Sanjib Senapati

The functional B-conformation of DNA succumbs to the A-form at low water activity. Methods for room temperature DNA storage that rely upon ‘anhydro-biosis’, thus, often encounter the loss of DNA activity due to the B→A-DNA transition. Here, we show that ionic liquids, an emerging class of green solvents, can induce conformational transitions in DNA and even rescue the dehydrated DNA in the functional B-form. CD spectroscopic analyses not only reveal rapid transition of A-DNA in 78% ethanol medium to B-conformation in presence of ILs, but also the high resistance of IL-bound B-form to transit to A-DNA under dehydration. Molecular dynamics simulations show the unique ability of ILs to disrupt Na+ ion condensation and form ‘IL spine’ in DNA minor groove to drive the A→B transition. Implications of these findings range from the plausible use of ILs as novel anhydrobiotic DNA storage medium to a switch for modulating DNA conformational transitions.

Alzheimer's disease is a neurodegenerative disease that leads to irreversible neuronal damage. Senile plaques, composed of amyloid beta peptide, is the principal abnormal characteristic of the disease. Among the factors involved, the secretase enzymes, namely, α secretase, beta-site amyloid precursor protein-cleaving enzyme, β secretase, and γ secretase, hold consequential importance. Beta-site amyloid precursor protein-cleaving enzyme 1 is considered to be the rate-limiting factor in the production of amyloid beta peptide. Research supporting the concept of inhibition of beta-site amyloid precursor protein-cleaving enzyme activity as one of the effective therapeutic targets in the mitigation of Alzheimer's disease is well accepted. The identification of natural compounds, such as β -amyloid precursor protein-selective beta-site amyloid precursor protein-cleaving enzyme inhibitors, and the idea of compartmentalisation of the beta-site amyloid precursor protein-cleaving enzyme 1 action have caused a dire need to closely examine the natural compounds and their effectiveness in the disease mitigation. Many natural compounds have been reported to effectively modulate beta-site amyloid precursor protein-cleaving enzyme 1. At lower doses, compounds like 2,2′,4′-trihydroxychalcone acid, quercetin, and myricetin have been shown to effectively reduce beta-site amyloid precursor protein-cleaving enzyme 1 activity. The currently used five drugs that are marketed and used for the management of Alzheimer's disease have an increased risk of toxicity and restricted therapeutic efficiency, hence, the search for new anti-Alzheimer's disease drugs is of primary concern. A variety of natural compounds having pure pharmacological moieties showing multitargeting activity and others exhibiting specific beta-site amyloid precursor protein-cleaving enzyme 1 inhibition as discussed below have superior biosafety. Many of these compounds, which are isolated from medicinal herbs and marine flora, have been long used for the treatment of various ailments since ancient times in the Chinese and Ayurvedic medical systems. The aim of this article is to review the available data on the selected natural compounds, giving emphasis to the inhibition of beta-site amyloid precursor protein-cleaving enzyme 1 activity as a mode of Alzheimer's disease treatment.

Rapid spread of ZIKA virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV retains its infectivity and remains structurally stable at temperatures up to 40 °C, unlike dengue and other flaviviruses. In spite of recent cryo-EM structures that showed similar architecture of ZIKA and dengue virus (DENV) E protein shells, little is known that makes ZIKV so temperature insensitive. Here, we attempt to unravel the molecular basis of greater thermal stability of ZIKV over DENV2 by executing atomistic molecular dynamics (MD) simulations on the viral E protein shells at 37 °C. Our results suggest that ZIKA E protein shell retains its structural integrity through stronger inter-raft communications facilitated by a series of electrostatic and H-bonding interactions among multiple inter-raft residues. In comparison, the DENV2 E protein shell surface was loosly packed that exhibited holes at all 3-fold vertices, in close agreement with another EM structure solved at 37 °C. The residue-level information obtained from our study could pave way for designing small molecule inhibitors and specific antibodies to inhibit ZIKV E protein assembly and membrane fusion.

Ionic liquids (ILs) are being considered as greener alternatives to the conventional organic solvents. However, highly viscous nature of ILs often limits their applications. Hence studies on IL/water binary mixtures have received tremendous attention. These mixtures exhibit much lower viscosity, but almost similar density, compressibility and other properties as that of the neat ILs, up to certain water content. Hence, determining the IL-water ratio till which the solution behaves like IL and subsequently changes to a state of solute IL dissolved in continuous water phase is of paramount importance. Noting the very different and characteristic behaviours of neat ILs and pure water over a temperature range, herein, we measured the various thermophysical properties of the binary mixtures of tetramethylguanidinium benzoate/water and tetramethylguanidinium salicylate/water with water content varying from 20 wt% to 95 wt% for a temperature range of 298 K to 343 K. The results show that similar to neat ILs, the measured densities and compressibility of these mixtures display a linear change, and viscosity decreases rapidly as temperature is increased for water content up to 50 wt%. At higher water concentrations, the measured density and compressibility exhibit nonlinear behaviour and the decrease in viscosity with increased temperature is minute, mimicking the behaviour of bulk water. MD simulations were carried out to explain the experimental observations. Simulation results show a greater temperature-induced disintegration of IL ion-water interactions in dense systems, explaining the rapid decay of the properties with temperature. The results also exhibit the presence of a neat, IL-like, H-bond mediated expanded structure in concentrated solution versus a collapsed IL structure in dilute solution.

Pancreastatin (PST), a chromogranin A–derived potent physiological dysglycemic peptide, regulates glucose/insu-lin homeostasis. We have identified a nonsynonymous functional PST variant (p.Gly297Ser; rs9658664) that occurs in a large section of human populations. Association analysis of this single nucleotide polymorphism with cardiovas-cular/metabolic disease states in Indian populations (n 5 ~4,300 subjects) displays elevated plasma glucose, glyco-sylated hemoglobin, diastolic blood pressure, and cate-cholamines in Gly/Ser subjects as compared with wild-type individuals (Gly/Gly). Consistently, the 297Ser allele confers an increased risk (~1.3–1.6-fold) for type 2 diabe-tes/hypertension/coronary artery disease/metabolic syn-drome. In corroboration, the variant peptide (PST-297S) displays gain-of-potency in several cellular events relevant for cardiometabolic disorders (e.g., increased expression of gluconeogenic genes, increased catecholamine secre-tion, and greater inhibition of insulin-stimulated glucose uptake) than the wild-type peptide. Computational docking analysis and molecular dynamics simulations show higher affinity binding of PST-297S peptide with glucose-regu-lated protein 78 (GRP78) and insulin receptor than the wild-type peptide, providing a mechanistic basis for the enhanced activity of the variant peptide. In vitro binding assays validate these in silico predictions of PST peptides binding to GRP78 and insulin receptor. In conclusion, the PST 297Ser allele influences cardiovascular/metabolic phenotypes and emerges as a novel risk factor for type 2 diabetes/hypertension/coronary artery disease in human populations.

HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8-21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies.

Coronaviruses have been receiving continuous attention worldwide as they have caused a serious threat to global public health. This group of viruses is named so as they exhibit charac-teristic crown-like spikes on their protein coat. SARS-CoV-2, a type of coronavirus that emerged in 2019, causes severe infection in the lower respiratory tract of humans and is often fatal in im-munocompromised individuals. No medications have been approved so far for the direct treatment of SARS-CoV-2 infection, and the currently available treatment options rely on relieving the symp-toms. The medicinal plants occurring in nature serve as a rich source of active ingredients that could be utilized for developing pharmacopeial and non-pharmacopeial/synthetic drugs with antiviral properties. Compounds obtained from certain plants have been used for directly and selectively inhibiting different coronaviruses, including SARS-CoV, MERS-CoV, and SARS-CoV-2. The pre-sent review discusses the potential natural inhibitors against the highly pathogenic human coron-aviruses, with a systematic elaboration on the possible mechanisms of action of these natural compounds while acting in the different stages of the life cycle of coronaviruses. Moreover, through a comprehensive exploration of the existing literature in this regard, the importance of such compounds in the research and development of effective and safe antiviral agents is discussed. We focused on the mechanism of action of several natural compounds along with their target of action. In addition, the immunomodulatory effects of these active components in the context of human health are elucidated. Finally, it is suggested that the use of traditional medicinal plants is a novel and feasible remedial strategy against human coronaviruses.

The increased threat of bacterial resistance against conventional antibiotics has warranted the need for development of membrane targeting antibacterial agents. Several self-assembled cationic amphiphiles with different supramolecular structures have been reported in recent years for potent antibacterial activity with increased specificity. In this study, we describe the self-assembly and antibacterial activity of four lower generation poly(aryl ether)-based amphiphilic dendrimers (AD-1, AD-2, AD-3, and AD-4) containing terminal amine (PAMAM-based), ester, and hydrazide functional groups with varied hydrophobicity. Among the four dendrimers under study, the amine-terminated dendrimer (AD-1) displayed potent antibacterial activity. The ratio of surface cationic charge to hydrophobicity had a significant effect on the antibacterial activity, where AD-3 dendrimer with increased surface cationic charges exhibited a higher minimum inhibitory concentration (MIC) than AD-1. AD-2 (ester terminated) and AD-4 (hydrazide terminated) dendrimers did not show any bactericidal activity. The amphiphilic dendrimer-bacteria interactions, further validated by binding studies, also showed significant changes in bacterial morphology, effective membrane permeation, and depolarization by AD-1 in comparison with AD-3. Molecular dynamics simulations of AD-1 and AD-3 on bacterial membrane patches further corroborated the experimental findings. The structural conformation of AD-1 dendrimer facilitated increased membrane interaction compared to AD-3 dendrimer. AD-1 also displayed selectivity to bacterial membranes over fibroblast cells (4× MIC), corroborating the significance of an optimal hydrophobicity for potent antibacterial activity with no cytotoxicity. The self-assembled (poly(aryl ether)-PAMAM-based) dendrimer (AD-1) also exhibited potent antibacterial activity in comparison with conventional higher generation dendrimers, establishing the implication of self-assembly for bactericidal activity. Moreover, the detailed mechanistic study reveals that optimal tuning of the hydrophobicity of amphiphilic dendrimers plays a crucial role in membrane disruption of bacteria. We believe that this study will provide valuable insights into the design strategies of amphiphilic dendrimers as antibacterial agents for efficient membrane disruption.

Acetate anion-based ionic liquids (ILs) have found wide range of applications. The microstructure and dynamics of this IL family have not been clearly understood yet. We report molecular dynamics simulation results of three acetate anion-based ionic liquids that encompass the most common IL cations. Simulations are performed based on a set of proposed force field parameters for IL acetate anion which can be combined with existing parameters for IL cations to simulate large variety of ILs. The computed liquid density and IR spectral data for [BMIM][Ac] are found to match very well with available experimental results. The strong amino-group-associated interactions in [TMG][Ac] are seen to bring about higher cohesive energy density, stronger ion packing, and more restricted translational and rotational mobilities of the constituent ions. The IL anions are found to track the cation movements in all systems, implying that ions in ILs travel in pairs or clusters. © 2010 Elsevier B.V. All rights reserved.