cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14891226
title: Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect

description: The small-molecule inhibitor of phosphoglycerate dehydrogenase, NCT-503, reduces incorporation of glucose-derived carbons into serine <i>in vitro</i>. Here we describe an off-target effect of NCT-503 in neuroblastoma cell lines expressing divergent phosphoglycerate dehydrogenase (PHGDH) levels and single-cell clones with CRISPR-Cas9-directed PHGDH knockout or their respective wildtype controls. NCT-503 treatment strongly reduced synthesis of glucose-derived citrate in all cell models investigated compared to the inactive drug control and independent of PHGDH expression level. Incorporation of glucose-derived carbons entering the TCA cycle via pyruvate carboxylase was enhanced by NCT-503 treatment. The activity of citrate synthase was not altered by NCT-503 treatment. We also detected no change in the thermal stabilisation of citrate synthase in cellular thermal shift assays from NCT-503-treated cells. Thus, the direct cause of the observed off-target effect remains enigmatic. Our findings highlight off-target potential within a metabolic assessment of carbon usage in cells treated with the small-molecule inhibitor, NCT-503.
DOI: 10.6084/m9.figshare.14891226.v1
title: Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle, independently of its on-target effect

description: The small-molecule inhibitor of phosphoglycerate dehydrogenase, NCT-503, reduces incorporation of glucose-derived carbons into serine <i>in vitro</i>. Here we describe an off-target effect of NCT-503 in neuroblastoma cell lines expressing divergent phosphoglycerate dehydrogenase (PHGDH) levels and single-cell clones with CRISPR-Cas9-directed PHGDH knockout or their respective wildtype controls. NCT-503 treatment strongly reduced synthesis of glucose-derived citrate in all cell models investigated compared to the inactive drug control and independent of PHGDH expression level. Incorporation of glucose-derived carbons entering the TCA cycle via pyruvate carboxylase was enhanced by NCT-503 treatment. The activity of citrate synthase was not altered by NCT-503 treatment. We also detected no change in the thermal stabilisation of citrate synthase in cellular thermal shift assays from NCT-503-treated cells. Thus, the direct cause of the observed off-target effect remains enigmatic. Our findings highlight off-target potential within a metabolic assessment of carbon usage in cells treated with the small-molecule inhibitor, NCT-503.
DOI: 10.6084/m9.figshare.13637095
title: Structural insights and molecular dynamics into the inhibitory mechanism of a Kunitz-type trypsin inhibitor from <i>Tamarindus indica</i> L

description: Trypsin inhibitors from tamarind seed have been studied <i>in vitro</i> and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced <i>de novo</i> by MALDI-TOF/TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n°287 was selected considering the RMSD analysis and interaction energy (–301.0128 kcal.mol<sup>−1</sup>). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.
DOI: 10.6084/m9.figshare.13637095.v2
title: Structural insights and molecular dynamics into the inhibitory mechanism of a Kunitz-type trypsin inhibitor from <i>Tamarindus indica</i> L

description: Trypsin inhibitors from tamarind seed have been studied <i>in vitro</i> and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced <i>de novo</i> by MALDI-TOF/TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n°287 was selected considering the RMSD analysis and interaction energy (–301.0128 kcal.mol<sup>−1</sup>). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.
DOI: 10.6084/m9.figshare.13637095.v1
title: Structural insights and molecular dynamics into the inhibitory mechanism of a Kunitz-type trypsin inhibitor from <i>Tamarindus indica</i> L

description: Trypsin inhibitors from tamarind seed have been studied <i>in vitro</i> and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced <i>de novo</i> by MALDI-TOF/TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n°287 was selected considering the RMSD analysis and interaction energy (–301.0128 kcal.mol<sup>−1</sup>). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.
DOI: 10.6084/m9.figshare.13490755
title: Synthesis of some quinazolinones inspired from the natural alkaloid L<i>-</i>norephedrine as EGFR inhibitors and radiosensitizers

description: A set of quinazolinones synthesized by the aid of L-norephedrine was assembled to generate novel analogues as potential anticancer and radiosensitizing agents. The new compounds were evaluated for their cytotoxic activity against MDA-MB-231, MCF-7, HepG-2, HCT-116 cancer cell lines and EGFR inhibitory activity. The most active compounds <b>5</b> and <b>6</b> were screened against MCF-10A normal cell line and displayed lower toxic effects. They proved their relative safety with high selectivity towards MDA-MB-231 breast cancer cell line. Measurement of the radiosensitizing activity for <b>5</b> and <b>6</b> revealed that they could sensitize the tumour cells after being exposed to a single dose of 8 Gy gamma radiation. Compound <b>5</b> was able to induce apoptosis and arrest the cell cycle at the G2-M phase. Molecular docking of <b>5</b> and <b>6</b> in the active site of EGFR was performed to gain insight into the binding interactions with the key amino acids.
DOI: 10.6084/m9.figshare.13490755.v1
title: Synthesis of some quinazolinones inspired from the natural alkaloid L<i>-</i>norephedrine as EGFR inhibitors and radiosensitizers

description: A set of quinazolinones synthesized by the aid of L-norephedrine was assembled to generate novel analogues as potential anticancer and radiosensitizing agents. The new compounds were evaluated for their cytotoxic activity against MDA-MB-231, MCF-7, HepG-2, HCT-116 cancer cell lines and EGFR inhibitory activity. The most active compounds <b>5</b> and <b>6</b> were screened against MCF-10A normal cell line and displayed lower toxic effects. They proved their relative safety with high selectivity towards MDA-MB-231 breast cancer cell line. Measurement of the radiosensitizing activity for <b>5</b> and <b>6</b> revealed that they could sensitize the tumour cells after being exposed to a single dose of 8 Gy gamma radiation. Compound <b>5</b> was able to induce apoptosis and arrest the cell cycle at the G2-M phase. Molecular docking of <b>5</b> and <b>6</b> in the active site of EGFR was performed to gain insight into the binding interactions with the key amino acids.
DOI: 10.6084/m9.figshare.16458535.v1
title: Microwave-assisted Phospha-Michael addition reactions in the 13α-oestrone series and <i>in vitro</i> antiproliferative properties

description: Microwave-assisted phospha-Michael addition reactions were carried out in the 13α-oestrone series. The exocyclic 16-methylene-17-ketones as α,β-unsaturated ketones were reacted with secondary phosphine oxides as nucleophilic partners. The addition reactions furnished the two tertiary phosphine oxide diastereomers in high yields. The main product was the 16α-isomer. The antiproliferative activities of the newly synthesised organophosphorus compounds against a panel of nine human cancer cell lines were investigated by means of MTT assays. The most potent compound, the diphenylphosphine oxide derivative in the 3-<i>O</i>-methyl-13α-oestrone series (<b>9</b>), exerted selective cell growth-inhibitory activity against UPCI-SCC-131 and T47D cell lines with low micromolar IC<sub>50</sub> values. Moreover, it displayed good tumour selectivity property determined against non-cancerous mouse fibroblast cells.
DOI: 10.6084/m9.figshare.13213424
title: Identification of a dual TAOK1 and MAP4K5 inhibitor using a structure-based virtual screening approach

description: The STE20 kinase family is a complex signalling cascade that regulates cytoskeletal organisation and modulates the stress response. This signalling cascade includes various kinase mediators, such as TAOK1 and MAP4K5. The dysregulation of the STE20 kinase pathway is linked with cancer malignancy. A small-molecule inhibitor targeting the STE20 kinase pathway has therapeutic potential. In this study, a structure-based virtual screening (SBVS) approach was used to identify potential dual TAOK1 and MAP4K5 inhibitors. Enzymatic assays confirmed three potential dual inhibitors (&gt;50% inhibition) from our virtual screening, and analysis of the TAOK1 and MAP4K5 binding sites indicated common interactions for dual inhibition. Compound 1 revealed potent inhibition of colorectal and lung cancer cell lines. Furthermore, compound 1 arrested cancer cells in the G0/G1 phase, which suggests the induction of apoptosis. Altogether, we show that the STE20 signalling mediators TAOK1 and MAP4K5 are promising targets for drug research.
DOI: 10.6084/m9.figshare.16458535
title: Microwave-assisted Phospha-Michael addition reactions in the 13α-oestrone series and <i>in vitro</i> antiproliferative properties

description: Microwave-assisted phospha-Michael addition reactions were carried out in the 13α-oestrone series. The exocyclic 16-methylene-17-ketones as α,β-unsaturated ketones were reacted with secondary phosphine oxides as nucleophilic partners. The addition reactions furnished the two tertiary phosphine oxide diastereomers in high yields. The main product was the 16α-isomer. The antiproliferative activities of the newly synthesised organophosphorus compounds against a panel of nine human cancer cell lines were investigated by means of MTT assays. The most potent compound, the diphenylphosphine oxide derivative in the 3-<i>O</i>-methyl-13α-oestrone series (<b>9</b>), exerted selective cell growth-inhibitory activity against UPCI-SCC-131 and T47D cell lines with low micromolar IC<sub>50</sub> values. Moreover, it displayed good tumour selectivity property determined against non-cancerous mouse fibroblast cells.
DOI: 10.6084/m9.figshare.13213424.v1
title: Identification of a dual TAOK1 and MAP4K5 inhibitor using a structure-based virtual screening approach

description: The STE20 kinase family is a complex signalling cascade that regulates cytoskeletal organisation and modulates the stress response. This signalling cascade includes various kinase mediators, such as TAOK1 and MAP4K5. The dysregulation of the STE20 kinase pathway is linked with cancer malignancy. A small-molecule inhibitor targeting the STE20 kinase pathway has therapeutic potential. In this study, a structure-based virtual screening (SBVS) approach was used to identify potential dual TAOK1 and MAP4K5 inhibitors. Enzymatic assays confirmed three potential dual inhibitors (&gt;50% inhibition) from our virtual screening, and analysis of the TAOK1 and MAP4K5 binding sites indicated common interactions for dual inhibition. Compound 1 revealed potent inhibition of colorectal and lung cancer cell lines. Furthermore, compound 1 arrested cancer cells in the G0/G1 phase, which suggests the induction of apoptosis. Altogether, we show that the STE20 signalling mediators TAOK1 and MAP4K5 are promising targets for drug research.
DOI: 10.6084/m9.figshare.13168111
title: The SNAP-<i>tag</i> technology revised: an effective <i>chemo-enzymatic approach</i> by using a universal azide-based substrate

description: SNAP-<i>tag</i><sup>®</sup> is a powerful technology for the labelling of protein/enzymes by using benzyl-guanine (BG) derivatives as substrates. Although commercially available or ad hoc produced, their synthesis and purification are necessary, increasing time and costs. To address this limitation, here we suggest a revision of this methodology, by performing a <i>chemo-enzymatic approach</i>, by using a BG-substrate containing an azide group appropriately distanced by a spacer from the benzyl ring. The SNAP-<i>tag</i><sup>®</sup> and its relative thermostable version (<i>Ss</i>OGT-<i>H<sup>5</sup></i>) proved to be very active on this substrate. The stability of these <i>tags</i> upon enzymatic reaction makes possible the exposition to the solvent of the azide-moiety linked to the catalytic cysteine, compatible for the subsequent conjugation with DBCO-derivatives by azide-alkyne Huisgen cycloaddition. Our studies propose a strengthening and an improvement in terms of biotechnological applications for this self-labelling <i>protein-tag</i>.
DOI: 10.6084/m9.figshare.13168111.v1
title: The SNAP-<i>tag</i> technology revised: an effective <i>chemo-enzymatic approach</i> by using a universal azide-based substrate

description: SNAP-<i>tag</i><sup>®</sup> is a powerful technology for the labelling of protein/enzymes by using benzyl-guanine (BG) derivatives as substrates. Although commercially available or ad hoc produced, their synthesis and purification are necessary, increasing time and costs. To address this limitation, here we suggest a revision of this methodology, by performing a <i>chemo-enzymatic approach</i>, by using a BG-substrate containing an azide group appropriately distanced by a spacer from the benzyl ring. The SNAP-<i>tag</i><sup>®</sup> and its relative thermostable version (<i>Ss</i>OGT-<i>H<sup>5</sup></i>) proved to be very active on this substrate. The stability of these <i>tags</i> upon enzymatic reaction makes possible the exposition to the solvent of the azide-moiety linked to the catalytic cysteine, compatible for the subsequent conjugation with DBCO-derivatives by azide-alkyne Huisgen cycloaddition. Our studies propose a strengthening and an improvement in terms of biotechnological applications for this self-labelling <i>protein-tag</i>.
DOI: 10.5281/zenodo.6956953
title: Catalog of microseismicity related to the Alto-Tiberina Fault

description: This template matching catalog contains information about new detected seismicity as the origin time (ot), latitude (lat_temp), longitude (lon_temp), depth (depth_tep), magnitude (mag), origin time of the template that can be used as the event_id (ot_template), the ratio between the average correlation coefficient (CC) and the daily median absolute deviation of the averaged CCs, as an indication for the quality of a detection (cc_mad_ratio), and an indication about the origin as some of the detection's seem to be related to human induced activity (hum_ind). Detailed information about the template matching processing can be gained from <strong>Spatio-temporal evolution of the</strong><strong> Seismicity in the Alto Tiberina Fault System revealed by a High-Resolution Template Matching Catalog</strong> by Essing & Poli (2022)
DOI: 10.5281/zenodo.6956952
title: Catalog of microseismicity related to the Alto-Tiberina Fault

description: This template matching catalog contains information about new detected seismicity as the origin time (ot), latitude (lat_temp), longitude (lon_temp), depth (depth_tep), magnitude (mag), origin time of the template that can be used as the event_id (ot_template), the ratio between the average correlation coefficient (CC) and the daily median absolute deviation of the averaged CCs, as an indication for the quality of a detection (cc_mad_ratio), and an indication about the origin as some of the detection's seem to be related to human induced activity (hum_ind). Detailed information about the template matching processing can be gained from <strong>Spatio-temporal evolution of the</strong><strong> Seismicity in the Alto Tiberina Fault System revealed by a High-Resolution Template Matching Catalog</strong> by Essing & Poli (2022)
DOI: 10.6084/m9.figshare.16927827
title: Deep-tissue localization of magnetic field hyperthermia using pulse sequencing

description: Deep-tissue localization of thermal doses is a long-standing challenge in magnetic field hyperthermia (MFH), and remains a limitation of the clinical application of MFH to date. Here, we show that pulse sequencing of MFH leads to a more persistent inhibition of tumor growth and less systemic impact than continuous MFH, even when delivering the same thermal dose. We used an <i>in vivo</i> orthotopic murine model of pancreatic PANC-1 cancer, which was designed with a view to the forthcoming ‘NoCanTher’ clinical study, and featured MFH alongside systemic chemotherapy (SyC: gemcitabine and nab-paclitaxel). In parallel, <i>in silico</i> thermal modelling was implemented. Tumor volumes 27 days after the start of MFH/SyC treatment were 53% (of the initial volume) in the pulse MFH group, compared to 136% in the continuous MFH group, and 337% in the non-treated controls. Systemically, pulse MFH led to ca. 50% less core-temperature increase in the mice for a given injected dose of magnetic heating agent, and inflicted lower levels of the stress marker, as seen in the blood-borne neutrophil-to-lymphocyte ratio (1.7, compared to 3.2 for continuous MFH + SyC, and 1.2 for controls). Our data provided insights into the influence of pulse sequencing on the observed biological outcomes, and validated the nature of the improved thermal dose localization, alongside significant lowering of the overall energy expenditure entailed in the treatment.
DOI: 10.6084/m9.figshare.16927827.v1
title: Deep-tissue localization of magnetic field hyperthermia using pulse sequencing

description: Deep-tissue localization of thermal doses is a long-standing challenge in magnetic field hyperthermia (MFH), and remains a limitation of the clinical application of MFH to date. Here, we show that pulse sequencing of MFH leads to a more persistent inhibition of tumor growth and less systemic impact than continuous MFH, even when delivering the same thermal dose. We used an <i>in vivo</i> orthotopic murine model of pancreatic PANC-1 cancer, which was designed with a view to the forthcoming ‘NoCanTher’ clinical study, and featured MFH alongside systemic chemotherapy (SyC: gemcitabine and nab-paclitaxel). In parallel, <i>in silico</i> thermal modelling was implemented. Tumor volumes 27 days after the start of MFH/SyC treatment were 53% (of the initial volume) in the pulse MFH group, compared to 136% in the continuous MFH group, and 337% in the non-treated controls. Systemically, pulse MFH led to ca. 50% less core-temperature increase in the mice for a given injected dose of magnetic heating agent, and inflicted lower levels of the stress marker, as seen in the blood-borne neutrophil-to-lymphocyte ratio (1.7, compared to 3.2 for continuous MFH + SyC, and 1.2 for controls). Our data provided insights into the influence of pulse sequencing on the observed biological outcomes, and validated the nature of the improved thermal dose localization, alongside significant lowering of the overall energy expenditure entailed in the treatment.
DOI: 10.6084/m9.figshare.14709241
title: Collagen/kerateine multi-protein hydrogels as a thermally stable extracellular matrix for 3D <i>in vitro</i> models

description: To determine whether the addition of kerateine (reduced keratin) in rat tail collagen type I hydrogels increases thermal stability and changes material properties and supports cell growth for use in cellular hyperthermia studies for tumor treatment. Collagen type I extracted from rat tail tendon was combined with kerateine extracted from human hair fibers. Thermal, mechanical, and biocompatibility properties and cell behavior was assessed and compared to 100% collagen type I hydrogels to demonstrate their utility as a tissue model for 3D <i>in vitro</i> testing. A combination (i.e., containing both collagen ‘C/KNT’) hydrogel was more thermally stable than pure collagen hydrogels and resisted thermal degradation when incubated at a hyperthermic temperature of 47°C for heating durations up to 60 min with a higher melting temperature measured by DSC. An increase in the storage modulus was only observed with an increased collagen concentration rather than an increased KTN concentration; however, a change in ECM structure was observed with greater fiber alignment and width with an increase in KTN concentration. The C/KTN hydrogels, specifically 50/50 C/KTN hydrogels, also supported the growth and of fibroblasts and MDA-MB-231 breast cancer cells similar to those seeded in 100% collagen hydrogels. This multi-protein C/KTN hydrogel shows promise for future studies involving thermal stress studies without compromising the 3D ECM environment or cell growth.
DOI: 10.6084/m9.figshare.14709241.v1
title: Collagen/kerateine multi-protein hydrogels as a thermally stable extracellular matrix for 3D <i>in vitro</i> models

description: To determine whether the addition of kerateine (reduced keratin) in rat tail collagen type I hydrogels increases thermal stability and changes material properties and supports cell growth for use in cellular hyperthermia studies for tumor treatment. Collagen type I extracted from rat tail tendon was combined with kerateine extracted from human hair fibers. Thermal, mechanical, and biocompatibility properties and cell behavior was assessed and compared to 100% collagen type I hydrogels to demonstrate their utility as a tissue model for 3D <i>in vitro</i> testing. A combination (i.e., containing both collagen ‘C/KNT’) hydrogel was more thermally stable than pure collagen hydrogels and resisted thermal degradation when incubated at a hyperthermic temperature of 47°C for heating durations up to 60 min with a higher melting temperature measured by DSC. An increase in the storage modulus was only observed with an increased collagen concentration rather than an increased KTN concentration; however, a change in ECM structure was observed with greater fiber alignment and width with an increase in KTN concentration. The C/KTN hydrogels, specifically 50/50 C/KTN hydrogels, also supported the growth and of fibroblasts and MDA-MB-231 breast cancer cells similar to those seeded in 100% collagen hydrogels. This multi-protein C/KTN hydrogel shows promise for future studies involving thermal stress studies without compromising the 3D ECM environment or cell growth.