Journal: Regenerative Biomaterials

Article Title: Bone-targeting engineered milk-derived extracellular vesicles for MRI-assisted therapy of osteoporosis

doi: 10.1093/rb/rbae112

Figure Lengend Snippet: Preparation and characterization of (DSS) 6 -mEV-SRT2104/MnB. ( A ) Schematic illustration of the preparation procedure of (DSS) 6 -mEV-SRT2104/MnB. ( B ) TEM images of mEVs. Scale bar = 100 nm. ( C ) Protein marker characterization of mEVs via Western blot. ( D ) Schematic illustration of the preparation of (DSS) 6 -mEVs via click chemistry. ( E ) The characterization of (DSS) 6 -mEVs by flow cytometry. ( F ) Schematic illustration of the synthesis of MnB NPs. ( G ) Hydrodynamic size of MnB NPs via DLS. ( H ) T 1 -weighted MR images and 1/T 1 of MnB NPs via 3.0 T clinical MRI scanner. ( I ) T 1 -weighted MR images of different samples and the corresponding SNR. ( J ) TEM images of (DSS) 6 -mEV-SRT2104/MnB. Scale bar = 100 nm (ns, no significant; *** P < 0.001).

Article Snippet: (DSS) 6 (98% purity assayed by HPLC, with azide groups and FITC fluorescence, the sequence is FITC-Ahx-{Lys(N3)}DSSDSSDSSDSSDSSDSS) was purchased from IGE Biotechnology Ltd. SRT2104 (T6679, China) was purchased from TargetMol Chemicals Inc. Antibodies used in this study were rabbit polyclonal antibody against Alix (92800, Cell Signaling Technology), CD81 (27855, Proteintech), CD63 (25682, Proteintech), GAPDH (2118, Cell Signaling Technology), RUNX2 (20700, Proteintech), Calnexin (ab75801, Abcam), CTSK (ab187647, Abcam) and OPN (ab283656, Abcam).

Techniques: Marker, Western Blot, Flow Cytometry

Journal: Regenerative Biomaterials

Article Title: Bone-targeting engineered milk-derived extracellular vesicles for MRI-assisted therapy of osteoporosis

doi: 10.1093/rb/rbae112

Figure Lengend Snippet: The effects of mEV-SRT2104 on osteoblasts and osteoclasts in vitro . ( A ) Schematic illustration of the osteogenic differentiation of MC3T3-E1 cells. ( B ) ALP staining of MC3T3-E1 cells after treatment for 7 days and ( C ) the quantification analysis of staining integrated density according to ( B ). Scale bar = 200 μm. ( D ) Relative mRNA expression of RUNX2, ALP and OPN after treatment for 7 days. ( E ) Western blot assay of protein RUNX2 and OPN after treatment for 7 days. ( F ) Schematic illustration of the osteoclast differentiation of RAW264.7 cells. ( G ) TRAP staining of RAW264.7 cells after treatment for 5 days and ( H ) the quantification analysis of TRAP-positive cell area. Scale bar = 200 μm. ( I ) Relative mRNA expression of CTSK, RANK and NFATC1. ( J ) Western blot assay of CTSK protein (ns, no significance; * P < 0.05, ** P < 0.01, *** P < 0.001).

Article Snippet: (DSS) 6 (98% purity assayed by HPLC, with azide groups and FITC fluorescence, the sequence is FITC-Ahx-{Lys(N3)}DSSDSSDSSDSSDSSDSS) was purchased from IGE Biotechnology Ltd. SRT2104 (T6679, China) was purchased from TargetMol Chemicals Inc. Antibodies used in this study were rabbit polyclonal antibody against Alix (92800, Cell Signaling Technology), CD81 (27855, Proteintech), CD63 (25682, Proteintech), GAPDH (2118, Cell Signaling Technology), RUNX2 (20700, Proteintech), Calnexin (ab75801, Abcam), CTSK (ab187647, Abcam) and OPN (ab283656, Abcam).

Techniques: In Vitro, Staining, Expressing, Western Blot

Journal: Regenerative Biomaterials

Article Title: Bone-targeting engineered milk-derived extracellular vesicles for MRI-assisted therapy of osteoporosis

doi: 10.1093/rb/rbae112

Figure Lengend Snippet: Bone-targeting capability of engineered mEVs in vitro and in vivo . ( A ) Schematic illustration of the culture of MC3T3-E1 cells. ( B ) Uptake of Dil-labelled (DSS) 6 -mEVs with MCST3-E1 cells by flow cytometry. ( C ) Schematic illustration of the binding of (DSS) 6 -mEV-SRT2104/MnB and mEV-SRT2104/MnB with hydroxyapatite. ( D ) T 1 -weighted MR images of the supernatant after the binding of mEVs or (DSS) 6 -mEVs with hydroxyapatite. ( E ) In vivo biodistribution of DiR-labelled (DSS) 6 -mEVs or mEVs by IVIS. ( F ) In vivo biodistribution of mEV-SRT2104/MnB or (DSS) 6 -mEV-SRT2104/MnB by MRI (ns, no significant; * P < 0.05, ** P < 0.01, *** P < 0.001).

Article Snippet: (DSS) 6 (98% purity assayed by HPLC, with azide groups and FITC fluorescence, the sequence is FITC-Ahx-{Lys(N3)}DSSDSSDSSDSSDSSDSS) was purchased from IGE Biotechnology Ltd. SRT2104 (T6679, China) was purchased from TargetMol Chemicals Inc. Antibodies used in this study were rabbit polyclonal antibody against Alix (92800, Cell Signaling Technology), CD81 (27855, Proteintech), CD63 (25682, Proteintech), GAPDH (2118, Cell Signaling Technology), RUNX2 (20700, Proteintech), Calnexin (ab75801, Abcam), CTSK (ab187647, Abcam) and OPN (ab283656, Abcam).

Techniques: In Vitro, In Vivo, Flow Cytometry, Binding Assay

Journal: Regenerative Biomaterials

Article Title: Bone-targeting engineered milk-derived extracellular vesicles for MRI-assisted therapy of osteoporosis

doi: 10.1093/rb/rbae112

Figure Lengend Snippet: (DSS) 6 -mEV-SRT2104 reduces bone loss in OVX mice by dual regulation of bone remodeling. ( A ) Representative micro-CT images showing 3D microarchitectures of trabeculae in the distal femurs. ( B ) Micro-CT quantitative analysis of BMD, BV/TV, Tb.N and Tb.Sp of distal femurs. ( C ) TRAP staining of bone sections. Scale bar = 250 μm. ( D ) H&E staining of bone sections of experimental mice. Scale bar = 250 μm. ( E ) Histomorphometric analysis of osteoclast surface per bone surface (Oc.S/BS). ( F ) Histomorphometric analysis of the trabecular bone area. ( G–K ) The relative serum protein expression evaluated by the Elisa test, including β-CTX ( G ), TRACP-5b ( H ), BALP ( I ), OCN ( J ) and P1NP ( K ) (ns, no significance; * P < 0.05, ** P < 0.01, *** P < 0.001).

Article Snippet: (DSS) 6 (98% purity assayed by HPLC, with azide groups and FITC fluorescence, the sequence is FITC-Ahx-{Lys(N3)}DSSDSSDSSDSSDSSDSS) was purchased from IGE Biotechnology Ltd. SRT2104 (T6679, China) was purchased from TargetMol Chemicals Inc. Antibodies used in this study were rabbit polyclonal antibody against Alix (92800, Cell Signaling Technology), CD81 (27855, Proteintech), CD63 (25682, Proteintech), GAPDH (2118, Cell Signaling Technology), RUNX2 (20700, Proteintech), Calnexin (ab75801, Abcam), CTSK (ab187647, Abcam) and OPN (ab283656, Abcam).

Techniques: Micro-CT, Staining, Expressing, Enzyme-linked Immunosorbent Assay

Journal: Regenerative Biomaterials

Article Title: Bone-targeting engineered milk-derived extracellular vesicles for MRI-assisted therapy of osteoporosis

doi: 10.1093/rb/rbae112

Figure Lengend Snippet: T 1 -weighted MRI of OVX mice. ( A ) The femur T 1 -weighted MR images were acquired from OVX mice administered with mEV-MnB, mEV-SRT2104/MnB or (DSS) 6 -mEV-SRT2104/MnB at various time points during week 4 and 10. ( B ) SNR analysis of (a). ( C ) The ΔSNR from 4 to 24 h in the distal femur of OVX mice administered with (DSS) 6 -mEV-SRT2104/MnB was assessed based on T 1 -weighted MRI images (ns, no significance; * P ＜ 0.05).

Article Snippet: (DSS) 6 (98% purity assayed by HPLC, with azide groups and FITC fluorescence, the sequence is FITC-Ahx-{Lys(N3)}DSSDSSDSSDSSDSSDSS) was purchased from IGE Biotechnology Ltd. SRT2104 (T6679, China) was purchased from TargetMol Chemicals Inc. Antibodies used in this study were rabbit polyclonal antibody against Alix (92800, Cell Signaling Technology), CD81 (27855, Proteintech), CD63 (25682, Proteintech), GAPDH (2118, Cell Signaling Technology), RUNX2 (20700, Proteintech), Calnexin (ab75801, Abcam), CTSK (ab187647, Abcam) and OPN (ab283656, Abcam).

Techniques:

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Interaction of SRT2104 with SIRT1. ( A ) Detailed binding profile of SRT2104 to SIRT1. ( B ) Illustrative representation of the molecular interaction between SRT2104 and SIRT1. Molecular docking simulations were conducted utilizing AutoDock software to model the interaction. A grid box measuring 126 Å in each dimension was established, with a grid point spacing of 0.375 Å. During the simulations, the ligands were allowed to flex, whereas the protein's amino acid residues were held fixed. The calculated binding energy served as a measure of affinity. Visualization of the interaction was enhanced using PyMol and Discover Studio, revealing that SRT2104 occupies the hydrophobic pocket of SIRT1. The amine group of SRT2104 forms hydrogen bonds with Gly269, Gln320, and Glu512 in the SIRT1 structure. Additionally, an oxygen atom of SRT2104 engages in a hydrogen bond with ARG282, contributing to the stability of the interaction. Hydrophobic contacts are further augmented by interactions between SRT2104 and SIRT1's Pro271, Arg282, Phe312, Lys314, and Phe321, including Pi-Pi stacking and alkyl interactions. Van der Waals forces involving Ile270, Ile279, Leu283, Ile316, Phe388, Ile510, and Thr511 also play a vital role in sustaining the interaction's stability.

Article Snippet: NCT00920660 , I , 20 , Healthy Volunteers between 18 and 60 years of age , Clinical Study to Assess the Effects of SRT2104 and Prednisolone on Biomarkers in Blood in Healthy Volunteers , 2009-04-06 to 2009-06-12 , GlaxoSmithKline , United Kingdom.

Techniques: Binding Assay, Software

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Clinical trials involving SRT2104.

Article Snippet: NCT00920660 , I , 20 , Healthy Volunteers between 18 and 60 years of age , Clinical Study to Assess the Effects of SRT2104 and Prednisolone on Biomarkers in Blood in Healthy Volunteers , 2009-04-06 to 2009-06-12 , GlaxoSmithKline , United Kingdom.

Techniques: Clinical Proteomics, Activity Assay, Capsules, Drug discovery, Suspension, Formulation

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Schematic representation of the molecular mechanisms mediated by SRT2104. SRT2104, through the activation of SIRT1, orchestrates a network of molecular pathways, including P53, STAT3, ZKSCANS, AMPK, GR, GSK3β/PTEN, NF-κB, β-catenin/Runx2, MAPK, Smad7, FOXO, and TORC1. These interactions collectively contribute to the amelioration of conditions such as lung injury, diabetic vascular complications, diabetic nephropathy, cognitive impairments associated with diabetes, musculoskeletal disorders, brain ischemia–reperfusion injury, Parkinson's disease (PD) neurodegeneration, and optic nerve damage. Key: "→" denotes activation or promotion, "⊥" indicates inhibition, "red arrow up" signifies upregulation, "green arrow down" signifies downregulation, and "Ac" refers to deacetylation.

Article Snippet: NCT00920660 , I , 20 , Healthy Volunteers between 18 and 60 years of age , Clinical Study to Assess the Effects of SRT2104 and Prednisolone on Biomarkers in Blood in Healthy Volunteers , 2009-04-06 to 2009-06-12 , GlaxoSmithKline , United Kingdom.

Techniques: Activation Assay, Inhibition

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Overview of the potential effects of SRT2104 on various organ systems. The diagram illustrates the compound's impact on key physiological processes across different tissues. “↓”denotes a decrease or impairment, while “↑” signifies an increase or enhancement. This figure summarizes the multifaceted pharmacological actions of SRT2104, suggesting its potential therapeutic applications.

Article Snippet: NCT00920660 , I , 20 , Healthy Volunteers between 18 and 60 years of age , Clinical Study to Assess the Effects of SRT2104 and Prednisolone on Biomarkers in Blood in Healthy Volunteers , 2009-04-06 to 2009-06-12 , GlaxoSmithKline , United Kingdom.

Techniques:

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Interaction of SRT2104 with SIRT1. ( A ) Detailed binding profile of SRT2104 to SIRT1. ( B ) Illustrative representation of the molecular interaction between SRT2104 and SIRT1. Molecular docking simulations were conducted utilizing AutoDock software to model the interaction. A grid box measuring 126 Å in each dimension was established, with a grid point spacing of 0.375 Å. During the simulations, the ligands were allowed to flex, whereas the protein's amino acid residues were held fixed. The calculated binding energy served as a measure of affinity. Visualization of the interaction was enhanced using PyMol and Discover Studio, revealing that SRT2104 occupies the hydrophobic pocket of SIRT1. The amine group of SRT2104 forms hydrogen bonds with Gly269, Gln320, and Glu512 in the SIRT1 structure. Additionally, an oxygen atom of SRT2104 engages in a hydrogen bond with ARG282, contributing to the stability of the interaction. Hydrophobic contacts are further augmented by interactions between SRT2104 and SIRT1's Pro271, Arg282, Phe312, Lys314, and Phe321, including Pi-Pi stacking and alkyl interactions. Van der Waals forces involving Ile270, Ile279, Leu283, Ile316, Phe388, Ile510, and Thr511 also play a vital role in sustaining the interaction's stability.

Article Snippet: NCT00937872 , I , 9 , Healthy Male Subjects between 18 and 65 years of age , A Clinical Study to Evaluate the Pharmacokinetics and the Absolute Bioavailability of SRT2104 Given as a 250 mg Oral Suspension and Intravenous Microdose of 100 μg Carbon-14 Radio-labeled SRT2104 in Healthy Male Subjects , 2008-11-22 to 2008-12-22 , Sirtris, a GSK Company , United Kingdom.

Techniques: Binding Assay, Software

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Clinical trials involving SRT2104.

Article Snippet: NCT00937872 , I , 9 , Healthy Male Subjects between 18 and 65 years of age , A Clinical Study to Evaluate the Pharmacokinetics and the Absolute Bioavailability of SRT2104 Given as a 250 mg Oral Suspension and Intravenous Microdose of 100 μg Carbon-14 Radio-labeled SRT2104 in Healthy Male Subjects , 2008-11-22 to 2008-12-22 , Sirtris, a GSK Company , United Kingdom.

Techniques: Clinical Proteomics, Activity Assay, Capsules, Drug discovery, Suspension, Formulation

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Schematic representation of the molecular mechanisms mediated by SRT2104. SRT2104, through the activation of SIRT1, orchestrates a network of molecular pathways, including P53, STAT3, ZKSCANS, AMPK, GR, GSK3β/PTEN, NF-κB, β-catenin/Runx2, MAPK, Smad7, FOXO, and TORC1. These interactions collectively contribute to the amelioration of conditions such as lung injury, diabetic vascular complications, diabetic nephropathy, cognitive impairments associated with diabetes, musculoskeletal disorders, brain ischemia–reperfusion injury, Parkinson's disease (PD) neurodegeneration, and optic nerve damage. Key: "→" denotes activation or promotion, "⊥" indicates inhibition, "red arrow up" signifies upregulation, "green arrow down" signifies downregulation, and "Ac" refers to deacetylation.

Article Snippet: NCT00937872 , I , 9 , Healthy Male Subjects between 18 and 65 years of age , A Clinical Study to Evaluate the Pharmacokinetics and the Absolute Bioavailability of SRT2104 Given as a 250 mg Oral Suspension and Intravenous Microdose of 100 μg Carbon-14 Radio-labeled SRT2104 in Healthy Male Subjects , 2008-11-22 to 2008-12-22 , Sirtris, a GSK Company , United Kingdom.

Techniques: Activation Assay, Inhibition

Journal: Scientific Reports

Article Title: Emerging roles of SIRT1 activator, SRT2104, in disease treatment

doi: 10.1038/s41598-024-55923-8

Figure Lengend Snippet: Overview of the potential effects of SRT2104 on various organ systems. The diagram illustrates the compound's impact on key physiological processes across different tissues. “↓”denotes a decrease or impairment, while “↑” signifies an increase or enhancement. This figure summarizes the multifaceted pharmacological actions of SRT2104, suggesting its potential therapeutic applications.

Article Snippet: NCT00937872 , I , 9 , Healthy Male Subjects between 18 and 65 years of age , A Clinical Study to Evaluate the Pharmacokinetics and the Absolute Bioavailability of SRT2104 Given as a 250 mg Oral Suspension and Intravenous Microdose of 100 μg Carbon-14 Radio-labeled SRT2104 in Healthy Male Subjects , 2008-11-22 to 2008-12-22 , Sirtris, a GSK Company , United Kingdom.

Techniques:

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Binding affinities (kcal/mol) of the compounds that were selected for further investigation.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques: Binding Assay, Protease Inhibitor

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Blind docking and docking of hypericin, SRT2104, and cyanidin-3-O-glucoside to the active site of the SARS-CoV-2 M pro dimer. Blind docking was performed using AutoDock Vina to produce 20 poses. Catalytic dyad residues His41 and Cys145 are highlighted in orange. Docking to the active site was performed using the QPLD protocol of Glide to each protomer of the M pro dimer.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques:

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Residue interactions between the M pro monomer and hypericin, SRT2104, and cyanidin-3-O-glucoside at 4.0 Å. Hydrogen bonds and π−π interactions are depicted by the yellow and cyan lines, respectively. The green residues are hydrophobic, the cyan residues are polar, and the red residues are negatively charged.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques: Residue

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Stability of SARS-CoV-2 M pro complex in the presence of hypericin, SRT2104, and cyanidin-3-O-glucoside. The protein-ligand complexes comprised of a single compound bound to the active site of each protomer of M pro , with cyanidin-3-O-glucoside depicted in purple (A) as an example. Average root mean square deviation (RMSD) for protein fit to backbone (B) for 100 ns, and average root mean square fluctuation of whole protein (C) following stabilisation. (D) shows the RMSF values the apo form subtracted from ligand bound forms of the protein. For the graphs (B – D), M pro in its apo form is shown in blue. M pro bound to hypericin, SRT2104, and cyanidin-3-O-glucoside is shown in red, green, and purple respectively.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques:

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Average energy contributions from MM-PBSA analysis were decomposed into a per-residue basis for binding of SARS-CoV-2 M pro with A) hypericin, B) SRT2104, and C) cyanidin-3-O-glucoside to the active site in protomer A (blue), and active site of protomer B (purple). Energy contributions were calculated in triplicate on 1000 ps segments of stabilised trajectories.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques: Residue, Binding Assay

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Inhibition of M pro activity by small molecules. Percentage inhibition at a ligand concentration of 50 μM and IC 50 values calculated using an ELISA.

Article Snippet: The small molecule test inhibitors that we tested were hypericin (89 %, HWI pharma services GmbH, Germany), cyanidin-3-O-glucoside (reference standard, PhytoLab, Germany), SRT2104 and SRT1720 (>99 %, AdooQ® Bioscience, Irvine, CA, USA), resveratrol (>99 %), and l -sulforaphane (>95 %, Sigma-Aldrich, St Luis, MO, USA).

Techniques: Inhibition, Activity Assay, Concentration Assay, Enzyme-linked Immunosorbent Assay

Journal: Annals of Clinical and Translational Neurology

Article Title: Sirtuin 1 activator SRT2104 protects Huntington's disease mice

doi: 10.1002/acn3.135

Figure Lengend Snippet: SRT2104 ameliorated motor deficits and increased survival in N171-82Q HD mice. Mice were fed 0.5% SRT2104 containing diet from 6 weeks of age until the end of life. (A) Mice were trained on 11-mm cylindrical beam and then tested at 12, 18, and 24 weeks of age. The traverse time on the beam was recorded. The longer traverse time indicates impaired motor function. The values are the mean ± SE, two-way (group and age) repeated ANOVA tests were used. * P < 0.01 compared with the values of wild-type (WT) diet group; ** P < 0.05 compared with the values of HD diet group. n = 10–12 mice. (B) Body weight was recorded weekly. The values are the mean ± SE, n = 10–12 mice. (C) Survival was monitored daily by experienced operators. The mice were considered to be at the end of life when they were unable to right themselves after being placed on their backs and initiate movement after being gently prodded for 30 sec. n = 10–12 mice. Log rank analysis was used to compare survival data between two groups.

Article Snippet: SRT2104 was quantified in brain homogenate via LC/MS/MS at Alliance Pharma (Malvern, PA).

Techniques:

Journal: Annals of Clinical and Translational Neurology

Article Title: Sirtuin 1 activator SRT2104 protects Huntington's disease mice

doi: 10.1002/acn3.135

Figure Lengend Snippet: SRT2104 attenuated brain atrophy in N171-82Q mice. Mice were fed 0.5% SRT2104 containing diet from 6 weeks of age. Then, mice were anesthetized with isoflurane (1%), respiration was monitored and the temperature was maintained during the entire scan. Images were acquired by a three-dimensional T2-weighted fast spin echo sequence with the following parameters: echo time (TE)/repetition time (TR) = 40/700 msec, resolution = 0.1 × 0.1 × 0.1 mm, echo train length = 4, number of average = 2 and flip angle = 40°. The imaging resolution and contrast were sufficient for automatic volumetric characterization of the mouse brains and substructures. The intensity-normalized images were submitted by the Diffeomap software to a linux cluster, which runs Large Deformation Diffeomorphic Metric Mapping (LDDMM). The transformations encode morphological differences between subject and template images and can be analyzed with deformation-based morphometry (DBM) to detect regional changes in brain volume. Twenty-nine different brain regions were automatically segmented and the volume of each brain region was calculated. (A) Representative MRI images in mice from indicated groups. (B) The volumes of neocortex and striatum were measured by structural MRI at 22 weeks of age. Values are mean ± SE from four to six mice. * P < 0.05 compared with the WT control group; ** P < 0.05 compared with the HD control group (ANOVA with Holm–Sidak Post-hoc test).

Article Snippet: SRT2104 was quantified in brain homogenate via LC/MS/MS at Alliance Pharma (Malvern, PA).

Techniques: Sequencing, Imaging, Software, Control

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Binding affinities (kcal/mol) of the compounds that were selected for further investigation.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques: Binding Assay, Protease Inhibitor

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Blind docking and docking of hypericin, SRT2104, and cyanidin-3-O-glucoside to the active site of the SARS-CoV-2 M pro dimer. Blind docking was performed using AutoDock Vina to produce 20 poses. Catalytic dyad residues His41 and Cys145 are highlighted in orange. Docking to the active site was performed using the QPLD protocol of Glide to each protomer of the M pro dimer.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques:

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Residue interactions between the M pro monomer and hypericin, SRT2104, and cyanidin-3-O-glucoside at 4.0 Å. Hydrogen bonds and π−π interactions are depicted by the yellow and cyan lines, respectively. The green residues are hydrophobic, the cyan residues are polar, and the red residues are negatively charged.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques: Residue

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Stability of SARS-CoV-2 M pro complex in the presence of hypericin, SRT2104, and cyanidin-3-O-glucoside. The protein-ligand complexes comprised of a single compound bound to the active site of each protomer of M pro , with cyanidin-3-O-glucoside depicted in purple (A) as an example. Average root mean square deviation (RMSD) for protein fit to backbone (B) for 100 ns, and average root mean square fluctuation of whole protein (C) following stabilisation. (D) shows the RMSF values the apo form subtracted from ligand bound forms of the protein. For the graphs (B – D), M pro in its apo form is shown in blue. M pro bound to hypericin, SRT2104, and cyanidin-3-O-glucoside is shown in red, green, and purple respectively.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques:

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Average energy contributions from MM-PBSA analysis were decomposed into a per-residue basis for binding of SARS-CoV-2 M pro with A) hypericin, B) SRT2104, and C) cyanidin-3-O-glucoside to the active site in protomer A (blue), and active site of protomer B (purple). Energy contributions were calculated in triplicate on 1000 ps segments of stabilised trajectories.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques: Residue, Binding Assay

Journal: Computational Biology and Chemistry

Article Title: Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

doi: 10.1016/j.compbiolchem.2020.107408

Figure Lengend Snippet: Inhibition of M pro activity by small molecules. Percentage inhibition at a ligand concentration of 50 μM and IC 50 values calculated using an ELISA.

Article Snippet: Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M pro active site.

Techniques: Inhibition, Activity Assay, Concentration Assay, Enzyme-linked Immunosorbent Assay