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"Javed, Saleem"
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Investigating binding dynamics of trans resveratrol to HSA for an efficient displacement of aflatoxin B1 using spectroscopy and molecular simulation
2022
Resveratrol is a polyphenol belonging to the class stilbenes. The active and stable form of resveratrol is
trans
-resveratrol. This polyphenol is bestowed with numerous biological properties. Aflatoxin B
1
is a hepato-carcinogen and mutagen that is produced by
Aspergillus
species. In this study, the interaction of
trans
-resveratrol with HSA followed by competitive dislodging of AFB
1
from HSA by
trans-
resveratrol has been investigated using spectroscopic studies. The UV-absorption studies revealed ground state complex formation between HSA and
trans
-resveratrol.
Trans
-resveratrol binds strongly to HSA with the binding constant of ~ 10
7
M
−1
to a single binding site (n = 1.58), at 298.15 K. The Stern–Volmer quenching constant was calculated as 7.83 × 10
4
M
−1
at 298.15 K, suggesting strong fluorescence quenching ability of
trans
-resveratrol. Site markers displacement assay projected subdomain IIA as the binding site of
trans
-resveratrol to HSA. The molecular docking approach envisages the amino acid residues involved in the formation of the binding pocket. As confirmed from the site marker displacement assays, both
trans
-resveratrol and AFB
1
binds to HSA in the same binding site, subdomain IIA. The study explores the ability of
trans
-resveratrol to displace AFB
1
from the HSA-AFB
1
complex, thereby affecting the toxicokinetic behavior of AFB
1
associated with AFB
1
exposure.
Journal Article
Biochemical Characterization of Cellulase From Bacillus subtilis Strain and its Effect on Digestibility and Structural Modifications of Lignocellulose Rich Biomass
by
Malik, Waseem Ayoub
,
Javed, Saleem
in
Bioengineering and Biotechnology
,
biofuels
,
carboxymethyl cellulose
2021
Microbial cellulases have become the mainstream biocatalysts due to their complex nature and widespread industrial applications. The present study reports the partial purification and characterization of cellulase from Bacillus subtilis CD001 and its application in biomass saccharification. Out of four different substrates, carboxymethyl cellulose, when amended as fermentation substrate, induced the highest cellulase production from B. subtilis CD001. The optimum activity of CMCase, FPase, and amylase was 2.4 U/ml, 1.5 U/ml, and 1.45 U/ml, respectively. The enzyme was partially purified by (NH 4 ) 2 SO 4 precipitation and sequenced through LC-MS/MS. The cellulase was found to be approximately 55 kDa by SDS-PAGE and capable of hydrolyzing cellulose, as confirmed by zymogram analysis. The enzyme was assigned an accession number AOR98335.1 and displayed 46% sequence homology with 14 peptide-spectrum matches having 12 unique peptide sequences. Characterization of the enzyme revealed it to be an acidothermophilic cellulase, having an optimum activity at pH 5 and a temperature of 60°C. Kinetic analysis of partially purified enzyme showed the Km and Vmax values of 0.996 mM and 1.647 U/ml, respectively. The enzyme activity was accelerated by ZnSO 4, MnSO 4, and MgSO 4, whereas inhibited significantly by EDTA and moderately by β-mercaptoethanol and urea. Further, characterization of the enzyme saccharified sugarcane bagasse, wheat straw, and filter paper by SEM, ATR-FTIR, and XRD revealed efficient hydrolysis and structural modifications of cellulosic materials, indicating the potential industrial application of the B. subtilis CD001 cellulase. The findings demonstrated the potential suitability of cellulase from B. subtilis CD001 for use in current mainstream biomass conversion into fuels and other industrial processes.
Journal Article
Silver nanoparticles synthesized using leaf extract of Azadirachta indica exhibit enhanced antimicrobial efficacy than the chemically synthesized nanoparticles
by
Khan, Kashan
,
Javed, Saleem
in
Anti-Bacterial Agents - pharmacology
,
Anti-Infective Agents - pharmacology
,
Antiinfectives and antibacterials
2021
A wide variety of methods have synthesized silver nanoparticles (Ag-NPs) in the recent past; however, biological methods have attracted much attention over the traditional chemical synthesis method due to being non-hazardous and eco-friendly. Here, a detailed and systemic study was performed to compare two different synthesis routes for Ag-NPs, that is, the chemical and the biological; their possible outcomes have also been described. Ag-NPs were synthesized chemically (cAg-NPs) using a chemical reductant and biologically (bAg-NPs) by using aqueous leaf extract of Azadirachta indica (neem). The synthesized nanoparticles were characterized using UVvisible spectrophotometry, FT-IR, EDX, and TEM. The average particle sizes (APS) of cAg-NPs were found to be 8 and 13nm and of bAg-NPs to be 19 and 43nm under different AgNO₃ concentrations. The antimicrobial tests of differently sized NPs were performed against Escherichia coli (Gram −ve) and Staphylococcus aureus (Gram + ve). The results revealed that bAg-NPs of APS 43 nm were highly antimicrobial against both the tested bacterial stains followed by cAg-NPs of 8 nm. We found the effect of cAg-NPs to be size-dependent, whereas bAg-NPs showed a more significant antimicrobial effect than cAg-NPs.
Journal Article
Crystal Structure, Topology, DFT and Hirshfeld Surface Analysis of a Novel Charge Transfer Complex (L3) of Anthraquinone and 4-{(anthracen-9-yl)meth-yl amino}-benzoic Acid (L2) Exhibiting Photocatalytic Properties: An Experimental and Theoretical Approach
by
Ahmed, Adeeba
,
Ahmad, Musheer
,
Javed, Saleem
in
Chemistry
,
Crystal structure
,
crystal studies
2022
Here, we report a facile route to the synthesizing of a new donor-acceptor complex, L3, using 4-{[(anthracen-9-yl)meth-yl] amino}-benzoic acid, L2, as donor moiety with anthraquinone as an acceptor moiety. The formation of donor-acceptor complex L3 was facilitated via H-bonding and characterized by single-crystal X-ray diffraction. The X-ray diffraction results confirmed the synthesized donor-acceptor complex L3 crystal belongs to the triclinic system possessing the P-1 space group. The complex L3 was also characterized by other spectral techniques, viz., FTIR and UV absorption spectroscopy, which confirmed the formation of new bonds between donor L2 moiety and acceptor anthraquinone molecule. The crystallinity and thermal stability of the newly synthesized complex L3 was confirmed by powdered XRD and TGA analysis and theoretical studies; Hirshfeld surface analysis was performed to define the type of interactions occurring in the complex L3. Interestingly, theoretical results were successfully corroborated with experimental results of FTIR and UV absorption. The density functional theory (DFT) calculations were employed for HOMO to LUMO; the energy gap (∆E) was calculated to be 3.6463 eV. The complex L3 was employed as a photocatalyst for the degradation of MB dye and was found to be quite efficient. The results showed MB dye degraded about 90% in 200 min and followed the pseudo-first-order kinetic with rate constant k = 0.0111 min
and R
= 0.9596. Additionally, molecular docking reveals that the lowest binding energy was -10.8 Kcal/mol which indicates that the L3 complex may be further studied for its biological applications.
Journal Article
Numerical analysis of electrochemically radiative and higher thermally conductive nanomaterials spinning motion due to rotating disk
2025
Optimization of heat and mass transfer via higher thermally conductive generalized nonlinear materials namely, the Cross fluid is one of the major contributions of this work. This particular work is further analyzed effectively in the presence of linear reactions as well as solar radiation. The flow configuration is assumed with anticlockwise rotation which guarantees more heat transfer as compared to the linear or translator motion of such materials. Specifically, the generalized concept of Brownian motion as well as thermophoretic forces are utilized in the swirling motion of shear rate-dependent viscosity material which plays a significant role in science and industries. However, an enhancement in the conduction is caused by the non-uniform nanoparticle concentration and this is due to the involvement of the thermo diffusion phenomenon. Moreover, the probability of an extra degree of freedom to the heat equation is reduced by the introduction of the radiation which alternately provided a significant contribution to the thermal conductivity maximization. Additionally, the appearance of linear reaction in the concentration equation is a foundation that is based on the first-order apparent kinetics is one of the hydrolysis of the anticancer cisplatin drugs. Mathematical equations are developed and then solved by using one of the modified collocation methods. The time relaxation constant reduced the pressure and enhanced the rotational flow speed. The reduction in pedesis and radiation caused enhancement in the pressure and temperature. As the first-order reaction rate increases, the material concentration decreases, while radiation enhances the heat transfer rate. The Schmidt number effectively reduces the mass flow rate, whereas the reaction rate enhances it. The entire scheme is validated by providing a well-matched comparison.
Journal Article
Chitinases: An update
2013
Chitin, the second most abundant polysaccharide in nature after cellulose, is found in the exoskeleton of insects, fungi, yeast, and algae, and in the internal structures of other vertebrates. Chitinases are enzymes that degrade chitin. Chitinases contribute to the generation of carbon and nitrogen in the ecosystem. Chitin and chitinolytic enzymes are gaining importance for their biotechnological applications, especially the chitinases exploited in agriculture fields to control pathogens. Chitinases have a use in human health care, especially in human diseases like asthma. Chitinases have wide-ranging applications including the preparation of pharmaceutically important chitooligosaccharides and N-acetyl D glucosamine, preparation of single-cell protein, isolation of protoplasts from fungi and yeast, control of pathogenic fungi, treatment of chitinous waste, mosquito control and morphogenesis, etc. In this review, the various types of chitinases and the chitinases found in different organisms such as bacteria, plants, fungi, and mammals are discussed.
Journal Article
Optimization of Fermentation Parameters for Higher Lovastatin Production in Red Mold Rice through Co-culture of Monascus purpureus and Monascus ruber
2010
Monascus, fermented rice (red mold rice), has been found to reduce the serum total cholesterol and triglyceride due to presence of lovastatin. Lovastatin acts as an inhibitor of 3-hydroxy-3-methyl glutaryl coenzyme A reductase. Coculture of Monascus purpureus MTCC 369 and Monascus ruber MTCC 1880 was used to produce red mold rice by solid-state fermentation. Optimization of different fermentation process parameters such as temperature, fermentation time, inoculum volume, and pH of the solid medium was carried out by Box-Behnken's factorial design of response surface methodology to maximize lovastatin concentration in red mold rice. Maximum lovastatin production of 2.83 mg/g was predicted at 14th day in solid medium under optimized process condition.
Journal Article
Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV–Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)
2023
For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule’s 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV–Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule’s charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO–LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.
Journal Article
Optimization of nutrient parameters for lovastatin production by Monascus purpureus MTCC 369 under submerged fermentation using response surface methodology
by
Panda, Bibhu Prasad
,
Sayyad, Sadik Ali
,
Ali, Mohd
in
Ammonium chloride
,
Biological and medical sciences
,
biosynthesis
2007
Lovastatin, an inhibitor of HMG-CoA reductase, was produced by submerged fermentation using Monascus purpureus MTCC 369. Five nutritional parameters screened using Plackett-Burman experimental design were optimized by Box-Behnken factorial design of response surface methodology for lovastatin production in shake flask cultures. Maximum lovastatin production of 351 mg/l were predicted in medium containing 29.59 g/l dextrose, 3.86 g/l NH₄Cl, 1.73 g/l KH₂PO₄, 0.86 g/l MgSO₄·7H₂O, and 0.19 g/l MnSO₄·H₂O using response surface plots and point prediction tool of DESIGN EXPERT 7.0 (Statease, USA) software.
Journal Article
Vibrational Spectroscopy, Quantum Computational and Molecular Docking Studies on 2-(1H-Benzimidazol-1-yl)-methylbenzoic Acid
2022
Experimental and theoretical investigations on the optimized geometrical structure, electronic and vibrational features of 2-[(1H-benzimidazol-1-yl)-methyl]benzoic acid are provided using the B3LYP/6-311++G(d,p) basis set. The Vibrational Energy Distribution Analysis (VEDA) program was used to perform the vibrational assignments and calculate the Potential Energy Distribution (PED). The acquired FT-IR and FT Raman data were used to complete the vibrational assignment and characterization of the compound fundamental modes. Theoretical and actual NMR chemical shifts were found to be quite similar. The UV-vis spectrum of 21HBMBA, as well as effects of solvents, have been investigated. The calculated HOMO and LUMO energies reveal that charge transfer happens within the molecule and MEP surface to be a chemically reactive area appropriate for drug action. Furthermore, a thorough examination of Non-Bonding Orbitals, excitation energies, AIM charges, Fukui functions and the Electron Localization Function (ELF) is carried out. The research is also expanded to compute first-order hyperpolarizability and forecast NLO characteristics. The details of the docking studies aided in the prediction of protein binding.
Journal Article