Bimlesh Ojha

Role of hydrophobic and polar interactions for BSA-amphiphile composites

To evaluate the role of hydrophobic and electrostatic or other polar interactions for protein-ligand binding, we have studied the interactions of bovine serum albumin (BSA) with 2-alkylmalonic acid and 2-alkylbenzimidazole amphiphiles having different head group and alkyl chain length. The binding affinity for the protein-amphiphile interactions is found to depend predominantly on the length of hydrocarbon chain, suggesting the crucial role of hydrophobic forces, supported by polar interactions at the protein surface. The BSA fluorescence exhibits appreciable hypsochromic shift along with a reduction in fluorescence intensity and mean lifetime upon binding with 2-alkylmalonic acid. UV-visible, steady state and time-resolved fluorescence measurements were performed to compare the effects of amphiphiles on BSA as a function of the amphiphiles head group and alkyl chain length.

A novel amphiphilic thiosemicarbazone derivative for binding and selective sensing of human serum albumin

The interaction of ligands and drug molecules with protein is of major interest in drug pharmacokinetics and pharmacodynamics. In this study, we synthesized a novel thiosemicarbazone-based amphiphilic molecule for selective binding and detection of human serum albumin (HSA) with significant increase in fluorescence intensity. The compound 5-(octyloxy) naphthalene substituted salicylaldehyde thiosemicarbazone was designed to interact with site I of HSA. The weak fluorescence of the probes in aqueous solution showed a dramatic increase in fluorescence intensity upon binding with HSA, while the responses to various other proteins and enzymes were negligible under similar experimental conditions. Changes in fluorescence intensity and formation of a new emission maximum of the compound in the presence of HSA as well as an increase in steady-state anisotropy values reflected well the nature of binding and location of the probe inside the protein environment.

Tuning the bactericidal repertoire and potency of quinoline-based amphiphiles for enhanced killing of pathogenic bacteria

The overwhelming challenge posed by drug-resistant pathogenic bacteria underscores the need for potent bactericidal agents, which exhibit broad-spectrum activity and a mode of action that does not favor development of resistance. In the present study we report the synthesis and bactericidal activity of structurally diverse quinoline-based amphiphiles, having a fluorescent head group and varying hydrophobic chain length. A structure-guided bactericidal efficacy and broad-spectrum activity of the amphiphiles was apparent in screening experiments against a panel of common pathogenic bacteria. Structure–function studies by fluorescence-based assays revealed that the charge and hydrophobic chain length of amphiphiles were key structural determinants that radically boosted the bactericidal activity. The most potent amphiphile N-methyl 8-dodecoxy quinolinium iodide (compound 6) exhibited a dose-dependent bactericidal activity on target pathogens and could even inhibit the growth of a presumptive methicillin-resistant S. aureus (MRSA) strain. Fluorescence-based mechanistic studies and transmission electron microscope (TEM) analysis indicated that the initial binding of compound 6 to bacteria probably involved electrostatic interaction, whereas the hydrophobic chain of the amphiphile promoted membrane insertion, which culminated in large scale membrane disruption and loss in cell viability. Although the bactericidal activity of compound 6 was independent of bacterial transmembrane potential, interaction of the amphiphile with pathogenic bacteria resulted in rapid dissipation of membrane potential. Interestingly, compound 6 displayed high antimicrobial selectivity and did not affect the viability of human HT-29 cells. It is envisaged that the therapeutic regime of the bactericidal scaffold of compound 6 can be further expanded by rational structural design for generating potent bactericidal agents.

A subtle interplay of C–H hydrogen bonds in complexation of anions of varied dimensionality by a nitro functionalized tripodal podand

The structural aspects of binding of halides (1 and 2), nitrate (3), perchlorate (4), trifluoroacetate (5) and hexafluorosilicate (6) with the protonated tripodal podand L are examined crystallographically. Anion binding with multiple receptor units is attributable entirely to the (NH)+⋯anion and multiple C–H⋯anion hydrogen bonding interactions in all six complexes. Protonation at the apical nitrogen and presence of nitro functionality renders the methylene and aryl hydrogen sufficiently acidic for their active participation in moderate to weak CH⋯anion interactions are noteworthy. All supramolecular networks of complexes 1–6 are guided by various non-convalent interactions, especially directional CH⋯Onitro hydrogen bonds and π-stacking interactions.

Positively Charged Chitosan and N-Trimethyl Chitosan Inhibit Aβ40 Fibrillogenesis

Amyloid fibrils, formed by aggregation of improperly folded or intrinsically disordered proteins, are closely related with the pathology of a wide range of neurodegenerative diseases. Hence, there is a great deal of interest in developing molecules that can bind and inhibit amyloid formation. In this regard, we have investigated the effect of two positively charged polysaccharides, chitosan (CHT) and its quarternary derivative N-trimethyl chitosan chloride (TMC), on the aggregation of Aβ40 peptide. Our aggregation kinetics and atomic force microscopy (AFM) studies show that both CHT and TMC exhibit a concentration-dependent inhibiting activity on Aβ40 fibrillogenesis. Systematic pH-dependent studies demonstrate that the attractive electrostatic interactions between the positively charged moieties in CHT/TMC and the negatively charged residues in Aβ40 play a key role in this inhibiting activity. The stronger inhibiting activity of TMC than CHT further suggests the importance of charge density of the polymer chain in interacting with Aβ40 and blocking the fibril formation. The possible interactions between CHT/TMC and Aβ40 are also revealed at the atomic level by molecular docking simulation, showing that the Aβ40 monomer could be primarily stabilized by electrostatic interactions with charged amines of CHT and quaternary amines of TMC, respectively. Binding of CHT/TMC on the central hydrophobic core region of Aβ40 peptide may be responsible for blocking the propagation of the nucleus to form fibrillar structures. These results suggest that incorporation of sugar units such as d-glucosamine and N-trimethyl-d-glucosamine into polymer structural template may serve as a new strategy for designing novel antiamyloid molecules.

Poly(4-styrenesulfonate) as an inhibitor of Aβ40 amyloid fibril formation.

The formation of amyloid, a cross-β-sheet fibrillar aggregate of proteins, is associated with a variety of neurodegenerative diseases. Amyloidogenic proteins such as β-amyloid (Aβ) are known to exist with a large amount of polyelectrolyte macromolecules in vivo. The exact nature of Aβ-polyelectrolyte interactions and their roles in Aβ-aggregation are largely unknown. In this regard, we report the inhibiting effect of an anionic polyelectrolyte poly(4-styrenesulfonate) (PSS) on the aggregation of Aβ40 peptide. The results demonstrate the strong inhibition potential of PSS on the aggregation of Aβ40 and imply the dominant role of hydrophobicity of the polyelectrolyte in reducing the propensity of Aβ40 amyloid formation. Additional studies with poly(vinyl sulfate) (PVS) and p-toluenesulfonate (PTS), which share similar charge density with PSS except the former lacking the nonpolar aromatic side chain and the latter the aliphatic hydrocarbon backbone, reveal that the presence of both aliphatic backbone and aromatic side chain group in PSS is essential for its Aβ-aggregation inhibition activity. The interactions involved in the Aβ40-PSS complex were further investigated using molecular dynamics (MD) simulation. Our results provide new insights into the structural interplay between polyelectrolytes and Aβ peptide, facilitating the ultimate understanding of amyloid formation in Alzheimers disease. The results should assist in developing novel polyelectrolytes as potential chemical tools to study amyloid aggregation.

Gold Nanoparticles as a Probe for Amyloid-β Oligomer and Amyloid Formation

The process of amyloid-β (Aβ) amyloid formation is pathologically linked to Alzheimers disease (AD). The identification of Aβ amyloids and intermediates that are crucial players in the pathology of AD is critical for exploring the underlying mechanism of Aβ aggregation and the diagnosis of the disease. Herein, we performed a gold nanoparticle (AuNP)-based study to detect the formation of Aβ amyloid fibrils and oligomers. Our results demonstrate that the intensity of the surface plasmon resonance (SPR) absorption band of the AuNPs is sensitive to the quantity of Aβ40 amyloids. This allows the SPR assay to be used for detection and semi-quantification of Aβ40 amyloids, and characterization of the kinetics of Aβ amyloid formation. Furthermore, our study demonstrates that the SPR band intensity of the AuNPs is sensitive to the presence of oligomers of both Aβ40 and an Aβ40 mutant, which forms more stable oligomers. The kinetics of the stable oligomer formation of the Aβ40 mutant can also be monitored following the SPR band intensity change of AuNPs. Our results indicate that this nanoparticle based method can be used for mechanistic studies of early protein self-assembly and fibrillogenesis.

2-Alkylmalonic Acid: Amphiphilic Chelator and a Potent Inhibitor of Metalloenzyme

The present investigation demonstrates the potential of 2-alkylmalonic acid amphiphile as inhibitor of metalloenzymes like Taq DNA polymerase and alpha-amylase. A dose-dependent inhibition of Taq DNA polymerase was observed when a polymerase chain reaction (PCR) was performed in the presence of amphiphiles while in the case of alpha-amylase the inhibition was found to be independent of the inhibitor concentration. Control experiments revealed that both the chelating as well as the amphiphilic nature of the inhibitor was essential for enzyme inhibition. The fluorescence intensity and lifetime of alpha-amylase were also found to decrease in the presence of the amphiphiles. Steady-state fluorescence quenching studies suggested that removal of the metal ion from the enzyme leads to a decrease in the solvent accessibility of tryptophans, indicating change in the tertiary structure of the protein. It is proposed that removal of metal ion from the active sites of the enzyme by the amphiphilic compound possibly leads to disruption of the native conformation of the enzyme which is responsible for loss of its activity.

Role of N-methyl-8-(alkoxy)quinolinium iodide in suppression of protein–protein interactions

AbstractThere is a great deal of interest in developing small molecule inhibitors of protein misfolding and aggregation due to a growing number of pathologic states known as amyloid disorders. In searching for alternative ways to reduce protein–protein interactions or to inhibit the amyloid formation, the inhibitory effects of cationic amphiphile viz. N-methyl-8-(alkoxy)quinolinium iodide on aggregation behaviour of hen egg white lysozyme (HEWL) at alkaline pH has been studied. Even though the compounds did not protect native HEWL from conformational changes, they were effective in diminishing HEWL amyloid formation, delaying both nucleation and elongation phases. It is likely that strong binding in the HEWL compound complex, raises the activation energy barrier for protein misfolding and subsequent aggregation, thereby retarding the aggregation kinetics substantially. Graphical AbstractCationic amphiphiles viz. N-methyl-8-(alkoxy)quinolinium iodide suppress the aggregation of HEWL. The control experiments show that the cationic head group as well as the aliphatic tail is indispensable for inhibition of aggregation process and removal of either head group or hydrocarbon chain obliterates its ability to do the same.