Investigating the interaction of anticancer drug temsirolimus with human transferrin: Molecular docking and spectroscopic approach.

In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures. Binding constant values obtained employing fluorescence spectroscopy depicts strong interaction between hTF and temsirolimus; temsirolimus binds to hTF at 298 K with a binding constant of .32 × 104  M-1 implying the strength of this interaction. The negative Gibbs free energy obtained through quenching experiments is evident of the fact that the binding is spontaneous. CD spectra of hTF also showed a downward shift in the presence of temsirolimus as compared with free hTF implying complex formation between hTF and temsirolimus. Molecular docking was performed with a view to find out which residues are key players in this interaction. The importance of our study stems from the fact it will provide an insight into binding pattern of commonly administered renal cancer drug with an important protein that plays a pivotal role in many physiological processes.

Aggregation as a consequence of glycation: insight into the pathogenesis of arthritis.

Advanced glycation end products (AGEs) as a result of Maillard reaction are currently at the heart of the pathogenesis of several diseases and hence are the objective of numerous investigations. Glycation of proteins has been an implication in long-term complications. Collagen is the most abundant protein in the human body. The purpose of this study was to monitor and characterize the oligomeric aggregates and AGEs of human collagen on addition of glyoxal using ultraviolet, fluorescence, circular dichroism (CD) spectroscopy, docking studies, ITC, and microscopy. Collagen was incubated for varying time periods up to 21 days with three different concentrations (5, 20, and 40 mM) of glyoxal. Collagen exists as molten globule at day 6, evident from native-like secondary structure, altered tryptophan, and high ANS fluorescence due to surface-exposed hydrophobic residues. Glycated collagen as AGEs and aggregates was observed at day 18 and 21, respectively. Formation of AGE and aggregates were confirmed by UV and fluorescence spectroscopy. The obtained AGEs were characterized with respect to the extent of side chain modifications (lysine and arginine) forming the Schiff base, the carboxymethyl lysine, and carbonyl content. Non-tryptophan fluorescence for AGEs was also monitored as the emission peak at 400 and 440 nm, respectively. SEM and TEM confirmed the oligomeric nature of aggregates. Glyoxal at 40 mM shows maximum alterations in protein structure followed by 20 and 5 mM concentration. In the present paper, we propose that a high concentration of glyoxal for a prolonged time results in the formation of harmful aggregates and AGEs.

Deciphering aggregates, prefibrillar oligomers and protofibrils of cytochrome c.

Aggregation of protein into insoluble intracellular complexes and inclusion bodies underlies the pathogenesis of human neurodegenerative diseases. Importance of cytochrome c (cyt c) arises from its involvement in apoptosis, sequence homology and for studying molecular evolution. A systemic investigation of polyethylene glycol (PEG) and trifluoroethanol (TFE) on the conformational stability of cyt c as a model hemeprotein was made using multi-methodological approach. Cyt c exists as molten globule (MG) at 60% PEG-400 and 40% TFE as confirmed by far-UV CD, attenuated total reflection Fourier transform infrared spectroscopy, Trp environment, 8-anilino-1-naphthalene-sulfonic acid (ANS) binding and blue shift in the soret band. Q-band splitting in MG states specifies conformational changes in the hydrophobic heme-binding pocket. Aggregates were detected at 90% PEG-400 and 50% TFE as confirmed by increase thioflavin T and ANS fluorescence and shift in Congo red absorbance. Detection of prefibrils and protofibrils at 90% PEG-400 and 50% TFE was possible after 72-h incubation. Single cell gel electrophoresis of prefibrils and protofibrils showed DNA damage confirming their toxicity and potential health hazards. Scanning electron microscopy and XRD analysis confirmed prefibrillar oligomers and protofibrils of cyt c.

An insight into the biophysical characterization of insoluble collagen aggregates: implication for arthritis.

Misfolding and aggregation of proteins is involved in some of the most prevalent neurodegenerative disorders. The importance of collagen stems from the fact that it is one of the dominant component used for tissue engineering and drug delivery applications and is a major component of skin, tendon, bone and other connective tissues. A systematic investigation on the conformation of collagen at various concentrations of glyoxal is studied by various biophysical techniques such as Trp fluorescence, ANS binding, Circular dichroism (CD), ATR-FTIR, Congo red (CR) assay, Rayleigh light scattering and Turbidity measurements. At 60% (v/v) glyoxal, collagen retains native-like secondary structure, altered Trp environment and high ANS fluorescence, characteristic of molten globule (MG) state. At 80% (v/v) glyoxal, insoluble collagen aggregates are detected as confirmed by decrease in Trp and ANS fluorescence, increase in non-native ß sheet structure as evident from far-UV CD and FTIR spectra, increase in Thioflavin T fluorescence, Rayleigh light scattering, Turbidity measurements, as well as red shift in CR absorbance.

Potassium bromate causes cell lysis and induces oxidative stress in human erythrocytes.

In the present study, we have studied the effect of KBrO3 on human erythrocytes under in vitro conditions. Erythrocytes were isolated from the blood of healthy nonsmoking volunteers and incubated with different concentrations of KBrO3 at 37°C for 60 min. This resulted in marked hemolysis in a KBrO3 -concentration dependent manner. Lysates were prepared from KBrO3 -treated and control erythrocytes and assayed for various parameters. KBrO3 treatment caused significant increase in protein oxidation, lipid peroxidation, hydrogen peroxide levels, and decrease in total sulfhydryl content, which indicates induction of oxidative stress in human erythrocytes. Methemoglobin levels and methemoglobin reductase activity were significantly increased while the total antioxidant power of lysates was greatly reduced upon KBrO3 treatment. Intracellular production of reactive oxygen species increased in a dose dependent manner. Exposure of erythrocytes to KBrO3 also caused decrease in the activities of catalase, glutathione peroxidase, thioredoxin reductase, glucose 6-phosphate dehydrogenase and glutathione reductase whereas the activities of Cu-Zn superoxide dismutase and glutathione-S-transferase were increased. These results show that KBrO3 induces oxidative stress in human erythrocytes through the generation of reactive oxygen species and alters the cellular antioxidant defense system.

Glycation promotes the formation of genotoxic aggregates in glucose oxidase.

This study investigates the effect of pentose sugars (ribose and arabinose) on the structural and chemical modifications in glucose oxidase (GOD) as well as genotoxic potential of this modified form. An intermediate state of GOD was observed on day 12 of incubation having CD minima peaks at 222 and 208 nm, characteristic of α-helix and a few tertiary contacts with altered tryptophan environment and high ANS binding. All these features indicate the existence of molten globule state of the GOD with ribose and arabinose on day 12. GOD on day 15 of incubation forms ß structures as revealed by CD and FTIR which may be due to its aggregation. Furthermore, GOD on day 15 showed a remarkable increase in Thioflavin T fluorescence at 485 nm. Comet assay of lymphocytes and plasmid nicking assay in presence of glycated GOD show DNA damage which confirmed the genotoxicity of advance glycated end products. Hence, our study suggests that glycated GOD results in the formation of aggregates and the advanced glycated end products, which are genotoxic in nature.

Potential drug targets of SARS-CoV-2: From genomics to therapeutics.

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from China has become a global threat due to the continuous rise in cases of Coronavirus disease 2019 (COVID-19). The problem with COVID-19 therapeutics is due to complexity of the mechanism of the pathogenesis of this virus. In this review, an extensive analysis of genome architecture and mode of pathogenesis of SARS-CoV-2 with an emphasis on therapeutic approaches is performed. SARS-CoV-2 genome consists of a single, ~29.9 kb long RNA having significant sequence similarity to BAT-CoV, SARS-CoV and MERS-CoV genome. Two-third part of SARS-Cov-2 genome comprises of ORF (ORF1ab) resulting in the formation of 2 polyproteins, pp1a and pp1ab, later processed into 16 smaller non-structural proteins (NSPs). The four major structural proteins of SARS-CoV-2 are the spike surface glycoprotein (S), a small envelope (E), membrane (M), and nucleocapsid (N) proteins. S protein helps in receptor binding and membrane fusion and hence plays the most important role in the transmission of CoVs. Priming of S protein is done by serine 2 transmembrane protease and thus plays a key role in virus and host cell fusion. This review highlights the possible mechanism of action of SARS-CoV-2 to search for possible therapeutic options.

Glycation With Fructose: The Bitter Side of Nature's Own Sweetener.

Fructose is a ketohexose and sweetest among all the natural sugars. Like other reducing sugars, it reacts readily with the amino- and nucleophilic groups of proteins, nucleic acids and other biomolecules resulting in glycation reactions. The non-enzymatic glycation reactions comprise Schiff base formation, their Amadori rearrangement followed by complex and partly incompletely understood reactions culminating in the formation of Advance Glycation End products (AGEs). The AGEs are implicated in complications associated with diabetes, cardiovascular disorders, Parkinson's disease, etc. Fructose is highly reactive and forms glycation products that differ both in structure and reactivity as compared to those formed from glucose. Nearly all tissues of higher organisms utilize fructose but only a few like the ocular lens, peripheral nerves erythrocytes and testis have polyol pathway active for the synthesis of fructose. Fructose levels rarely exceed those of glucose but, in tissues that operate the polyol pathway, its concentration may rise remarkably during diabetes and related disorders. Diet contributes significantly to the body fructose levels however, availability of technologies for the large scale and inexpensive production of fructose, popularity of high fructose syrups as well as the promotion of vegetarianism have resulted in a remarkable increase in the consumption of fructose. In vivo glycation reactions by fructose, therefore, assume remarkable significance. The review, therefore, aims to highlight the uniqueness of glycation reactions with fructose and its role in some pathophysiological situations.

Detergent induces the formation of IgG aggregates: a multi-methodological approach.

Role of micellar environment created by Triton X-100 (TX-100) and CHAPSO on protein conformation using IgG as a model system has been studied in this paper. A substantial amount of secondary structure with the reduction in constant tertiary contacts was obtained in both bovine and human IgG in the presence of 0.12 mM TX-100 where as 6 and 8 mM CHAPSO concentration was required for this type of secondary structure. Further addition of either of the detergents result in the induction of α-helix in both the IgGs as evident by helix specific peaks in the amide I region of FTIR and circular dichroism spectra. Tryptophan and 8-anilino-1-naphthalene-sulphonic acid (ANS) fluorescence confirmed changes in protein conformation upon addition of detergents. Maximum ANS binding at 0.12 mM TX-100 in both while 6 and 8 mM CHAPSO in bovine and human IgG respectively, indicate a compact ''molten-globule''-like conformation. An increase addition of these detergents results in the burial of hydrophobic patches of both IgG owing to aggregation. Presence of aggregates at 0.2 and 0.16 mM TX-100 and 8 and 9 mM CHAPSO, for bovine and human IgG respectively, was further confirmed by reduction in ANS fluorescence, dynamic light scattering study, thioflavin T fluorescence and congo red absorbance.

Deciphering structural intermediates and genotoxic fibrillar aggregates of albumins: a molecular mechanism underlying for degenerative diseases.

The misfolding and aggregation of proteins is involved in some of the most prevalent neurodegenerative disorders. The importance of human serum albumin (HSA) stems from the fact that it is involved in bio-regulatory and transport phenomena. Here the effect of acetonitrile (ACN) on the conformational stability of HSA and by comparison, ovalbumin (OVA) has been evaluated in the presence and absence of NaCl. The results show the presence of significant amount of secondary structure in HSA at 70% ACN and in OVA at 50% ACN, as evident from far-UV Circular Dichroism (CD) and Attenuated Total Reflection Fourier transformed infra red spectroscopy (ATR-FTIR). Tryptophan and 8-Anilino-1-Naphthalene-Sulphonic acid (ANS) fluorescence indicate altered tryptophan environment and high ANS binding suggesting a compact "molten globule"-like conformation with enhanced exposure of hydrophobic surface area. However, in presence of NaCl no intermediate state was observed. Detection of aggregates in HSA and OVA was possible at 90% ACN. Aggregates possess extensive ß-sheet structure as revealed by far-UV CD and ATR-FTIR. These aggregates exhibit increase Thioflavin T (Th T) fluorescence with a red shift of Congo red (CR) absorption spectrum. X-ray diffraction (XRD) and Scanning Electron Microscopy (SEM) analysis confirmed the presence of fibrillar aggregates. Single cell gel electrophoresis (SCGE) assay of these fibrillar aggregates showed the DNA damage resulting in cell necrosis confirming their genotoxic nature. Some proteins not related to any human disease form fibrils in vitro. In the present study ACN gives access to a model system to study the process of aggregation.

Detection and analysis of amorphous aggregates and fibrils of cytochrome c in the presence of phenolic acids.

Cytochrome c (cyt c) exists as a partially unfolded intermediate at 45 mM gallic acid (GA) possessing disrupted secondary structure, altered Trp environment and high ANS binding. Increasing the concentration of either GA or ferulic acid (FA) up to 50 mM results in cyt c aggregation as confirmed by shift in Congo red, increase thioflavin T, decrease ANS and Trp fluorescence. SEM confirmed the formation of fibrils and amorphous aggregates of cyt c in presence of 50 mM FA and GA respectively. Single cell gel electrophoresis establishes very less probability of this noble protein to cause misfolding and aggregation-prone diseases.

Equilibrium studies of cellulase aggregates in presence of ascorbic and boric acid.

The aggregate formation of cellulase was detected at 300 and 10 mM ascorbic and boric acid respectively. These aggregates showed reduced enzyme activity, loss in near-UV signal, decrease tryptophan and ANS fluorescence. They possess increase in non-native ß-sheet structure as evident from far-UV CD and FTIR spectra, large hydrodynamic radii, increase thioflavin T fluorescence and shift in Congo red. Cellulase at 90 mM ascorbic acid exists as molten globule with retention of secondary structure, altered tryptophan environment, high ANS binding and loss in tertiary structure. Ascorbic acid acts as an antioxidant up to 90 mM and beyond this as a pro-oxidant.

Acetonitrile can promote formation of different structural intermediate states on aggregation pathway of immunoglobulin G from human and bovine.

A sequential addition of acetonitrile to human and bovine immunoglobulin G induces molten globule-like state at 50% (v/v) and 60% (v/v) respectively having secondary structure similar to native protein as evident from far-UV circular dichroism and Fourier transform infra red spectroscopy. Further addition of acetonitrile up to 80% forms aggregate of IgG as confirmed by increase in thioflavin T, loss of signals in near-UV CD spectra, decrease in ANS and tryptophan fluorescence. Thus at high acetonitrile concentration, a relatively large amount of partially unfolded intermediates of IgG are present which result in aggregates formation.