The ISWI family protein SMARCA5 contains the ATP-binding pocket that coordinates the catalytic Mg2+ ion and water molecules for ATP hydrolysis. In this study, we demonstrate that SMARCA5 can also possess an alternative metal-binding ability. First, we isolated SMARCA5 on the cobalt column (IMAC) to near homogeneity. Examination of the interactions of SMARCA5 with metal-chelating supports showed that, apart from Co2+, it binds to Cu2+, Zn2+ and Ni2+. The efficiency of the binding to the last-listed metal was influenced by the chelating ligand, resulting in a strong preference for Ni-NTA over the Ni-CM-Asp equivalent. To gain insight in the preferential affinity for the Ni-NTA ligand, QM calculations were performed on model systems and metal-ligand complexes with a limited protein fragment of SMARCA5 containing the double-histidine (dHis) motif. The calculations correlated the observed affinity with the relative stability of the d-block metals to tetradentate ligand coordination over tridentate, as well as their overall octahedral coordination capacity. Likewise, binding free energies derived from model imidazole complexes mirrored the observed Ni-NTA/Ni-CM-Asp preferential affinity. Finally, similar calculations on complexes with a SMARCA5 peptide fragment derived from the AlphaFold structural prediction, captured almost accurately the expected relative stability of the TM complexes, and produced a large energetic separation (~10 kcal∙mol-1) between Ni-NTA and Ni-CM-Asp in favour of the former.
- MeSH
- Adenosine Triphosphatases MeSH
- Chromosomal Proteins, Non-Histone metabolism chemistry MeSH
- Metals chemistry metabolism MeSH
- Quantum Theory MeSH
- Humans MeSH
- Ligands MeSH
- Models, Molecular MeSH
- Chromatin Assembly and Disassembly MeSH
- Protein Binding * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Interferon induced transmembrane proteins (IFITMs) play a dual role in the restriction of RNA viruses and in cancer progression, yet the mechanism of their action remains unknown. Currently, there is no data about the basic biochemical features or biophysical properties of the IFITM1 protein. In this work, we report on description and biochemical characterization of three conformational variants/oligomeric species of recombinant IFITM1 protein derived from an Escherichia coli expression system. The protein was extracted from the membrane fraction, affinity purified, and separated by size exclusion chromatography where two distinct oligomeric species were observed in addition to the expected monomer. These species remained stable upon re-chromatography and were designated as "dimer" and "oligomer" according to their estimated molecular weight. The dimer was found to be less stable compared to the oligomer using circular dichroism thermal denaturation and incubation with a reducing agent. A two-site ELISA and HDX mass spectrometry suggested the existence of structural motif within the N-terminal part of IFITM1 which might be significant in oligomer formation. Together, these data show the unusual propensity of recombinant IFITM1 to naturally assemble into very stable oligomeric species whose study might shed light on IFITM1 anti-viral and pro-oncogenic functions in cells.
- MeSH
- Antiviral Agents pharmacology chemistry metabolism MeSH
- Antigens, Differentiation * metabolism chemistry MeSH
- Protein Conformation * MeSH
- Humans MeSH
- Recombinant Proteins chemistry isolation & purification metabolism biosynthesis MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
There is increasing research interest in using mesoporous silica for the delivery of poorly water-soluble drugs that are stabilized in a noncrystalline form. Most research has been done on ordered silica, whereas far fewer studies have been published on using nonordered mesoporous silica, and little is known about intrinsic drug affinity to the silica surface. The present mechanistic study uses inverse gas chromatography (IGC) to analyze the surface energies of three different commercially available disordered mesoporous silica grades in the gas phase. Using the more drug-like probe molecule octane instead of nitrogen, the concept of a "drug-accessible surface area" is hereby introduced, and the effect on drug monolayer capacity is addressed. In addition, enthalpic interactions of molecules with the silica surface were calculated based on molecular mechanics, and entropic energy contributions of volatiles were estimated considering molecular flexibility. These free energy contributions were used in a regression model, giving a successful comparison with experimental desorption energies from IGC. It is proposed that a simplified model for drugs based only on the enthalpic interactions can provide an affinity ranking to the silica surface. Following this preformulation research on mesoporous silica, future studies may harness the presented concepts to guide formulation scientists.
- MeSH
- Pharmaceutical Preparations MeSH
- Silicon Dioxide * chemistry MeSH
- Porosity MeSH
- Solubility MeSH
- Water * chemistry MeSH
- Publication type
- Journal Article MeSH
Hlavním cílem tohoto článku je prezentovat výsledky syntézy nových alkylových derivátů 5-(2-brom-4-fluorfenyl)-4-ethyl-4H-1,2,4-triazol-3-thiolu a molekulárního dokování studie proti COX-1 a COX-2. Předchozí studie prokázaly široký rozsah biologické aktivity 1,2,4-triazolových derivátů. Proto bylo důležité zjistit, jak nová řada 1,2,4-triazolových derivátů poskytne potenciální protizánětlivou aktivitu. K dosažení cíle byly připraveny alkylové deriváty 5-(2-brom-4-fluorfenyl)-4-ethyl-4H-1,2,4-triazol-3-thiolů (2a-2i) z 5-(2Byl získán brom-4-fluorfenyl)-4-ethyl-4H-l,2,4-triazol-3-thiol (1e). Struktura syntetizovaných sloučenin byla potvrzena 1H-NMR elementární analýzou. Totožnost a čistota sloučenin byla potvrzena metodou kapalinové chromatografie-hmotnostní spektrometrie. Tyto sloučeniny mají relativně jednoduché schéma syntézy, což jim dává výhodu v procesu tvorby potenciálního léčiva a výskyt alkylových radikálů v molekule by měl mít pozitivní vliv na farmakokinetické ukazatele, stabilitu, selektivitu a biologickou dostupnost. U syntetizovaných sloučenin byla provedena studie in silico, konkrétně molekulární dokování týkající se interakce s COX-1 a COX-2. Na základě indexů selektivity vazebných režimů pozorovaných pro vybrané sloučeniny (2e, 2g) s aktivními místy COX1 bylo zjištěno, že sloučeniny mohou pravděpodobně uplatňovat svůj protizánětlivý účinek cestou biosyntézy prostaglandinů, inhibicí COX-1 místo COX-2. Rovněž byl prokázán vliv hydrofobních interakcí alkylových skupin 1,2,4-triazolových derivátů na změnu afinity a selektivity k COX-1 nebo COX-2. Proto jsou deriváty 1,2,4 slibnými kandidáty na zlepšení, další studium a budoucí vývoj nových, účinnějších protizánětlivých léčiv pro terapeutické použití.
The main goal of this article is to present the results of the synthesis of new alkyl derivatives of 5-(2-bromo4-fluorophenyl)-4-ethyl-4H-1,2,4-triazole-3-thiol and molecular docking studies against COX-1 and COX-2. Previous studies have established a wide range of biological activity of 1,2,4-triazole derivatives. Therefore, it was essential to determine how a new series of 1,2,4-triazole derivatives would provide potential anti-inflammatory activity. To reach the goal, raw alkyl derivatives of 5-(2-bromo-4-fluorophenyl)-4-ethyl-4H-1,2,4-triazole-3-thiols (2a-2i) from 5-(2-bromo-4-fluorophenyl)-4-ethyl-4H-1,2,4-triazole3-thiol (1e) were obtained. The structure of the synthesized compounds was confirmed by 1H-NMR elemental analyses. The individuality and purity of compounds were confirmed by the method of liquid chromatography-mass spectrometry. These compounds have a relatively simple synthesis scheme, which gives them an advantage in creating a potential drug, and the appearance of alkyl radicals in the molecule should positively affect pharmacokinetic indicators, stability, selectivity, and bioavailability. An in silico study was conducted for the synthesized compounds, namely molecular docking, in relation to the interaction with COX-1 and COX-2. Based on the selectivity indexes of binding modes observed for the selected compounds (2e, 2g) with active COX-1 centers, it was found that compounds can reliably exhibit their anti-inflammatory effect through the prostaglandin biosynthesis pathway, inhibiting COX-1 instead of COX-2. The effect of hydrophobic interactions of alkyl groups of 1,2,4-triazole derivatives on changes in affinity and selectivity to COX-1 or COX-2 has also been proven. Therefore, derivatives of 1,2,4 are promising candidates for improvement, further study, and future development of new, more powerful antiinflammatory drugs for therapeutic use.
Prostate cancer (PCa) tops the list of cancer-related deaths in men worldwide. Prostate-specific membrane antigen (PSMA) is currently the most prominent PCa biomarker, as its expression levels are robustly enhanced in advanced stages of PCa. As such, PSMA targeting is highly efficient in PCa imaging as well as therapy. For the latter, PSMA-positive tumors can be targeted directly by using small molecules or macromolecules with cytotoxic payloads or indirectly by engaging the immune system of the host. Here we describe the engineering, expression, purification, and biological characterization of bispecific T-cell engagers (BiTEs) that enable targeting PSMA-positive tumor cells by host T lymphocytes. To this end, we designed the 5D3-αCD3 BiTE as a fusion of single-chain fragments of PSMA-specific 5D3 and anti-CD3 antibodies. Detailed characterization of BiTE was performed by a combination of size-exclusion chromatography, differential scanning fluorimetry, and flow cytometry. Expressed in insect cells, BiTE was purified in monodisperse form and retained thermal stability of both functional parts and nanomolar affinity to respective antigens. 5D3-αCD3's efficiency and specificity were further evaluated in vitro using PCa-derived cell lines together with peripheral blood mononuclear cells isolated from human blood. Our data revealed that T-cells engaged via 5D3-αCD3 can efficiently eliminate tumor cells already at an 8 pM BiTE concentration in a highly specific manner. Overall, the data presented here demonstrate that the 5D3-αCD3 BiTE is a candidate molecule of high potential for further development of immunotherapeutic modalities for PCa treatment.
- Publication type
- Journal Article MeSH
Bovine papillomavirus type 1 L1 protein was produced in a baculovirus expression system and purified as virus-like particles (VLPs) by affinity chromatography using lectins. The morphological integrity of VLPs was confirmed by electron microscopy. Differences between the two detected variants were deciphered by mass spectrometry of peptides (MALDI-TOF). Mice were immunized with purified VLPs in doses of 10, 25, or 50 μg in combination with 1% saponin and 15% alhydrogel per dose as adjuvants. Analysis of the humoral immune response revealed increased levels of specific antibodies detected 3 weeks after the first immunization in all groups of animals. This was further significantly increased by the booster applied 3 weeks after the first dose, with the best immune response in a group of mice immunized by the largest dose of antigen. BPV1 L1 VLPs purified by affinity chromatography using lectins could be used for prophylactic immunization in veterinary medicine.
- Publication type
- Journal Article MeSH
Stable isotope labeling by amino acids in cell culture (SILAC) and iodoacetyl tandem mass tag (iodoTMT) are well-implemented mass spectrometry-based approaches for quantification of proteins and for site-mapping of cysteine modification. We describe here a combination of SILAC and iodoTMT to assess ongoing changes in the global proteome and cysteine modification levels using liquid chromatography separation coupled with high-resolution mass spectrometry (LC-MS/MS).
Affinity purification, combined with mass spectrometry (AP-MS) is considered a pivotal technique in protein-protein interaction studies enabling systematic detection at near physiological conditions. The addition of a quantitative proteomic method, like SILAC metabolic labeling, allows the elimination of non-specifically bound contaminants which greatly increases the confidence of the identified interaction partners. Compared to eukaryotic cells, the SILAC labeling of bacteria has specificities that must be considered. The protocol presented here describes the labeling of bacterial cultures with stable isotope-labeled amino acids, purification of an affinity-tagged protein, and sample preparation for MS measurement. Finally, we discuss the analysis and interpretation of MS data to identify and select the specific partners interacting with the protein of interest. As an example, this workflow is applied to the discovery of potential interaction partners of glyceraldehyde-3-phosphate dehydrogenase in the gram-negative bacterium Francisella tularensis.
INTRODUCTION AND AIMS: Viral hepatitis, which appears most frequently at birth or during childhood, is a disease whose transmission routes include tears, bile, sexual fluids, sweat, milk, urine, feces, and saliva. The aim of the present study was to analyze the specificity of the immunochromatographic and ELISA diagnostic tests for hepatitis B surface antigen and compare them with PCR testing. MATERIALS AND METHODS: The study sample was made up of 140 men and 60 women referred to the Urmia Medical University hospital to undergo PCR testing for HBV diagnosis. The ELISA test was performed using the Pioneer Medicine Company kit (Tehran, Iran). RESULTS: The results of the HBs-Ag rapid test and the ELISA test were compared with the PCR test. The HBs-Ag rapid test had 97% sensitivity and 91% specificity, whereas the ELISA test had 78% sensitivity and 76% specificity. DISCUSSION AND CONCLUSION: According to our results, the immunochromatographic test was accurate for diagnosing HBs-Ag in blood and the ELISA test had acceptable sensitivity and specificity, compared with PCR testing.
- MeSH
- Chromatography, Affinity MeSH
- Diagnostic Tests, Routine MeSH
- Enzyme-Linked Immunosorbent Assay MeSH
- Hepatitis B Surface Antigens * MeSH
- Hepatitis B * diagnosis MeSH
- Humans MeSH
- Infant, Newborn MeSH
- Polymerase Chain Reaction MeSH
- Hepatitis B virus genetics MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Infant, Newborn MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Comparative Study MeSH
- Geographicals
- Iran MeSH
Medicinal plants have been exploited for therapeutic purposes since the dawn of civilization and have long been acknowledged essential to human health. The purpose of this research is to examine the scientific evidence for using the therapeutic herbal plants Thalictrum foliolosum DC. and Cordia dichotoma G. Forst. to treat hepatitis illness. The fundamental explanation for the therapeutic relevance of these plants is phytochemicals, which were evaluated qualitatively and quantitatively in three separate extracts with different solvent properties (methanol-polar, chloroform-non-polar, and aqueous-polar as one of the bases of traditional use). Flavonoids, phenols, tannins, saponins, and alkaloids were all evaluated for their presence in plant extracts, and it was observed that methanolic extract had the highest content of phytochemicals among different extracts whereas, the aqueous extract showed least amount of phytochemicals. Additionally, the antioxidant activity of these plants was also evaluated and methanolic extract was revealed with potential antioxidant activity, as also evidenced by the lowest half inhibitory concentration (IC50) values in the DPPH, ABTS, and high %inhibition in μM Fe equivalent of FRAP assays. Following that, the dominant phytochemicals were investigated using ultra-high performance liquid chromatography from the selected plants. Furthermore, default docking algorithms were used to appraise the dominant phytoconstituents for their in-silico investigation, in which rutin was found with the highest binding affinity (8.2 kcal/mol) and interaction with receptor which is further involved in causing jaundice. The receptor is infact an enzyme that is sphingomyelin phosphodiesterase Leptospira interrogans (PDB: 5EBB) which is holded back in its position by rutin and do not interact with Leptospira inferrogans spp which causes jaundice. Overall, the study suggested that these herbs have significant therapeutic properties, and their in-silico analysis strongly recommends further clinical investigations to get insight into the mechanisms of action in curing variety of diseases.
- MeSH
- Antioxidants pharmacology analysis MeSH
- Cordia * MeSH
- Flavonoids pharmacology analysis MeSH
- Phytochemicals analysis MeSH
- Humans MeSH
- Methanol MeSH
- Plant Extracts chemistry MeSH
- Rutin MeSH
- Molecular Dynamics Simulation MeSH
- Thalictrum * MeSH
- Jaundice * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
