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Benzamidine

Benzamidine is a chemical compound with the formula C6H7N2.
It is a white crystalline solid that is used in various research applications, including as a protease inhibitor and as a precursor for the synthesis of other chemical compounds.
Benzamidine has been studied for its potential therapeutic applications, such as in the treatment of inflammation and blood disorders.
Researchers can use PubCompare.ai's AI-driven optimization platform to discover the most accurate and reproducible protocols for working with Benzamidine, guiding them to the best solutions for their research needs by comparing protocols from literature, pre-prints, and patents.

Most cited protocols related to «Benzamidine»

1
Structural Insights into GABAA Receptor
Cited 30 times
The GABAAR-β3cryst structure was solved by molecular replacement using the C. elegans glutamate-gated chloride channel α (GluClα66 (link), PDB accession code 3RHW) as a search model in Phaser67 (link). An initial round of automated model building, structure refinement and density modification was performed using Phenix AutoBuild68 (link) followed by iterative steps of manual model building in Coot69 (link) and refinement in Buster70 . During the refinement/building process it became clear that the N-terminal region of one GABAAR-β3cryst monomer (chain A) adopted a distinct, well-ordered, conformation because of its involvement in crystal contacts. As a result, the strict five-fold non-crystallographic symmetry (NCS) restraints strategy was replaced at later stages by a local structural similarity restraints NCS approach, to allow pruning of genuine differences among matching chains from the NCS relation71 (link). The final model contains one GABAAR-β3cryst homopentamer per asymmetric unit. The complete polypeptide chains could be built, except the C-terminal TETSQVAPA purification tag and the first nine N-terminal residues (QSVNDPGNM) in chains B, C, D and E. Furthermore, clear electron density is visible for benzamidine molecules, one of which occupies every orthosteric ligand binding site, as well as 11 out of the 15 N-linked glycosylation sites, the remaining four being located in the N-terminal disordered regions of chains B-E. Glycans attached to Asn 149 in each chain were protected from endoglycosidase F1 cleavage due to extensive interactions with the protein core, underlying their important structural role. Stereochemical properties of the model were assessed in Coot69 (link) and Molprobity72 (link). Protein geometry analysis revealed no Ramachandran outliers, with 96.98% residues in favoured regions and 3.02% residues in allowed regions. Molprobity clash score after adding hydrogens is 5.74 (100th percentile) and the overall Molprobity score is 1.85 (100th percentile).
Sequence and structural alignments were performed in ClustalW73 (link) and SHP74 (link), respectively. Protein interfaces were analysed using the PDBePISA web server at the European Bioinformatics Institute (http://www.ebi.ac.uk/pdbe/prot_int/pistart.html)75 (link) and residue conservation was mapped onto the crystal structure using ProtSkin76 (link). Electrostatic surface potential calculations were performed using the APBS Tools plug-in in PyMOL77 (link) and pore/tunnel dimensions were analysed using the Caver 3.0 software for a probe radius of 1.4 Å78 (link). Structural figures were prepared with the PyMOL Molecular Graphics System, Version 1.6, Schrödinger, LLC.
Miller P.S, & Aricescu A.R. (2014). Crystal structure of a human GABAA receptor. Nature, 512(7514), 270-275.
Publication 2014
benzamidine Binding Sites Caenorhabditis elegans Crystallography Cytokinesis Electrons Electrostatics Endoglycosidases Europeans glutamate-gated chloride channel Hydrogen Ligands Polypeptides Polysaccharides Protein Glycosylation Proteins Radius
2
Purification of Sth1 and Rtt102-Arp7/9 Complexes
Cited 20 times
Sth1 constructs and complexes were cloned and expressed as described24 (link). For Sth1301-1097P1Swap, the Sth1 fragments 301–645 and 693-1097 were primer-extended to add S. solfataricus Rad54 residues 610–644. A silent EcoRI site was introduced during extension to ligate the two Sth1 fragments. For protein purification, cells were resuspended in lysis buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 5% glycerol, 25 mM imidazole, and 4 mM benzamidine), lysed using a Microfluidizer apparatus (Microfluidics), and clarified by centrifugation. Lysates were purified on a Ni-NTA affinity column (Qiagen) and washed extensively with lysis buffer. Proteins were eluted with 250 mM imidazole and bound to a HiTrap Heparin HP column (GE Healthcare) equilibrated in sample buffer (20 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 2 mM dithiothreitol (DTT), and 4 mM benzamidine). Proteins were eluted using a 200–800 mM NaCl gradient, and further purified on a SD-200 gel filtration column (GE Healthcare) equilibrated with sample buffer. To reconstitute the Rtt102-Arp7/9 ternary complex, Rtt102 and Arp7/924 (link) were mixed at a 2:1 molar ratio and purified through a SD-200 gel filtration column equilibrated in sample buffer (without benzamidine).
Turegun B., Baker R.W., Leschziner A.E, & Dominguez R. (2018). Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Communications Biology, 1, 1.
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Publication 2018
benzamidine Buffers Cells Centrifugation Deoxyribonuclease EcoRI Dithiothreitol Gel Chromatography Glycerin Heparin HEPES imidazole Molar Oligonucleotide Primers Proteins Sodium Chloride
3
Reconstitution of LIL3.2 from Arabidopsis
Cited 19 times
Reconstitution assays were performed based on protocols as described [4 (link), 5 (link), 9 (link)]. For both LIL3.1 and LIL3.2 isoforms from Arabidopsis thaliana, very similar results were obtained [10 (link)]. Based on the higher purification yield only experimental work with LIL3.2 is shown here. In brief; LIL3 inclusion bodies (30 μM) were solubilized in a reaction buffer containing 100 mM Tris pH 11, 5 mM 6-aminocaproic acid, 1 mM benzamidine and 12.5% sucrose and n-Dodecyl β-d-maltoside (DDM) at a final concentration of 6 mM DDM respectively. 100 mM DTT and 6 μM Chl a (solubilized in diethyl ether/Ethanol 1:1) were added prior to heating samples to 100 °C for 1 min followed by a 2-h incubation at RT in the dark.
Mork-Jansson A.E, & Eichacker L.A. (2019). A strategy to characterize chlorophyll protein interaction in LIL3. Plant Methods, 15, 1.
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Publication 2019
6-Aminocaproic Acid Arabidopsis thalianas benzamidine Biological Assay Buffers Ethanol Ethyl Ether Inclusion Bodies Protein Isoforms Sucrose Tromethamine
4
Rac1 Activation Assay on ECM Coatings
Cited 17 times
Cell culture dishes were coated o/n at 4°C with fibronectin, laminin 1, or collagen I (10 μg/ml). Cells were seeded in small clusters of 2–4 cells on the different matrices and analyzed after 4 h. The PI3-kinase inhibitor wortmannin was added as indicated at an initial concentration of 50 nM at 30 min after seeding. Because of the high instability of wortmannin, 3× fresh inhibitor (10 nM) was added every hour. 4 h after seeding, the cells were washed in ice-cold phosphate-buffered saline (containing 1 mM MgCl2 and 0.5 mM CaCl2), incubated 5 min on ice in lysis buffer (50 mM Tris-HCl, pH 7.4, 2 mM MgCl2, 1% NP-40, 10% glycerol, 100 mM NaCl, 1 mM benzamidine, 1 μg/ml leupeptin, 1 μg/ml pepstatin, 1 μg/ml aprotinin), and then centrifuged for 5 min at 21,000 g at 4°C. Aliquots were taken from the supernatant to compare protein amounts. The supernatant was incubated with bacterially produced GST–PAK-CD fusion protein, bound to glutathione-coupled Sepharose beads at 4°C for 30 min. The beads and proteins bound to the fusion protein were washed three times in an excess of lysis buffer, eluted in Laemmli sample buffer (60 mM Tris, pH 6.8, 2% sodium dodecylsulfate, 10% glycerin, 0.1% bromphenol blue), and then analyzed for bound Rac1 molecules by Western blotting using a monoclonal mouse antibody against human Rac1 (Transduction Laboratories).
Sander E.E., van Delft S., ten Klooster J.P., Reid T., van der Kammen R.A., Michiels F, & Collard J.G. (1998). Matrix-dependent Tiam1/Rac Signaling in Epithelial Cells Promotes Either Cell–Cell Adhesion or Cell Migration and Is Regulated by Phosphatidylinositol 3-Kinase. The Journal of Cell Biology, 143(5), 1385-1398.
Publication 1998
Aprotinin benzamidine Biological Assay Bromphenol Blue Buffers Cell Culture Techniques Cells Cold Temperature Collagen Type I Fibronectins Glutathione Glycerin Homo sapiens Hyperostosis, Diffuse Idiopathic Skeletal Laemmli buffer laminin-1 leupeptin Magnesium Chloride Monoclonal Antibodies Mus Nonidet P-40 pepstatin Phosphates Phosphatidylinositol 3-Kinases Proteins Saline Solution Sepharose Sodium Chloride Sulfate, Sodium Dodecyl Tromethamine Wortmannin
5
Ribosome Profiling Protocol
Cited 13 times

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Publication 2012
Aprotinin benzamidine Buffers Cells Centrifugation Cycloheximide Edetic Acid Ethanol Formaldehyde HEPES leupeptin Magnesium Chloride pepstatin polyacrylamide gels Promega Protease Inhibitors Ribosomal RNA Sepharose Sodium Chloride Sucrose Technique, Dilution Tissue, Membrane Transfer RNA Urea

Most recents protocols related to «Benzamidine»

1
In silico Docking of NBA against Kgp Protein
Not available on PMC !
In this study, in silico docking experiment was done using AutoDock Vina. The chemicals and biologicals were procured from Friendemann Schmidt Chemical, Sigma-Aldrich, Merck KGaA, Qrec Chemicals and HmbG® Chemicals. The progress of reaction was monitored by thin layer chromatography (TLC) and melting point measurements using Spectroline UV CM-26 and Stuart Analogue Melting Point SMP11, respectively. The chemical structures of the synthesized compounds were confirmed based on attenuated total reflectance-infrared (ATR-IR) spectral, 1 H & 13 C nuclear magnetic resonance (NMR) spectral and direct infusion mass spectrometry (DIMS) spectral data.
In silico molecular docking of NBA against Kgp protein of P. gingivalis: In this in silco docking experiment, the docking of benzamidine analogues was carried out to assess their interaction and binding modes with the target protein gingipain K (Kgp) of P. gingivalis (PDB ID: 4RBM) using an Intel i7 with RAM of 16 GB. To prepare protein, structure drawing and conversion to working format software including Discovery studio, ChemDraw and OpenBabel were used [19, (link)20] (link). All designed chemical structures were modelled using Chemsketch software. The 2D structures of NBA were generated and conversion into respective 3D structures was done using Ligplot. The designed structures of NBA were optimized, followed by energy minimization using AutoDock software and the process of molecular docking [21] (link). The 3D structures of gingipain K (Kgp) of P. gingivalis (PDB ID: 4RBM) was downloaded from RCSB Protein Data Bank (PDB). The Discovery Studio Visualizer was used to prepare the downloaded KgP protein by removing the heteroatoms and water molecules. Whereas for addition of hydrogen and assignment of the charges molecular graphics laboratory (MGL) tools were used. AutoDock Vina was used only for defining grid parameters and docking. The docking results were further analyzed using Discovery Studio Visualizer [22] (link).
Jain A., Ravichandran M., Ugrappa S., Lalitha P., Wu Y.S., Noor S.N.F.M., Fuloria S., Subramaniyan V., & Fuloria N.K. (2024). Synthesis, Characterization and Response of Newer Benzamidine Analogues against Porphyromonas gingivalis mediated Peri-Implantitis. Asian Journal of Chemistry, 36(4), 829-836.
Publication 2024
2
Synthesis and Antimicrobial Evaluation of Novel Benzamidine Analogues
Not available on PMC !
Novel benzamidine analogues (NBA, 3a-c) were synthesized as per the method stated in standard literature with minor modification [23, (link)24] (link). Briefly, compound (0.0002 M) (previously synthesized by Schiff reaction of compound 1 with 4-nitrobenzaldehyde) was dissolved in 1,4-dioxane and chloroacetyl chloride (0.00025 M), followed by dropwise addition of triethyl amine (0.0003 M) with constant stirring at low temperature (0-5 ºC). Next, the mixture was stirred for 40 h (until the completion of reaction). The reaction was carried out in the presence of molecular sieves. The reaction mixture was added into crushed ice and stirred to obtain the crude product. The crude was recrystallized by dissolving crude product in absolute ethanol and refluxing with activated charcoal for 10 min to yield pure compound 3a. A similar procedure was followed to synthesize compounds 3b and 3c using 4-chlolrobenzaldehyde and 4-dimethylaminobenzaldehyde (Scheme-I). The above procedure was repeated three times and optimized by raising the concentration of compound 3a-c, chloroacetyl chloride and triethylamine, from 0.0002 M to 0.002 M, 0.00025 M to 0.0025 M and 0.0003 M to 0.003 M, respectively. The TLC analysis for all the synthesized azetidinones was performed in absolute ethanol:chloroform (9.5:0.5 ratio) solvent system and melting points of all the synthesized compounds were recorded. In vitro antimicrobial activity: In current investigation, the minimum inhibitory concentration (MIC) of NBA for P. gingivalis was assessed through standard micro-broth dilution assay with small changes [25] (link). Briefly, culturing of P. gingivalis was done in soy broth (at pH 7.4), followed by adjustment of P. gingivalis culture density (1.5 × 10 8 CFU/mL), dilution of NBA (from 500 µg/mL to 1.95 µg/mL), addition of P. gingivalis culture (100 µL) to wells of microplate, incubation for 46 h (in anaerobic conditions) and finally each well absorbance was recorded at 620 nm to calculate the MIC. Next, the minimum bactericidal concentration (MBC) towards P. gingivalis, was determined by further incubating the clear well content (20 µL) in anaerobic conditions for 46 h plated in soy broth agar. Finally, the MBC was determined as NBA concentration with no visible growth. The experiments were commenced three times.
Jain A., Ravichandran M., Ugrappa S., Lalitha P., Wu Y.S., Noor S.N.F.M., Fuloria S., Subramaniyan V., & Fuloria N.K. (2024). Synthesis, Characterization and Response of Newer Benzamidine Analogues against Porphyromonas gingivalis mediated Peri-Implantitis. Asian Journal of Chemistry, 36(4), 829-836.
Publication 2024
3
Thermal Shift Assay for CK2α Protein
Thermal shift binding assay (TSA) was performed with a Bio-Rad CFX real-time PCR system (Hercules, CA, USA). CK2α protein was equilibrated in a buffer (pH 7.5, 100 mM Tris-HCl, 100 mM NaCl) with SYPRO Orange dye (Invitrogen) after addition of DMSO or benzamidine. Samples were freshly prepared and dispensed into 384-well PCR plates at a final volume of 10 μL per well. Fluorescence intensity of each well was measured with a temperature gradient range from 25 to 95 °C with a heating rate increase of 1 °C per minute. To determine the effect of benzamidine on melting temperature (Tm) of CK2α protein, a Boltzmann model was used to generate the protein unfolding curves with GraphPad Prism (v10.0) software.
Kim H.Y., Kim Y.M, & Hong S. (2024). CK2α-mediated phosphorylation of GRP94 facilitates the metastatic cascade in triple-negative breast cancer. Cell Death Discovery, 10, 185.
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Publication 2024
4
Isolation of Nuclear Envelopes
Nuclear envelopes were prepared by the method described by Dreger et al. (42 (link)). Briefly, the nuclei (5–8 mg of protein) were suspended in 25 ml of ice-cold TP buffer (10 mM Tris–HCl, pH 8.0, 10 mM Na2HPO4, 1 mM PMSF, 1 mM benzamidine) containing 250 μg/ml of heparin, 1 mM Na3VO4, 10 mM NaF and 400 units of benzonase (ThermoFisher Scientific). The suspension was stirred for 90 min at 4°C. Nuclear envelopes were then pelleted by centrifugation at 10 000 × g for 30 min at 4°C, and resuspended in STM 0.25 buffer (50 mM Tris–HCl, pH 7.5, 0.25 M sucrose, 5 mM MgCl2, 2 mM DTT, 1 mM PMSF, 1 mM benzamidine) at ∼0.2–0.5 mg/ml.
Sanchez-Lopez I., Orantos-Aguilera Y., Pozo-Guisado E., Alvarez-Barrientos A., Lilla S., Zanivan S., Lachaud C, & Martin-Romero F.J. (2024). STIM1 translocation to the nucleus protects cells from DNA damage. Nucleic Acids Research, 52(5), 2389-2415.
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Publication 2024
5
Purification and Characterization of Factor Xa
Not available on PMC !

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Publication 2024

Top products related to «Benzamidine»

1
Benzamidine by Merck Group
Sourced in United States, Germany, United Kingdom
Benzamidine is a chemical compound used in laboratory settings. It functions as a serine protease inhibitor, which means it can inhibit the activity of certain enzymes involved in protein digestion.
2
Leupeptin by Merck Group
Sourced in United States, Germany, Italy, China, Japan, France, Israel, Switzerland, Canada, Sao Tome and Principe, United Kingdom, Australia, Ireland
Leupeptin is a protease inhibitor that can be used in laboratory settings to inhibit the activity of certain proteases. It is a tripeptide compound that binds to and inhibits the catalytic sites of proteases.
3
Protease inhibitor cocktail by Merck Group
Sourced in United States, Germany, China, United Kingdom, Italy, Japan, Sao Tome and Principe, France, Canada, Macao, Switzerland, Spain, Australia, Israel, Hungary, Ireland, Denmark, Brazil, Poland, India, Mexico, Senegal, Netherlands, Singapore
The Protease Inhibitor Cocktail is a laboratory product designed to inhibit the activity of proteases, which are enzymes that can degrade proteins. It is a combination of various chemical compounds that work to prevent the breakdown of proteins in biological samples, allowing for more accurate analysis and preservation of protein integrity.
4
Aprotinin by Merck Group
Sourced in United States, Germany, United Kingdom, Italy, China, Canada, Japan, Spain, France, Israel, Belgium, Austria, Switzerland, Finland, India, Australia, Macao, Hungary, Sweden, Sao Tome and Principe
Aprotinin is a protease inhibitor derived from bovine lung tissue. It is used as a laboratory reagent to inhibit protease activity in various experimental procedures.
5
Bradford assay by Bio-Rad
Sourced in United States, Germany, United Kingdom, Italy, Canada, China, France, Switzerland, Austria, Spain, Japan, Australia, Brazil, Ireland, Sweden
The Bradford assay is a colorimetric protein assay used to measure the concentration of protein in a solution. It is based on the color change of the Coomassie Brilliant Blue G-250 dye in response to various concentrations of protein.
6
Bca protein assay kit by Thermo Fisher Scientific
Sourced in United States, China, Germany, United Kingdom, Japan, Belgium, France, Switzerland, Italy, Canada, Australia, Sweden, Spain, Israel, Lithuania, Netherlands, Denmark, Finland, India, Singapore
The BCA Protein Assay Kit is a colorimetric detection and quantification method for total protein concentration. It utilizes bicinchoninic acid (BCA) for the colorimetric detection and quantification of total protein. The assay is based on the reduction of Cu2+ to Cu1+ by protein in an alkaline medium, with the chelation of BCA with the Cu1+ ion resulting in a purple-colored reaction product that exhibits a strong absorbance at 562 nm, which is proportional to the amount of protein present in the sample.
7
Odyssey infrared imaging system by LI COR
Sourced in United States, Germany, United Kingdom, China, Italy, Niger, France, Netherlands, Austria, Australia, Liechtenstein
The Odyssey Infrared Imaging System is a versatile laboratory equipment designed for high-sensitivity detection and quantification of fluorescent and luminescent signals. The system utilizes infrared technology to capture and analyze various molecular targets, such as proteins, nucleic acids, and small molecules, in a range of sample types.
8
Pierce bca protein assay kit by Thermo Fisher Scientific
Sourced in United States, United Kingdom, Germany, China, Australia, Switzerland, France, Italy, Canada, Spain, Japan, Belgium, Sweden, Lithuania, Austria, Denmark, Poland, Ireland, Portugal, Finland, Czechia, Norway, Macao, India, Singapore
The Pierce BCA Protein Assay Kit is a colorimetric-based method for the quantification of total protein in a sample. It utilizes the bicinchoninic acid (BCA) reaction, where proteins reduce Cu2+ to Cu+ in an alkaline environment, and the resulting purple-colored reaction is measured spectrophotometrically.
9
Pvdf membrane by Merck Group
Sourced in United States, Germany, China, United Kingdom, Morocco, Ireland, France, Italy, Japan, Canada, Spain, Switzerland, New Zealand, India, Hong Kong, Sao Tome and Principe, Sweden, Netherlands, Australia, Belgium, Austria
PVDF membranes are a type of laboratory equipment used for a variety of applications. They are made from polyvinylidene fluoride (PVDF), a durable and chemically resistant material. PVDF membranes are known for their high mechanical strength, thermal stability, and resistance to a wide range of chemicals. They are commonly used in various filtration, separation, and analysis processes in scientific and research settings.
10
Protease inhibitor cocktail by Roche
Sourced in United States, Switzerland, Germany, China, United Kingdom, France, Canada, Japan, Italy, Australia, Austria, Sweden, Spain, Cameroon, India, Macao, Belgium, Israel
Protease inhibitor cocktail is a laboratory reagent used to inhibit the activity of proteases, which are enzymes that break down proteins. It is commonly used in protein extraction and purification procedures to prevent protein degradation.

More about "Benzamidine"

Benzamidine is a versatile chemical compound with the formula C6H7N2.
It is a white crystalline solid used in various research applications, including as a protease inhibitor and a precursor for the synthesis of other compounds.
Researchers can leverage the power of PubCompare.ai's AI-driven optimization platform to discover the most accurate and reproducible protocols for working with Benzamidine, guiding them to the best solutions for their needs.
Benzamidine is closely related to other protease inhibitors like Leupeptin and Aprotinin, which are often used in combination with Benzamidine as part of a Protease Inhibitor Cocktail.
These compounds are essential tools for researchers studying blood disorders, inflammation, and other biological processes involving proteases.
To quantify the effects of Benzamidine and other compounds, researchers commonly use protein assays like the Bradford assay or the BCA protein assay kit.
These techniques allow for the accurate measurement of protein concentrations, which is crucial for interpreting the results of experiments involving Benzamidine.
The data generated from Benzamidine experiments can be analyzed using advanced imaging systems, such as the Odyssey Infrared Imaging System.
This tool enables researchers to visualize and quantify the results of their studies, providing valuable insights into the mechanisms of action and potential therapeutic applications of Benzamidine.
By combining the power of PubCompare.ai's optimization platform with a comprehensive understanding of Benzamidine and related research tools, scientists can navigate the complex landscape of protease inhibitor research and develop the most effective strategies for their projects.
Whether working with Benzamidine, Leupeptin, Aprotinin, or other related compounds, researchers can rely on PubCompare.ai to guide them to the best solutions and protocols for their needs.