Jasdeep Singh

The DNA intercalators ethidium bromide and propidium iodide also bind to core histones

Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non‐histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA‐interactive small molecules may bind to chromatin‐associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB) and its structural analogue propidium iodide (PI) with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post‐translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones) property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.

Fluorescence Spectroscopic and Calorimetry Based Approaches to Characterize the Mode of Interaction of Small Molecules with DNA

Ethidium bromide displacement assay by fluorescence is frequently used as a diagnostic tool to identify the intercalation ability of DNA binding small molecules. Here we have demonstrated that the method has pitfalls. We have employed fluorescence, absorbance and label free technique such as isothermal titration calorimetry to probe the limitations. Ethidium bromide, a non-specific intercalator, netropsin, a (A-T) specific minor groove binder, and sanguinarine, a (G-C) specific intercalator, have been used in our experiments to study the association of a ligand with DNA in presence of a competing ligand. Here we have shown that netropsin quenches the fluorescence intensity of an equilibrium mixture of ethidium bromide - calf thymus DNA via displacement of ethidium bromide. Isothermal titration calorimetry results question the accepted interpretation of the observed decrease in fluorescence of bound ethidium bromide in terms of competitive binding of two ligands to DNA. Furthermore, isothermal titration calorimetry experiments and absorbance measurements indicate that the fluorescence change might be due to formation of ternary complex and not displacement of one ligand by another.

Polyphenols in combination with β-cyclodextrin can inhibit and disaggregate α-synuclein amyloids under cell mimicking conditions: A promising therapeutic alternative

Parkinsons disease is characterized by the presence of insoluble and neurotoxic aggregates (amyloid fibrils) of an intrinsically disordered protein α-synuclein. In this study we have examined the effects of four naturally occurring polyphenols in combination with β-cyclodextrin (β-CD) on the aggregation of α-synuclein in the presence of macromolecular crowding agents. Our results reveal that even at sub-stoichiometric concentrations of the individual components, the polyphenol-β-CD combination(s) not only inhibited the aggregation of the proteins but was also effective in disaggregating preformed fibrils. Curcumin was found to be the most efficient, followed by baicalein with (-)-epigallocatechin gallate and resveratrol coming in next, the latter two exhibiting very similar effects. Our results suggest that the efficiency of curcumin results from a balanced composition of the phenolic OH groups, benzene rings and flexibility. The latter ensures proper positioning of the functional groups to maximize the underlying interactions with both the monomeric form of α-synuclein and its aggregates. The uniqueness of β-CD was reinforced by the observation that none of the other cyclodextrin variants [α-CD and HP-β-CD] used was as effective, in spite of these possessing better water solubility. Moreover, the fact that the combinations remained effective under conditions of macromolecular crowding suggests that these have the potential to be developed into viable drug compositions in the near future. MTT assays on cell viability independently confirmed this hypothesis wherein these combinations (and the polyphenols alone too) appreciably impeded the toxicity of the prefibrillar α-synuclein aggregates on the mouse neuroblastoma cell lines (N2a cells).

Arjunolic acid, a peroxisome proliferator-activated receptor α agonist, regresses cardiac fibrosis by inhibiting non-canonical TGF-β signaling

Cardiac hypertrophy and associated heart fibrosis remain a major cause of death worldwide. Phytochemicals have gained attention as alternative therapeutics for managing cardiovascular diseases. These include the extract from the plant Terminalia arjuna, which is a popular cardioprotectant and may prevent or slow progression of pathological hypertrophy to heart failure. Here, we investigated the mode of action of a principal bioactive T. arjuna compound, arjunolic acid (AA), in ameliorating hemodynamic load-induced cardiac fibrosis and identified its intracellular target. Our data revealed that AA significantly represses collagen expression and improves cardiac function during hypertrophy. We found that AA binds to and stabilizes the ligand-binding domain of peroxisome proliferator-activated receptor α (PPARα) and increases its expression during cardiac hypertrophy. PPARα knockdown during AA treatment in hypertrophy samples, including angiotensin II-treated adult cardiac fibroblasts and renal artery-ligated rat heart, suggests that AA-driven cardioprotection primarily arises from PPARα agonism. Moreover, AA-induced PPARα up-regulation leads to repression of TGF-β signaling, specifically by inhibiting TGF-β-activated kinase1 (TAK1) phosphorylation. We observed that PPARα directly interacts with TAK1, predominantly via PPARα N-terminal transactivation domain (AF-1) thereby masking the TAK1 kinase domain. The AA-induced PPARα-bound TAK1 level thereby shows inverse correlation with the phosphorylation level of TAK1 and subsequent reduction in p38 MAPK and NF-κBp65 activation, ultimately culminating in amelioration of excess collagen synthesis in cardiac hypertrophy. In conclusion, our findings unravel the mechanism of AA action in regressing hypertrophy-associated cardiac fibrosis by assigning a role of AA as a PPARα agonist that inactivates non-canonical TGF-β signaling.

L-Asparaginase of Leishmania donovani: Metabolic target and its role in Amphotericin B resistance

Emergence of Amphotericin B (AmB) resistant Leishmania donovani has posed major therapeutic challenge against the parasite. Consequently, combination therapy aimed at multiple molecular targets, based on proteome wise network analysis has been recommended. In this regard we had earlier identified and proposed L-asparaginase of Leishmania donovani (LdAI) as a crucial metabolic target. Here we report that both LdAI overexpressing axenic amastigote and promastigote forms of L. donovani survives better when challenged with AmB as compared to wild type strain. Conversely, qRT-PCR analysis showed an upregulation of LdAI in both forms upon AmB treatment. Our data demonstrates the importance of LdAI in imparting immediate protective response to the parasite upon AmB treatment. In the absence of structural and functional information, we modeled LdAI and validated its solution structure through small angle X-ray scattering (SAXS) analysis. We identified its specific inhibitors through ligand and structure-based approach and characterized their effects on enzymatic properties (Km, Vmax, Kcat) of LdAI. We show that in presence of two of the inhibitors L1 and L2, the survival of L. donovani is compromised whereas overexpression of LdAI in these cells restores viability. Taken together, our results conclusively prove that LdAI is a crucial metabolic enzyme conferring early counter measure against AmB treatment by Leishmania.

Modulation of prion polymerization and toxicity by rationally designed peptidomimetics

Misfolding and aggregation of cellular prion protein is associated with a large array of neurological disorders commonly called the transmissible spongiform encephalopathies. Designing inhibitors against prions has remained a daunting task owing to limited information about mechanism(s) of their pathogenic self-assembly. Here, we explore the anti-prion properties of a combinatorial library of bispidine-based peptidomimetics (BPMs) that conjugate amino acids with hydrophobic and aromatic side chains. Keeping the bispidine unit unaltered, a series of structurally diverse BPMs were synthesized and tested for their prion-modulating properties. Administration of Leu- and Trp-BPMs delayed and completely inhibited the amyloidogenic conversion of human prion protein (HuPrP), respectively. We found that each BPM induced the HuPrP to form unique oligomeric nanostructures differing in their biophysical properties, cellular toxicities and response to conformation-specific antibodies. While Leu-BPMs were found to stabilize the oligomers, Trp-BPMs effected transient oligomerization, resulting in the formation of non-toxic, non-fibrillar aggregates. Yet another aromatic residue, Phe, however, accelerated the aggregation process in HuPrP. Molecular insights obtained through MD (molecular dynamics) simulations suggested that each BPM differently engages a conserved Tyr 169 residue at the α2-β2 loop of HuPrP and affects the stability of α2 and α3 helices. Our results demonstrate that this new class of molecules having chemical scaffolds conjugating hydrophobic/aromatic residues could effectively modulate prion aggregation and toxicity.

The Gelsolin Pathogenic D187N Mutant Exhibits Altered Conformational Stability and Forms Amyloidogenic Oligomers

Gelsolin is an actin-severing protein that attains an open functional conformation in the presence of Ca2+ or low pH. Mutations (D187N/Y) in the second domain of gelsolin trigger the proteolytic pathway producing amyloidogenic fragments that form the pathological hallmark of gelsolin amyloidosis and lattice corneal dystrophy type 2 (LCD2). Here, we show that the D187N mutant gelsolin in a Ca2+ depleted, low pH-activated, open conformation could assemble into amyloidogenic oligomers without necessarily undergoing the specific proteolytic step. Although both wild-type (WT) and mutant proteins exhibit closely overlapping globular shapes at physiological conditions, the latter exhibits subjugated actin depolymerization, loss of thermodynamic stability, and folding cooperativity. Mutant gelsolin displayed aberrant conformational unwinding and formed structural conformers with high associative properties at low pH conditions. A SAXS intensity profile and Guinier analysis of these conformers showed the formation of unusual, higher order aggregates. Extended incubation at low pH resulted in the formation of thioflavin T and Congo red positive, β-sheet rich aggregates with a fibrillar, amyloid-like morphology visible under electron and atomic force microscopy. Mass spectrometric analysis of disaggregated end-stage fibrils displayed peptide fragments encompassing the entire protein sequence, indicating the involvement of full length mutant gelsolin in fibril formation. Atomistic and REMD simulations indicated a larger increase in solvent accessibility and loss of fold architecture in mutant gelsolin at low pH as compared to WT gelsolin. Our findings support the existence of a secondary oligomerization-dependent aggregation pathway associated with gelsolin amyloidosis and can pave the way for better therapeutic strategies.

DNA intercalators as amyloid assembly modulators: mechanistic insights

Amyloid assemblies are stabilized through inter-molecular H-bonding with initial structural organizations governed by extensive hydrophobic and π-stacking interactions. Apparently, the structural integrity and stability of DNA duplexes are also governed by a cooperative balance of similar interactions. Structural perturbations in both amyloids and DNA by planar molecules or intercalators essentially rely on their ability to interfere with this balance. However, poor information on amyloid interference mechanisms by intercalators has subjected researchers to undertake random trials with such anti-amyloidogenic agents. Here, we employed four different classes of DNA intercalators to investigate if their non-native, hetero-aromatic associations could modulate the amyloid aggregation pathway. We utilized micro-second scale MD simulations using the steric-zipper structure of the diabetes associated amylin fragment to identify such associations and their plausible role in subjugating higher order assemblies. The simulation estimates were experimentally validated and extended to other disease-associated amyloid systems including gelsolin, prion and lysozyme. We find that the intercalators essentially stabilize monomeric and prefibrillar assemblies, reducing their ability to transform into structured supramolecular structures. Our results conclusively establish the dominant role of aromatic-associations in diverting the course of the amyloid assembly process at the expense of stabilizing H-bonding networks. Overall this report presents comprehensive experimental and theoretical insights on the regulation of amyloidogenesis by aromatic planar moieties.

Identification and validation of l-asparaginase as a potential metabolic target against Mycobacterium tuberculosis : KATARIA et al.

Multidrug‐resistant Mycobacterium tuberculosis (Mtb) has emerged as a major health challenge, necessitating the search for new molecular targets. A secretory amidohydrolase, l‐asparaginase of Mtb (MtA), originally implicated in nitrogen assimilation and neutralization of acidic microenvironment inside human alveolar macrophages, has been proposed as a crucial metabolic enzyme. To investigate whether this enzyme could serve as a potential drug target, it was studied for structural details and active site–specific inhibitors were tested on cultured Mycobacterial strain. The structural details of MtA obtained through comparative modeling and molecular dynamics simulations provided insights about the orchestration of an alternate reaction mechanism at the active site. This was contrary to the critical Tyr flipping mechanism reported in other asparaginases. We report the novel finding of Tyr to Val replacement in catalytic triad I along with the structural reorganization of a β‐hairpin loop upon substrate binding in MtA active site. Further, 5 MtA‐specific, active‐site–based inhibitors were obtained by following a rigorous differential screening protocol. When tested on Mycobacterium culture, 3 of these, M3 (ZINC 4740895), M26 (ZINC 33535), and doxorubicin showed promising results with inhibitory concentrations (IC 50) of 431, 100, and 56 µM, respectively. Based on our findings and considering stark differences with human asparaginase, we project MtA as a promising molecular target against which the selected inhibitors may be used to counteract Mtb infection effectively.