Characterization and classification of pathogenic bacteria using native fluorescence and spectral deconvolution.

Identification and classification of pathogenic bacterial strains is of current interest for the early treatment of diseases. In this work, protein fluorescence from eight different pathogenic bacterial strains were characterized using steady state and time resolved fluorescence spectroscopy. The spectral deconvolution method was also employed to decompose the emission contribution from different intrinsic fluorophores and extracted various key parameters, such as intensity, emission maxima, emission line width of the fluorophores, and optical redox ratio. The change in average lifetime values across different bacterial strains exhibits good statistical significance (p ≤ 0.01). The variations in the photophysical characteristics of bacterial strains are due to the different conformational states of the proteins. The stepwise multiple linear discriminate analysis of fluorescence emission spectra at 280 nm excitation across eight different bacterial strains classifies the original groups and cross validated group with 100% and 99.5% accuracy, respectively.

A biophysical approach of tyrphostin AG879 binding information in: bovine serum albumin, human ErbB2, c-RAF1 kinase, SARS-CoV-2 main protease and angiotensin-converting enzyme 2.

Viral infections cause significant health problems all over the world, and it is critical to develop treatments for these problems. Antivirals that target viral genome-encoded proteins frequently cause the virus to become more resistant to treatment. Because viruses rely on several cellular proteins and phosphorylation processes that are essential to their life cycle, drugs targeting host-based targets could be a viable treatment option. To reduce costs and improve efficiency, existing kinase inhibitors could be repurposed as antiviral medications; however, this method rarely works, and specific biophysical approaches are required in the field. Because of the widespread use of FDA-approved kinase inhibitors, it is now possible to better understand how host kinases contribute to viral infection. The purpose of this article is to investigate the tyrphostin AG879 (Tyrosine kinase inhibitor) binding information in Bovine Serum Albumin (BSA), human ErbB2 (HER2), C-RAF1 Kinase (c-RAF), SARS-CoV-2 main protease (COVID 19), and Angiotensin-converting enzyme 2 (ACE-2).Communicated by Ramaswamy H. Sarma.

Exploring the Binding Interaction Mechanism of Taxol in ß-Tubulin and Bovine Serum Albumin: A Biophysical Approach.

In this present study on understanding the taxol (PTX) binding interaction mechanism in both the ß-tubulin and bovine serum albumin (BSA) molecule, various optical spectroscopy and computational techniques were used. The fluorescence steady-state emission spectroscopy result suggests that there is a static quenching mechanism of the PTX drug in both ß-tubulin and BSA, and further time-resolved emission spectroscopy studies confirm that the quenching mechanism exists. The excitation-emission matrix (EEM), Fourier transform infrared, and resonance light scattering spectra (FT-IR) confirm that there are structural changes in both the BSA and ß-tubulin molecule during the binding process of PTX. The molecular docking studies revealed the PTX binding information in BSA, ß-tubulin, and modeled ß-tubulin and the best binding pose to further subject the molecular dynamics simulation, and this study confirms the stability of PTX in the protein complex during the simulation. Density functional theory (DFT) calculations were performed between the free PTX drug and PTX drug (single point) in the protein molecule active site region to understand the internal stability.

Comparative Binding Analysis of N-Acetylneuraminic Acid in Bovine Serum Albumin and Human α-1 Acid Glycoprotein.

The present study focuses on the determination of the biologically significant N-acetylneuraminic acid (NANA) drug binding interaction mechanism between bovine serum albumin (BSA) and human α-1 acid glycoprotein (HAG) using various optical spectroscopy and computational methods. The steady state fluorescence spectroscopy result suggests that the fluorescence intensity of BSA and HAG was quenched by NANA in a static mode of quenching. Further time-resolved emission spectroscopy measurements confirm that mode of quenching mechanism of NANA in the BSA and HAG system. The FT-IR, excitation-emission matrix and circular dichroism (CD) analysis confirms the presence of NANA in the HAG, BSA system, and fluorescence resonance energy transfer analysis shows that NANA transfers energy between the HAG and BSA system. The molecular docking result shows good binding affinity in both protein complexes, and further molecular dynamics simulations and charge distribution analysis were performed to gain more insight into the binding interaction mechanism of NANA in the HAG and BSA complex.

A cytotoxicity, optical spectroscopy and computational binding analysis of 4-[3-acetyl-5-(acetylamino)-2-methyl-2,3-dihydro-1,3,4-thiadiazole-2-yl]phenyl benzoate in calf thymus DNA.

In this study the interaction mechanism between newly synthesized 4-(3-acetyl-5-(acetylamino)-2-methyl-2, 3-dihydro-1,3,4-thiadiazole-2-yl) phenyl benzoate (thiadiazole derivative) anticancer active drug with calf thymus DNA was investigated by using various optical spectroscopy techniques along with computational technique. The absorption spectrum shows a clear shift in the lower wavelength region, which may be due to strong hypochromic effect in the ctDNA and the drug. The results of steady state fluorescence spectroscopy show that there is static quenching occurring while increasing the thiadiazole drug concentration in the ethidium bromide-ctDNA system. Also the binding constant (K), thermo dynamical parameters of enthalpy change (ΔH°), entropy change (ΔS°) Gibbs free energy change (ΔG°) were calculated at different temperature (293 K, 298 K) and the results are in good agreement with theoretically calculated MMGBSA binding analysis. Time resolved emission spectroscopy analysis clearly explains the thiadiazole derivative competitive intercalation in the ethidium bromide-ctDNA system. Further, molecular docking studies was carried out to understand the hydrogen bonding and hydrophobic interaction between ctDNA and thiadiazole derivative molecule. In addition the docking and molecular dynamics charge distribution analysis was done to understand the internal stability of thiadiazole derivative drug binding sites of ctDNA. The global reactivity of thiadiazole derivative such as electronegativity, electrophilicity and chemical hardness has been calculated.

Determination on the binding of thiadiazole derivative to human serum albumin: a spectroscopy and computational approach.

4-[3-acetyl-5-(acetylamino)-2,3-dihydro-1,3,4-thiadiazole-2-yl]phenyl benzoate from the family of thiadiazole derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiadiazole derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance, r between the donor (HSA) and acceptor (thiadiazole derivative) was estimated according to Forster's theory of non-radiative energy transfer. The Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes of temperature-dependent Kb was calculated, which explains that the reaction is spontaneous and exothermic. The microenvironment of HSA have also been studied using synchronous fluorescence spectroscopy, and the feature of thiadiazole derivative-induced structural changes of HSA have been carried using Fourier transform infrared spectroscopy and the Molecular modelling simulations explore the hydrophobic and hydrogen bonding interactions.

Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies.

4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate [Ace semi],4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl propanoate [Pro semi] from the family of thiosemicarbazones derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and it is also less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiosemicarbazone derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance (r) between donor (HSA) and acceptor (thiosemicarbazone derivative) was estimated according to Forster's theory of non-radiative energy transfer using fluorescence spectroscopy. The binding dynamics has been elaborated using synchronous fluorescence spectroscopy, and the feature of thiosemicarbazone derivative induced structural changes of HSA has been studied by circular dichorism, Fourier transform infrared spectroscopy. Molecular modelling simulations explore the hydrophobic interaction and hydrogen bonding which stabilizes the interaction.

Investigation of Optical Spectroscopic and Computational Binding Mode of Bovine Serum Albumin with 1, 4-Bis ((4-((4-Heptylpiperazin-1-yl) Methyl)-1H-1, 2, 3-Triazol-1-yl) Methyl) Benzene.

A newly synthesized 1, 4-bis ((4-((4-heptylpiperazin-1-yl) methyl)-1H-1, 2, 3-triazol-1-yl) methyl) benzene from the family of piperazine derivative has good anticancer activity, antibacterial and low toxic nature; its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of piperazine derivative to bovine serum albumin (BSA) was investigated using fluorescence spectroscopy. The molecular distance r between the donor (BSA) and acceptor (piperazine derivative) was estimated according to Forster's theory of nonradiative energy transfer. The physicochemical properties of piperazine derivative, which induced structural changes in BSA, have been studied by circular dichroism and those chemical environmental changes were probed using Raman spectroscopic analysis. Further, the binding dynamics was expounded by synchronous fluorescence spectroscopy and molecular modeling studies explored the hydrophobic interaction and hydrogen bonding results, which stabilize the interaction.

Steady-state and time-resolved fluorescence spectroscopic characterization of urine of healthy subjects and cervical cancer patients.

Steady-state and time-resolved fluorescence spectroscopy were employed in the discrimination of cervical cancer patients from healthy subjects using urine samples. Fluorescence emission at 390 and 440 nm was considered to monitor the fluorescence of indoxyl sulfate and neopterin. Significant spectral differences were observed between healthy and cancer subjects. Different ratio parameters were calculated from the spectral intensity at 280- and 350-nm excitation and were subjected to stepwise linear discriminant analysis. In total, 84.0% of samples were correctly classified at 280 nm and 96.4% were correctly classified at 350 nm. The fluorescence decay kinetics of urine samples at 390-nm emission was best described by bi- exponential fits, whereas the decay characteristics at 440 nm of urine samples was best explained by bi-exponential fits and, in some cases, by tri-exponential fits. However, the decay kinetics of both indoxyl sulfate and neopterin standards was well described by bi-exponential decays. Based on the fluorescence emission characteristics and statistical analysis, the fluorophores indoxyl sulfate, neopterin, and riboflavin may be considered as potential biomarkers for cervical cancer diagnosis.

Fluorescence spectroscopic characterization of salivary metabolites of oral cancer patients.

A pilot study has been carried out using human saliva in differentiating the normal subjects from that of oral squamous cell carcinoma (OSCC) patients, using the autofluorescence spectroscopy at 405nm excitation. A markable difference in the spectral signatures between the saliva of normal subjects and that of oral cancer patients has been noticed. The possible reasons for the altered spectral signature may be due to the presence of endogenous porphyrin, NAD(P)H and FAD in the exfoliated cells from saliva. The elevated level of porphyrin in saliva of OSCC patients may be attributed to the disturbances in the amino acid degradation pathway and heme biosynthetic pathway, during the transformation of normal into malignant cells. The integrated area under the curve of fluorescence emission spectrum at 405nm excitation and also fluorescence excitation spectrum for 625nm emission were compared for the saliva of normal and oral cancer patients. The area under the curve for the emission spectrum provides 85.7% sensitivity and 93.3% specificity, where as the fluorescence excitation spectrum discriminates the same with 84.1% sensitivity and 93.2% specificity.

Evaluation of dosimetric parameters for various 192Ir brachytherapy sources under unbounded phantom geometry by Monte Carlo simulation.

As per TG-43 dose calculation formalism, it is essential to obtain various dosimetric parameters such as the air-kerma strength, dose rate constant, radial dose function, and anisotropy function, as they account for accurate determination of dose rate distribution around brachytherapy sources. Most of the available reported Monte Carlo simulations were performed in liquid water phantoms with a bounded region of 30-cm diameter. In this context, an attempt was made to report the dosimetric parameters for various commercially available pulsed-dose rate (PDR) and high-dose rate (HDR) sources under unbounded phantom conditions, as the data may be used as input to treatment planning systems (TPSs) for quality control assistance. The air-kerma strength per unit activity, S(k)/A, was computed for various Iridium-192 ((192)Ir) sources in dry air medium. The air-kerma strength and dose rate constant for old PDR is (9.77 +/- 0.03) 10(-8) U/Bq and 1.124 +/- 0.001 cGyh(-1)U(-1); for new PDR, the values are (9.96 +/- 0.03) 10(-8) U/Bq and 1.124 +/- 0.001 cGyh(-1)U(-1); for old MHDR, the values are (9.80 +/- 0.01) 10(-8) U/Bq and 1.115 +/- 0.001 cGyh(-1)U(-1); for new MHDR, (9.80 +/- 0.01) 10(-8) U/Bq and 1.112 +/- 0.001cGyh(-1)U(-1); for old VHDR, the values are (10.32 +/- 0.01) 10(-8) U/Bq and 1.035 +/- 0.002 cGyh(-1)U(-1); for new VHDR, the values are (10.34 +/- 0.02) 10(-8) U/Bq and 1.096 +/- 0.001 cGyh(-1)U(-1). The computed radial dose function values and anisotropy function values are also in good agreement with available data.

Characterization of responses and comparison of calibration factor for commercial MOSFET detectors.

A commercial metal oxide silicon field effect transistor (MOSFET) dosimeter of model TN502-RD has been characterized for its linearity, reproducibility, field size dependency, dose rate dependency, and angular dependency for Cobalt-60 (60Co), 6-MV, and 15-MV beam energies. The performance of the MOSFET clearly shows that it is highly reproducible, independent of field size and dose rate. Furthermore, MOSFET has a very high degree of linearity, with r-value>0.9 for all 3 energies. The calibration factor for 2 similar MOSFET detectors of model TN502-RD were also estimated and compared for all 3 energies. The calibration factor between the 2 similar MOSFET detectors shows a variation of about 1.8% for 60Co and 15 MV, and for 6 MV it shows variation of about 2.5%, indicating that calibration should be done whenever a new MOSFET is used. However, the detector shows considerable angular dependency of about 8.8% variation. This may be due to the variation in radiation sensitivity between flat and bubble sides of the MOSFET, and indicates that positional care must be taken while using MOSFET for stereotactic radiosurgery and stereotactic radiotherapy dosimetric applications.