Faizan Abul Qais

Multi-spectroscopic and molecular modelling approach to investigate the interaction of riboflavin with human serum albumin

Riboflavin (RF) plays an important role in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Human serum albumin (HSA) is an important protein involved in the transportation of drugs, hormones, fatty acid and other molecules which determine the biodistribution and physiological fate of these molecules. In this study, we have investigated the interaction of riboflavin RF with HSA under simulative physiological conditions using various biophysical, calorimetric and molecular docking techniques. Results demonstrate the formation of riboflavin–HSA complex with binding constant in the order of 104 M−1. Fluorescence spectroscopy confirms intermediate strength having a static mode of quenching with stoichiometry of 1:1. Experimental results suggest that the binding site of riboflavin mainly resides in sub-domain IIA of HSA and that ligand interaction increases the α-helical content of HSA. These parameters were further verified by isothermal titration calorimetry ITC which confirms the thermodynamic parameters obtained by fluorescence spectroscopy. Molecular docking was employed to suggest a binding model. Based on thermodynamic, spectroscopic and computational observations it can be concluded that HSA-riboflavin complex is mainly stabilized by various non-covalent forces with binding energy of −7.2 kcal mol−1.

Understanding the mechanism of non-enzymatic glycation inhibition by cinnamic acid: an in vitro interaction and molecular modelling study

Under hyperglycaemic conditions non-enzymatic glycation of proteins gives rise to advanced glycation end products (AGEs). The AGEs thus formed generate free radicals, which foster the development of diabetes and its associated complications. Inhibition of glycation is expected to play a role in controlling diabetes. Plant derived antioxidants like cinnamic acid (CA) are known for limiting AGE formation, however, the mechanism involved is poorly understood. Therefore, we aimed to investigate the possible mechanism of inhibition of AGEs formation by CA through various experimental approaches. Glycation of HSA was achieved by incubating the reaction mixture with glucose for 30 days at 37 °C. The protein samples were tested for levels of free lysine & thiol groups, carbonyl content and reactive oxygen species (ROS). Interaction between CA and HSA was also studied through various biophysical techniques. Thermodynamic studies showed a strong exothermic interaction between CA and HSA. The positive value of TΔS° and negative value of ΔH° indicates that the HSA–CA complex is mainly stabilized by a hydrophobic interaction and hydrogen bond. Further, molecular docking reveals that CA binds to HSA subdomain IIA (Sudlows site I) with a binding energy of −7.0 kcal mol−1, nearly the same as obtained in isothermal titration calorimetry (ITC) and fluorescence spectroscopy. The results of various spectroscopic techniques along with molecular docking and examination of many biomarkers highlights the role of CA in preventing disease progression.

Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study

Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waals forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted.

Unraveling the thermodynamics, binding mechanism and conformational changes of HSA with chromolyn sodium: Multispecroscopy, isothermal titration calorimetry and molecular docking studies

Cromolyn sodium is an anti-allergic drug effective for treatment in asthma and allergic rhinitis. In this project, interaction of chromolyn sodium (CS) with human serum albumin (HSA) has been investigated by various techniques such as UV-vis, fluorescence, circular dichorism (CD), fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetric (ITC) and molecular docking. The fluorescence quenching results revealed that there was static quenching mechanism in the interactions of CS with HSA. The binding constant (Kb), enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy change (ΔG°) were calculated. The negative values of TΔS° and ΔH° obtained from fluorescence spectroscopy and isothermal titration calorimetry, indicate that hydrogen bonding and van der Waals forces played major role in the binding process and the reaction is exothermic in nature. The binding constant (Kb) was found to be in the order of 104M-1 which depicts a good binding affinity of CS towards HSA. The conformational changes in the HSA due to interaction of CS were investigated from CD and FT-IR spectroscopy. The binding site of CS in HSA was sub-domain IIA as evident from site probing experiment and molecular docking studies.

In vitro interaction of cefotaxime with calf thymus DNA: Insights from spectroscopic, calorimetric and molecular modelling studies

HighlightsWe have found that cefotaxime interacts to minor groove of DNA.The values of banding constants show a direct interaction between cefotaxime and DNA.This complexation reaction was found to be spontaneous, thermodynamically favourable and enthalpy driven.The binding of cefotaxime provides stability to DNA that might contribute in its DNA protection. ABSTRACT Cefotaxime is third generation antibiotic with known therapeutic efficacy against bacterial infections including cerebral abscesses and bacterial meningitis. The &bgr;‐lactam group of drugs are considered safest antibiotics. Many antibiotics directly interact with DNA and alter their expression profile. Thus, it is necessary to understand the binding mode and its relevance to drug activity and toxicity. There is considerably a remarkable focus on deciphering the binding mechanism of these therapeutic agents as DNA is one of the major target for wide range of drugs. Cefotaxime has been extensively studied for its pharmacological properties while its binding mode to DNA has not been explicated so far. In this study, we have unveiled the binding mechanism of cefotaxime to DNA by using various biophysical, thermodynamic and in silico techniques. UV–vis spectroscopy confirmed the formation cefotaxime‐DNA complex along with a brief idea about the extent of interaction. Fluorescence spectroscopy yielded the values of various binding constants and explained mode of fluorescence quenching to be static. CD spectroscopy, thermal denaturation, KI quenching and viscosity measurement explained that cefotaxime is groove binder. Measuring the effect of ions on cefotaxime‐DNA complex ensured that it does not bind to DNA electrostatically. Dye displacement experiments finally confirmed that cefotaxime binds to the minor groove of DNA. ITC gave the thermodynamic profile of this binding in which negative value of Gibbs free energy change revealed that the process is spontaneous. Molecular modelling finally strengthened our experimental results that cefotaxime was located in curved contour of minor groove of DNA. The findings support on safety of drug and may have a little interference on normal biological functions.

Titanium dioxide nanoparticles preferentially bind in subdomains IB, IIA of HSA and minor groove of DNA

Titanium dioxide nanoparticles (TiO2-NPs) interaction with human serum albumin (HSA) and DNA was studied by UV–visible spectroscopy, spectrofluorescence, circular dichroism (CD), and transmission electron microscopy (TEM) to analyze the binding parameters and protein corona formation. TEM revealed protein corona formation on TiO2-NPs surface due to adsorption of HSA. Intrinsic fluorescence quenching data suggested significant binding of TiO2-NPs (avg. size 14.0 nm) with HSA. The Stern–Volmer constant (Ksv) was determined to be 7.6 × 102 M−1 (r2 = 0.98), whereas the binding constant (Ka) and number of binding sites (n) were assessed to be 5.82 × 102 M−1 and 0.97, respectively. Synchronous fluorescence revealed an apparent decrease in fluorescence intensity with a red shift of 2 nm at Δλ = 15 nm and Δλ = 60 nm. UV–visible analysis also provided the binding constant values for TiO2-NPs–HSA and TiO2-NPs-DNA complexes as 2.8 × 102 M−1 and 5.4 × 103 M−1. The CD data demonstrated loss in α-helicity of HSA and transformation into β-sheet, suggesting structural alterations by TiO2-NPs. The docking analysis of TiO2-NPs with HSA revealed its preferential binding with aromatic and non-aromatic amino acids in subdomain IIA and IB hydrophobic cavity of HSA. Also, the TiO2-NPs docking revealed the selective binding with A-T bases in minor groove of DNA.

Nanoparticles as Quorum Sensing Inhibitor: Prospects and Limitations

The emergence and worldwide spread of multi-drug resistant bacterial pathogens and slow pace of drug discovery with novel mode of action has necessitated search for alternative or new strategies to combat bacterial infection. Targeting virulence and pathogenicity of pathogens controlled by quorum sensing (QS) is considered as a promising anti-infective drug target. Several molecules both natural and synthetic were reported to interfere quorum sensing and are potential candidates for anti-infective drugs. The inhibition of QS might successfully attenuate and eradicate the microbial pathogens in combination with host immune system. It is expected that QS inhibition will exert less selection pressure for development of resistance among pathogenic bacteria. The recent progress in nanobiotechnology have given a greater hope for the development of novel anti-QS agents/formulations with improved therapeutic potential, enhanced targeted delivery with lesser toxicity to host system. The improved action of nano-formulations is a fascinating ability compared to their bulk. Recently, nanoparticles such as metal nanoparticles are reported to exhibit promising anti-QS activity both in vitro and in vivo. Nanomaterials are also been tested as vehicle for targeted delivery of conventionally used antimicrobial agents. There is greater scope of manipulation in nano-based formulations according to desired needs making such therapeutic strategies more efficient. Of note, the risks associated with the application of nanoparticles in drug delivery, diagnostics, production of improved biocompatible material or preventing biofilm formation on medical devices, etc. are needed to be scrutinized. In this article, we have made an attempt to review the recent advancements in nanoparticle as anti-QS agents and progress made on nano-based formulations with promising prospects and limitations.

Quorum Sensing Interference by Natural Products from Medicinal Plants: Significance in Combating Bacterial Infection

Plant derived natural products and phytocompounds are known for their broad spectrum biological activities and are of great therapeutic value in traditional system of medicine. The role of medicinal plants and phytocompounds in the treatment of various diseases including bacterial infection are widely documented. Anti-infective compounds from medicinal plants may provide new drug leads. Bacterial cell to cell communication has been become attractive target for the development of novel anti-infective measures that do not rely on the use of antibiotics. Targeting Quorum sensing has been emerge as promising strategy to combat bacterial infections as it is unlikely to develop multidrug resistance pathogens since it does not impose any selection pressure. In this review, we have surveyed the recent literature available on plant extracts, essential oils and phytocompounds exhibiting anti-quorum sensing properties. Further, significance of phytocompounds to combat bacterial infections caused by MDR bacteria has been discussed.

Biofabrication of Zinc Oxide Nanoparticle from Ochradenus baccatus Leaves: Broad-Spectrum Antibiofilm Activity, Protein Binding Studies, and In Vivo Toxicity and Stress Studies

Biofilms are complex aggregation of cells that are embedded in EPS matrix. These microcolonies are highly resistant to drugs and are associated with various diseases. Biofilms have greatly affected the food safety by causing severe losses due to food contamination and spoilage. Therefore, novel antibiofilm agents are needed. This study investigates the antibiofilm and protein binding activity of zinc nanoparticles (ZnNPs) synthesized from leaf extract of Ochradenus baccatus. Standard physical techniques, including UV-visible spectroscopy Fourier transform infrared spectroscopy and X-ray diffraction and transmission electron microscopy, were used to characterize the synthesized OB-ZnNPs. Synthesized OB-ZnNPs demonstrated significant biofilm inhibition in human and food-borne pathogens (Chromobacterium violaceum, Escherichia coli, P. aeruginosa, Klebsiella pneumoniae, Serratia marcescens, and Listeria monocytogenes) at subinhibitory concentrations. OB-ZnNPs significantly reduced the virulence factors like violacein, prodigiosin, and alginate and impaired swarming migration and EPS production. OB-ZnNPs demonstrated efficient binding with HSA protein and no change in their structure or stability was observed. In addition, in vivo toxicity evaluation confirmed that OB-ZnNPs possessed no serious toxic effect even at higher doses. Moreover, they were found to have excellent antioxidant properties that can be employed in the fields of food safety and medicine. Hence, it is envisaged that the OB-ZnNPs can be used as potential nanomaterials to combat drug resistant bacterial infections and prevent contamination/spoilage of food.

Study of pyridoxamine against glycation and reactive oxygen species production in human serum albumin as model protein: An in vitro & ex vivo approach

Hyperglycaemia is considered to be a driving factor for advanced glycated end products (AGEs). Inhibiting the process of glycation play an important role in reducing the diabetes related complications. We have explored the glucose mediated glycation and antiglycation activity of pyridoxamine using human serum albumin (HSA). Protein was incubated with glucose for 28 days at physiological temperature to achieve glycation. Antiglycation activity was assessed by the estimation of carbonyl content, free lysine and AGE specific fluorescence. Molecular docking was used to study the interaction of pyridoxamine with HSA and to get a detailed understanding of binding sites and binding energy. Glycation was reduced by pyridoxamine to commendable levels which was evident by the quantification of free lysine and carbonyl content. Pyridoxamine treatment also prevented the loss in secondary structure induced by glycation. It has also emerged as the quencher of reactive oxygen species which lead to the protection of DNA from oxidative damage. Pyridoxamine was found to be located at subdomain IIA of HSA with binding energy of -5.6 kcal/mol. These results are high points in the antiglycation activity of pyridoxamine. Its antioxidant nature and antiglycation activity are proof of its potential in preventing disease progression in diabetes.