs) regulate intracellular communications to control cellular metabolic activities. Some of the malignant cells have upregulated and overexpressed RTKs which are responsible for angiogenesis in many metastatic cancers. Axl RTK is present in most of the eukaryotic cells and all metastatic cancer cells have overexpressed Axl tyrosine kinase to trigger uncontrolled growth and angiogenesis in the malignant cells. The upregulated kinases can be inhibited in its active and inactive states in the presence of small organic molecule inhibitors. Kinase inhibitors have been discovered to arrest the signal transduction pathways in the malignant cells as a therapy and cure for cancer. In this work, small molecule databases were screened using the pharmacophore features of a macrocyclic inhibitor (7YS) taken as reference from the crystal structure of Axl kinase domain. Pharmacophore based virtual screening of small molecule libraries (CHEMBL32, ChemDiv, Chemspace, Mcule, MolProt, PubChem and Zinc), followed by molecular docking, molecular dynamics simulations, binding energies from MM-PBSA calculations and trajectory analysis as principal component analysis were studied. The molecular basis for the binding of macrocyclic inhibitor, ATP and seven screened hit molecules bound at Axl kinase domain in two different modes at catalytic and regulatory sites was analyzed.
DOI: 10.3535/trh-x7m-ma2
title: Cucullia gnaphalii (Hübner, 1813)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.