Journal: iScience

Article Title: Loratadine inhibits Staphylococcus aureus virulence and biofilm formation

doi: 10.1016/j.isci.2022.103731

Figure Lengend Snippet:

Article Snippet: Clindamycin , MedChemExpress , HY-B0408; CAS: 21462-39-5.

Techniques: Recombinant, Analogues, Enzyme-linked Immunosorbent Assay, Sample Prep, Sequencing, Amplification, Over Expression, Plasmid Preparation, Clone Assay, Software

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Article Title: Quantification of vancomycin and clindamycin in human plasma and synovial fluid applying ultra-performance liquid chromatography tandem mass spectrometry.

doi: 10.1016/j.jchromb.2022.123493

Figure Lengend Snippet: Fig. 1. Representative MRM chromatograms of a blank plasma sample: vancomycin (A1), vancomycin-d10 (A2) and clindamycin (A3). Representative MRM chromatograms of a plasma sample at the LLOQ level: vancomycin (B1), vancomycin-d10 (B2) and clindamycin (B3). Representative MRM chromatograms of a patient’s plasma sample: vancomycin (C1), vancomycin-d10 (C2) and clindamycin (C3).

Article Snippet: Vancomycin hydrochloride (purity: 96.1 %) was purchased from Cayman Chemical (Uden, the Netherlands) and clindamycin hydrochloride (purity: 98.8 %) was purchased from Santa Cruz Biotechnology (Huissen, the Netherlands).

Techniques: Clinical Proteomics

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Article Title: Quantification of vancomycin and clindamycin in human plasma and synovial fluid applying ultra-performance liquid chromatography tandem mass spectrometry.

doi: 10.1016/j.jchromb.2022.123493

Figure Lengend Snippet: Fig. 2. Representative MRM chromatograms of a blank synovial fluid sample: vancomycin (A1), vancomycin-d10 (A2) and clindamycin (A3). Representative MRM chromatograms of a synovial fluid sample at the LLOQ level: vancomycin (B1), vancomycin-d10 (B2) and clindamycin (B3). Representative MRM chromatograms of a patient’s synovial fluid sample: vancomycin (C1), vancomycin-d10 (C2) and clindamycin (C3).

Article Snippet: Vancomycin hydrochloride (purity: 96.1 %) was purchased from Cayman Chemical (Uden, the Netherlands) and clindamycin hydrochloride (purity: 98.8 %) was purchased from Santa Cruz Biotechnology (Huissen, the Netherlands).

Techniques:

Journal: Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Article Title: Quantification of vancomycin and clindamycin in human plasma and synovial fluid applying ultra-performance liquid chromatography tandem mass spectrometry.

doi: 10.1016/j.jchromb.2022.123493

Figure Lengend Snippet: Fig. 3. The measured clindamycin concentration in plasma and synovial fluid in three patients presented in a graph.

Article Snippet: Vancomycin hydrochloride (purity: 96.1 %) was purchased from Cayman Chemical (Uden, the Netherlands) and clindamycin hydrochloride (purity: 98.8 %) was purchased from Santa Cruz Biotechnology (Huissen, the Netherlands).

Techniques: Concentration Assay, Clinical Proteomics

Journal: Communications Biology

Article Title: 3D collagen high-throughput screen identifies drugs that induce epithelial polarity and enhance chemotherapy response in colorectal cancer

doi: 10.1038/s42003-025-08699-0

Figure Lengend Snippet: A - B Plots of median colony area ( A ) and percent colonies with lumens ( B ) for hit identification. Fold change plotted on the Y -axis and corresponding B-score on the X -axis. Dotted lines indicate the top 5% of values along its axis. C Venn diagram depicting selection of hits wells based on plots in ( A , B ). D , E Comparison of ( D ) median colony area and ( E ) percent colonies with lumens for top three hits to the plate they were located on during the screen. Well number was assigned based on order of the wells. Solid line indicates the median for all wells of the plate and the dotted lines denote the interquartile range. F Insets of brightfield and fluorescent (Calcein AM) confocal images of wells treated with top three hits at three concentrations from the screen. (Scale bars: 250 µm). Images taken with ImageXpress confocal HT.ai automated high-content imaging system at 4x magnification. Full well images shown in Fig. . G − I Quantification of CRC (SC cells) colony circularity when treated with ( G ) azithromycin, ( H ) clindamycin, or ( I ) linezolid. SC cells were seeded in type I collagen and incubated with either 10 µM, 1 µM, or 0.1 µM of the indicated antibiotic for 14 days. Results are quantified as circularity index. Higher circularity indicates rounder colonies and lower circularity index indicates spiky colonies. Left panel depicts density plot of the circularity for all colonies from each treatment for all three biological replicates. Vertical line indicates the median circularity for each treatment condition. Right panel depicts median circularity for each biological replicate. n > 150 for each biological replicate from 3 technical replicates (wells). Plotted as mean ± SEM. One-way ANOVA with Tukey’s post hoc test, p -values indicated. J Brightfield and fluorescent confocal images of SC cell colonies treated with indicated antibiotics. SC cells were seeded in type I collagen and incubated with 10 µM of the indicated antibiotic for 14 days. Collagen layer containing colonies was isolated, fixed, and stained for DAPI (blue), Phalloidin (red), and E-cadherin (green). Colonies were imaged through the equatorial plane using a 10x objective. (Scale bars: 100 µm).

Article Snippet: Azithromycin, clindamycin, and linezolid were purchased from Selleck Chemicals LLC (Houston, TX, USA, #S1835, #S2830, #S1408).

Techniques: Selection, Comparison, Imaging, Incubation, Isolation, Staining

Journal: Communications Biology

Article Title: 3D collagen high-throughput screen identifies drugs that induce epithelial polarity and enhance chemotherapy response in colorectal cancer

doi: 10.1038/s42003-025-08699-0

Figure Lengend Snippet: A Principal component analysis (PCA) plot of RNA-seq data from SC cell 3D cultures treated with azithromycin, clindamycin, and linezolid for 12 days. Each dot represents a biological replicate. B Volcano plot for all comparisons all correlation PCA for control and azithromycin treated 3D cultures. Differential expression analysis criteria: absolute fold change ≥ 2 and FDR adjusted p- value ≤ 0.05. C Heatmap of top 50 differentially expressed transcripts in control vs azithromycin-treated 3D cultures in triplicate; purple = up, blue = down (expression scale in inset). D WebGestalt-based control vs azithromycin-treated pathway over-representation analysis. Top 10 biological processes significantly overrepresented (FDR ≤ 0.5) are depicted with their respective enrichment ratios. E Hallmark gene set enrichment analysis comparison of RNA-seq data from control and azithromycin-treated 3D cultures. Hallmark pathways are indicated on the left and are represented as bubbles on the Normalized enrichment score on x -axis. Bubble size indicates core enrichment or number of leading-edge genes and bubble color represents FDR (false discovery rate); scales of both are indicated on the right. F Gene set enrichment analysis (GSEA) of RNA-seq data from control and azithromycin-treated cultures. Three select categories of interest are shown. Abbreviations: NES Normalized enrichment score, FDR False discovery rate q -values.

Article Snippet: Azithromycin, clindamycin, and linezolid were purchased from Selleck Chemicals LLC (Houston, TX, USA, #S1835, #S2830, #S1408).

Techniques: RNA Sequencing, Control, Quantitative Proteomics, Expressing, Comparison

Journal: Materials

Article Title: Clindamycin-Based 3D-Printed and Electrospun Coatings for Treatment of Implant-Related Infections

doi: 10.3390/ma14061464

Figure Lengend Snippet: Attenuated total reflectance–Fourier transform infrared spectroscopy (ATR-FTIR) spectra of clindamycin (CLIN), the electrospun (ES), the ES-loaded with CLIN (ES–CLIN), the 3D-printed coating (3D), and the 3D-printed coating loaded with CLIN (3D–CLIN). CLIN-related peaks (S–C–H) in ES and 3D-printed polymer coatings are designated in ellipses.

Article Snippet: Clindamycin hydrochloride monohydrate (C 18 H 33 ClN 2 O 5 ∙HCl∙H 2 O) was purchased from Alfa Aesar, Haverhill, MA, USA.

Techniques: Fourier Transform Infrared Spectroscopy, Spectroscopy, Polymer

Journal: iScience

Article Title: Loratadine inhibits Staphylococcus aureus virulence and biofilm formation

doi: 10.1016/j.isci.2022.103731

Figure Lengend Snippet:

Article Snippet: Clindamycin , MedChemExpress , HY-B0408; CAS: 21462-39-5.

Techniques: Recombinant, Analogues, Enzyme-linked Immunosorbent Assay, Sample Prep, Sequencing, Amplification, Over Expression, Plasmid Preparation, Clone Assay, Software

Journal: Medical Principles and Practice

Article Title: Multilocus Sequence Types of Invasive and Colonizing Neonatal Group B Streptococci in Poland

doi: 10.1159/000362368

Figure Lengend Snippet: Distribution of MIC in invasive and colonizing GBS strains from neonates

Article Snippet: The macrolide resistance phenotypes cMLS B (constitutive), iMLS B (inducible) and M were determined using a double-disc test with erythromycin (15 μg) and clindamycin (2 μg) (Oxoid).

Techniques:

Journal: Nature Structural & Molecular Biology

Article Title: Structural conservation of antibiotic interaction with ribosomes

doi: 10.1038/s41594-023-01047-y

Figure Lengend Snippet: a-k , Superimposition of previous structures of diverse antibiotic-ribosome complexes, including ( a ) gentamicin (yellow) on the E. coli 70S ribosome at 3.5 Å (PDB ID 4V53) with gentamicin (green) on the T. thermophilus 30S at 3.3 Å (PDB ID 4LF9), ( b ) kasugamycin (yellow) on the E. coli 70S ribosome at 3.5 Å (PDB ID 4V4H) with kasugamycin (red) on the T. thermophilus 30S at 3.4 Å (PDB ID 2HHH) , ( c ) streptomycin on the T. thermophilus 30S at 3.0 Å (yellow; PDB ID 1FJG) at 3.3 Å (green, PDB ID 4DR6) at 3.35 Å (blue, PDB ID 4JI1) with streptomycin (red) on the human mitochondrial small subunit at 2.4 Å (PDB ID 7P2E) , ( d ) apramycin (yellow) on the T. thermophilus 30S at 3.5 Å (PDB ID 4AQY) with apramycin on the E. coli 70S ribosome at 2.4 Å (red, PDB ID 7PJS) and 3.1 Å (green, PDB ID 7PJV) , ( e ) hygromycin B on the T. thermophilus 30S at 3.3 Å (yellow, PDB ID 1HNZ) and 3.7 Å (blue, PDB ID 4LFA) with hygromycin B on the E. coli 70S ribosome at 3.5 Å (red, PDB ID 4V64) , ( f ) spectinomycin (red) on the T. thermophilus 30S at 3.0 Å (PDB ID 1FJG) with spectinomycin on E. coli 70S ribosome at 3.5 Å (green, PDB ID 4V57) , E. faecalis 70S ribosome at 2.4 Å (yellow, PDB ID 7P7Q) and within an E. coli 70S translocation intermediate at 2.5 Å (blue, PDB ID 7N2V) , ( g ) tetracycline on the T. thermophilus 30S at 3.4 Å (red, PDB ID 1HNW) and 4.5 Å (yellow, PDB ID 1I97) with tetracycline (blue) on the T. thermophilus 70S at 3.3 Å (PDB ID 4V9A) and tetracycline (green) on the E. coli 70S at 2.8 Å (PDB ID 5J5B) , ( h ) the pleuromutilins tiamulin (yellow) on the D. radiodurans 50S at 3.5 Å (PDB ID 1XBP) , retapamulin (blue) on the D. radiodurans 50S at 3.7 Å (PDB ID 2OGO) , tiamulin (red) on the archaeal H. marismortui 50S at 3.2 Å (PDB ID 3G4S) and lefamulin (green) on the S. aureus 50S at 3.6 Å (PDB ID 5HL7) , ( i ) capreomycin (yellow) on the T. thermophilus 70S at 3.5 Å (PDB ID 4V7M) with capreomycin (red) on the M. tuberculosis 70S at 4.0 Å (PDB ID 5V93) , ( j ) the orthosomycins avilamycin (blue, PDB ID 5KCR) and evernimicin (red, PDB ID 5KCS) on the E. coli 70S at 3.9 Å with avilamycin (green, PDB ID 5JVG) and evernimicin (yellow, PDB ID 5JVH) on the D. radiodurans 50S at at 3.6 Å and 3.4 Å, respectively , ( k ) the lincosamide clindamycin on the D. radiodurans 50S at 3.1 Å (yellow, PDB ID 1JZY) , on the H. marismortui 50S at 3.0 Å (red, PDB ID 1YJN) and on the E. coli 70S at 3.3 Å (green, PDB ID 4V7V) with lincomycin on the S. aureus 50S at 3.7 Å (blue, PDB ID 5HKV) . Alignments were made using the rRNA within 10 Å of the antibiotic. rRNA and r-proteins comprising the binding site are colored grey, whereas antibiotics (including waters and ions if present) are color-coded as indicated.

Article Snippet: Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).

Techniques: Translocation Assay, Binding Assay

Journal: Nature Structural & Molecular Biology

Article Title: Structural conservation of antibiotic interaction with ribosomes

doi: 10.1038/s41594-023-01047-y

Figure Lengend Snippet: Segmented cryo-EM map densities (transparent gray) and molecule models (colored by atom) are shown for tetracyclines (tetracycline, omadacycline, eravacycline and pentacycline), aminoglycosides (hygromycin B, gentamicin, spectinomycin, streptomycin, apramycin and kasugamycin), tuberactinomycin (capreomycin), orthosomycin (avilamycin and evernimicin), pleuromutilin (tiamulin and retapamulin) and lincosamide (lincomycin and clindamycin) antibiotics.

Article Snippet: Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).

Techniques: Cryo-EM Sample Prep

Journal: Nature Structural & Molecular Biology

Article Title: Structural conservation of antibiotic interaction with ribosomes

doi: 10.1038/s41594-023-01047-y

Figure Lengend Snippet: a , View of tetracycline binding site (16S rRNA, grey) in the absence (left panel) and presence of tetracycline (right panel). Waters (spheres) that are displaced upon tetracycline (Tet, blue) binding are colored red. b , View of streptomycin binding site (16S rRNA, grey) in the absence (left panel) and presence of streptomycin (right panel). Waters (spheres) that are displaced upon streptomycin (Str, blue) binding are colored red. c , View of spectinomycin binding site (16S rRNA, grey) in the absence (left panel) and presence of spectinomycin (right panel). Waters (spheres) that are displaced upon spectinomycin (Spc, blue) binding are colored red. d , View of kasugamycin binding site (16S rRNA, grey) in the absence (left panel) and presence of kasugamycin (right panel). Waters (spheres) that are displaced upon kasugamycin (Ksg, blue) binding are colored red. e-h , View of ( e ) lincomycin, ( f ) clindamycin, ( g ) tiamulin and ( h ) retapamulin binding site (23S rRNA, grey) in the absence (left panel) and presence of the drug (right panel). Waters (spheres) that are displaced upon binding of the antibiotic are colored red. In ( a )-( h ), waters (spheres) that are stabilized upon drug binding are colored green.

Article Snippet: Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).

Techniques: Binding Assay

Journal: Nature Structural & Molecular Biology

Article Title: Structural conservation of antibiotic interaction with ribosomes

doi: 10.1038/s41594-023-01047-y

Figure Lengend Snippet: a , Interaction of streptomycin (Str A ) on the SSU at 2.0 Å. b , Superimposition of streptomycin (Str A ) from a with streptomcyin (Str B ) determined at 1.8 Å (from Fig. ). c , Superimposition of streptomycin determined here on E. coli (Str Eco ) at 1.8 Å (Str B from Fig. ) with streptomycin on the human mitochondrial SSU body (Str mito ) at 2.23 Å (ref. ). d , e , Interaction of eravacycline (Era) ( d ) and omadacycline ( e ) on the SSU at 2.1 and 2.2 Å, respectively. f , Superimposition of eravacycline (Era) from d , omadacycline from (and tetracycline (Tet) (from Fig. ). g , Interaction of clindamycin (Cln) on the LSU at 2.0 Å. h , Superimposition of clindamycin (Cln) from g with lincomycin (Lnc) determined at 1.6 Å (from Fig. ). i , Superimposition of lincomycin determined here on E. coli (Lnc Eco ) at 1.8 Å (from Fig. ) with lincomycin on the L. monocytogenes 70S ribosome (Lnc Lm . at 2.1 Å, ref. ). j , Interaction of retapamulin (Ret) on the LSU at 1.9 Å. k , Superimposition of retapamulin (Ret) from j with tiamulin (Tia) (from Fig. ). l , Superimposition of Ret (blue) and 23S rRNA (cyan) from Ret-LSU structure with E. coli 70S ribosome lacking any drug in the A-site of the PTC (gray, PDB ID 7K00 ) .

Article Snippet: Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).

Techniques:

Journal: Nature Structural & Molecular Biology

Article Title: Structural conservation of antibiotic interaction with ribosomes

doi: 10.1038/s41594-023-01047-y

Figure Lengend Snippet: a , Interaction of pentacycline on the SSU head at 1.89 Å. b-d , Superimposition of pentacycline from ( a ) with ( b ) tetracycline on the SSU head determined at 1.8 Å (from Fig. ), ( c ) eravacycline on the SSU head determined at 2.2 Å (from Fig. ), and ( d ) omadacycline on the SSU head determined at 2.1 Å (from Fig. ), e-f , Zoom of the coordination of the Mg2 for ( e ) omadacycline and ( f ) pentacycline. g , Interaction of evernimicin (Evn) on the LSU at 1.9 Å. h , Superimposition of evernimicin (Evn) from ( g ) with avilamycin (Avi) (from Fig. ). i , Superimposition of Evn (blue) from ( g ) with previous structures of Evn in complex with the ribosome (PDB ID 5KCS and 5JVH) , . j , Interaction of iboxamycin (green) on the 70S ribosome at 2.5 Å (PDB ID 7RQ8) . k-l , superimposition of iboxamycin (green) from ( j ) with ( k ) clindamycin (light blue) and ( l ) lincomycin (dark blue) determined here at 2.0 Å and 1.6 Å, respectively.

Article Snippet: Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).

Techniques:

Journal: Molecules

Article Title: Determination of Pharmaceuticals, Heavy Metals, and Oxysterols in Fish Muscle

doi: 10.3390/molecules26051229

Figure Lengend Snippet: Pharmaceuticals and selected metabolites which were not detected in fish muscle with their limit of detection (ng/g).

Article Snippet: Acetaminophen D4, caffeine D9, salbutamol D7, trimethoprim D9, fluoxetine D5, bisoprolol D5, ciprofloxacin D8, mycophenolic acid D3, clindamycin D3, valsartan D3, erythromycin C13D3, dulfamethoxazole D4 were used as internal standards and were purchased from Toronto Research Chemicals (Toronto, Ontario, ON, Canada).

Techniques: