Co-exposure of decabromodiphenyl ethane and cadmium increases toxicity to earthworms: Enrichment, oxidative stress, damage and molecular binding mechanisms

The increase of electronic waste worldwide has resulted in the exacerbation of combined decabromodiphenyl ethane (DBDPE) and cadmium (Cd) pollution in soil, posing a serious threat to the safety of soil organisms. However, whether combined exposure increases toxicity remains unclear. Therefore, this study primarily investigated the toxic effects of DBDPE and Cd on earthworms at the individual, tissue, and cellular levels under single and combined exposure. The results showed that the combined exposure significantly increased the enrichment of Cd in earthworms by 50.32-90.42 %. The toxicity to earthworms increased with co-exposure, primarily resulting in enhanced oxidative stress, inhibition of growth and reproduction, intensified intestinal and epidermal damage, and amplified coelomocyte apoptosis. PLS-PM analysis revealed a significant and direct relationship between the accumulation of target pollutants in earthworms and oxidative stress, damage, as well as growth and reproduction of earthworms. Furthermore, IBR analysis indicated that SOD and POD were sensitive biomarkers in earthworms. Molecular docking elucidated that DBDPE and Cd induced oxidative stress responses in earthworms through the alteration of the conformation of the two enzymes. This study enhances understanding of the mechanisms behind the toxicity of combined pollution and provides important insights for assessing e-waste contaminated soils.

HIV-1 Tat amino acid residues that influence Tat-TAR binding affinity: a scoping review

HIV-1 remains a global health concern and to date, nearly 38 million people are living with HIV. The complexity of HIV-1 pathogenesis and its subsequent prevalence is influenced by several factors including the HIV-1 subtype. HIV-1 subtype variation extends to sequence variation in the amino acids of the HIV-1 viral proteins. Of particular interest is the transactivation of transcription (Tat) protein due to its key function in viral transcription. The Tat protein predominantly functions by binding to the transactivation response (TAR) RNA element to activate HIV-1 transcriptional elongation. Subtype-specific Tat protein sequence variation influences Tat-TAR binding affinity. Despite several studies investigating Tat-TAR binding, it is not clear which regions of the Tat protein and/or individual Tat amino acid residues may contribute to TAR binding affinity. We, therefore, conducted a scoping review on studies investigating Tat-TAR binding. We aimed to synthesize the published data to determine (1) the regions of the Tat protein that may be involved in TAR binding, (2) key Tat amino acids involved in TAR binding and (3) if Tat subtype-specific variation influences TAR binding. A total of thirteen studies met our inclusion criteria and the key findings were that (1) both N-terminal and C-terminal amino acids outside the basic domain (47-59) may be important in increasing Tat-TAR binding affinity, (2) substitution of the amino acids Lysine and Arginine (47-59) resulted in a reduction in binding affinity to TAR, and (3) none of the included studies have investigated Tat subtype-specific substitutions and therefore no commentary could be made regarding which subtype may have a higher Tat-TAR binding affinity. Future studies investigating Tat-TAR binding should therefore use full-length Tat proteins and compare subtype-specific variations. Studies of such a nature may help explain why we see differential pathogenesis and prevalence when comparing HIV-1 subtypes.

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.

Chemical, biological and protein-receptor binding profiling of Bauhinia scandens L. stems provide new insights into the management of pain, inflammation, pyrexia and thrombosis

Bauhinia scandens L. (Family, Fabaceae) is a medicinal plant used for conventional and societal medication in Ayurveda. The present study has been conducted to screen the chemical, pharmacological and biochemical potentiality of the methanol extracts of B. scandens stems (MEBS) along with its related fractions including carbon tetrachloride (CTBS), di-chloromethane (DMBS) and n-butanol (BTBS). UPLC-QTOF-MS has been implemented to analyze the chemical compounds of the methanol extracts of Bauhinia scandens stems. Additionally, antinociceptive and anti-inflammatory effects were performed by following the acetic acid-induced writhing test and formalin-mediated paw licking test in the mice model. The antipyretic investigation was performed by Brewer Yeast induced pyrexia method. The clot lysis method was implemented to screen the thrombolytic activity in human serum. Besides, the in silico study was performed for the five selected chemical compounds of Bauhinia scandens, found by UPLC-QTOF-MS By using Discover Studio 2020, UCSF Chimera, PyRx autodock vina and online tools. The MEBS and its fractions exhibited remarkable inhibition in dose dependant manner in the antinociceptive and antiinflammatory investigations. The antipyretic results of MEBS and DMBS were close to the standard drug indomethacin. Investigation of the thrombolytic effect of MEBS, CTBS, DMBS, and BTBS revealed notable clot-lytic potentials. Besides, the phenolic compounds of the plant extracts revealed strong binding affinity to the COX-1, COX-2, mPGES-1 and plasminogen activator enzymes. To recapitulate, based on the research work, Bauhinia scandens L. stem and its phytochemicals can be considered as prospective wellsprings for novel drug development and discovery by future researchers.

In vivo magnetic resonance imaging and spectroscopy. Technological advances and opportunities for applications continue to abound

Over the past decades, the field of in vivo magnetic resonance (MR) has built up an impressive repertoire of data acquisition and analysis technologies for anatomical, functional, physiological, and molecular imaging, the description of which requires many book volumes. As such it is impossible for a few authors to have an authoritative overview of the field and for a brief article to be inclusive. We will therefore focus mainly on data acquisition and attempt to give some insight into the principles underlying current advanced methods in the field and the potential for further innovation. In our view, the foreseeable future is expected to show continued rapid progress, for instance in imaging of microscopic tissue properties in vivo, assessment of functional and anatomical connectivity, higher resolution physiologic and metabolic imaging, and even imaging of receptor binding. In addition, acquisition speed and information content will continue to increase due to the continuous development of approaches for parallel imaging (including simultaneous multi-slice imaging), compressed sensing, and MRI fingerprinting. Finally, artificial intelligence approaches are becoming more realistic and will have a tremendous effect on both acquisition and analysis strategies. Together, these developments will continue to provide opportunity for scientific discovery and, in combination with large data sets from other fields such as genomics, allow the ultimate realization of precision medicine in the clinic.

First report of a lactonic disecosteroid from the buccinid gastropod Babylonia spirata

A lactonic steroid with an unprecedented 1, 10: 8, 9-disecoergostane framework was identified from the ethyl acetate-methanol extract of buccinid gastropod mollusk, Babylonia spirata collected from the southwestern coast of Indian peninsular region. The compound was characterized as 1, 10: 8, 9-disecoergosta-8-en-A-homo-6a-oxa-1-one by exhaustive spectroscopic methods including two-dimensional nuclear magnetic resonance and mass spectroscopic investigations. The disecosteroid displayed moderate carbolytic enzyme inhibition activity as distinguished by its inhibitive effects against α-amylase and α-glucosidase (IC₅₀ 0.40 and 0.54 mg/mL, respectively). The anti-inflammatory (5-lipoxidase inhibitory) activity of the titled secondary metabolite was found to be superior (IC₅₀ < 0.85 mg/mL) than the commercial anti-inflammatory drug (ibuprofen IC₅₀ > 0.85 mg/mL). However, significantly greater antioxidant property was recorded for the studied disecosteroid as evaluated by in vitro 2, 2-diphenyl-1-picrylhydrazyl radical inhibition potential (IC₅₀ 0.30 mg/mL) than that of standard, α-tocopherol (IC₅₀ > 0.50 mg/mL). The in silico molecular docking studies were conducted to explain the anti-5-lipoxidase and anti-α-amylase properties of the isolated compound. The molecular binding interactions of the ligands with the pro-inflammatory 5-lipoxidase and the carbolytic enzyme α-amylase, demonstrated that their binding energies/docking scores were positively associated with their in vitro bioactivities. A plausible pathway for the biosynthetic origin of lactonic disecosteroid in B. spirata was proposed from an ergosterol precursor. Structure-activity correlation study demonstrated that the biological activities of the disecosteroid were directly proportional to their electronic properties allied with lesser steric restrictions.

Thermodynamic and Kinetic Analysis of Isothermal Titration Calorimetry Experiments by Using KinITC in AFFINImeter

Standard molecular binding isothermal titration calorimetric (ITC) experiments are designed to get thermodynamic information: changes in Gibbs energy, enthalpy, and entropy associated to the studied process. Traditionally, the kinetic information contained in the ITC raw signal has been ignored. For a usual one-step process, this corresponds to the rate constants for the association and the dissociation of the complex (k_on and k_off). The availability of highly sensitive ITC instruments with low response time, together with the development of theoretical methods and of public software for the proper analysis of the signal, cancels any reason for not retrieving this kinetic information. Here we describe how to further exploit ITC experiments of simple one-step interactions by using the software AFFINImeter.The method is exemplified using a standard reference system for thermodynamic and kinetic molecular binding analysis: the interaction of carbonic anhydrase (CA) with its inhibitor 4-carboxybenzenesulfonamide (4-CBS) at several temperatures. It is to be emphasized that old experiments initially designed and executed just for thermodynamic analysis can be readily recycled by using AFFINImeter to retrieve the previously ignored kinetic information.

Affinity assisted selection of antibodies for Point of Care TSH immunoassay with limited wash

BACKGROUND

Molecular binding characteristics of several thyroid stimulating hormone (TSH) antibodies were determined for the TSH antigen, along with its closely related endogenous interfering hormones, follicle stimulating hormone (FSH), luteinizing hormone (LH) and chorionic gonadotropin (CG).

METHODS

This data was compared to the same antibodies used in the low wash sandwich ELISA immunoassay system, the Point of Care i-STAT® immunoassay. From this information we developed binding criteria useful in the low wash i-STAT® immunoassay to permit good signal generation from TSH and low cross-reactivity from its interfering hormones. For the TSH Assay we have developed characteristics that enable antibody selection in the i-STAT® immunoassay cartridge. Our antibody screening approach used a dot blot approach as a first screen to select for the most useful antibodies. We then compared a FRET (Förster Resonance Energy Transfer) and electrochemical cartridge approach to determine the appropriate antibody combinations.

RESULTS

Both methods generated similar data, but the FRET method was not capable of differentiating the antibody with the best characteristics as a capture antibody or a detection conjugate in a sandwich ELISA assay. Finally, we performed binding characterizations of the antibodies using each of the above mentioned glycoproteins.

CONCLUSIONS

We found that we need sub-picomolar detection of TSH, and at least 100 fold or higher values for the cross-reacting species.