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Frontiers in Pharmacology 2016Traditional medicine has a history extending back to thousands of years, and during the intervening time, man has identified the healing properties of a very broad range... (Review)
Review
Traditional medicine has a history extending back to thousands of years, and during the intervening time, man has identified the healing properties of a very broad range of plants. Globally, the use of herbal therapies to treat and manage cardiovascular disease (CVD) is on the rise. This is the second part of our comprehensive review where we discuss the mechanisms of plants and herbs used for the treatment and management of high blood pressure. Similar to the first part, PubMed and ScienceDirect databases were utilized, and the following keywords and phrases were used as inclusion criteria: hypertension, high blood pressure, herbal medicine, complementary and alternative medicine, endothelial cells, nitric oxide (NO), vascular smooth muscle cell (VSMC) proliferation, hydrogen sulfide, nuclear factor kappa-B (NF-κB), oxidative stress, and epigenetics/epigenomics. Each of the aforementioned keywords was co-joined with plant or herb in question, and where possible with its constituent molecule(s). This part deals in particular with plants that are used, albeit less frequently, for the treatment and management of hypertension. We then discuss the interplay between herbs/prescription drugs and herbs/epigenetics in the context of this disease. The review then concludes with a recommendation for more rigorous, well-developed clinical trials to concretely determine the beneficial impact of herbs and plants on hypertension and a disease-free living.
PubMed: 27014064
DOI: 10.3389/fphar.2016.00050 -
Nature Chemistry Jun 2022For molecular collisions, the deflection of a molecule's trajectory provides one of the most sensitive probes of the interaction potential and there are general rules of...
For molecular collisions, the deflection of a molecule's trajectory provides one of the most sensitive probes of the interaction potential and there are general rules of thumb that relate the direction of deflection to precollision conditions. Following intuition, forward scattering results from glancing collisions, whereas near head-on collisions result in back scattering. Here we present the observation of forward scattering in inelastic processes that defies this common wisdom. For deeply inelastic collisions between NO radicals and CO or HD molecules, we observed forward scattering in fully resolved pair-correlated differential cross-sections, despite the low impact parameters that are needed to induce a sufficient energy transfer. We rationalized these findings by extending the textbook model of hard-sphere scattering-taking inelastic energy transfer into account-and attribute the forward scattering to glory-type trajectories caused by attractive forces. This phenomenon, which we refer to as hard-collision glory scattering, is predicted to be ubiquitous. We derive under which conditions hard-collision glory scattering occurs and retrospectively identify such behaviour in previously studied systems.
Topics: Energy Transfer; Quantum Theory; Retrospective Studies
PubMed: 35315436
DOI: 10.1038/s41557-022-00907-2 -
Philosophical Transactions. Series A,... Mar 2017Feedback traps are tools for trapping and manipulating single charged objects, such as molecules in solution. An alternative to optical tweezers and other... (Review)
Review
Feedback traps are tools for trapping and manipulating single charged objects, such as molecules in solution. An alternative to optical tweezers and other single-molecule techniques, they use feedback to counteract the Brownian motion of a molecule of interest. The trap first acquires information about a molecule's position and then applies an electric feedback force to move the molecule. Since electric forces are stronger than optical forces at small scales, feedback traps are the best way to trap single molecules without 'touching' them (e.g. by putting them in a small box or attaching them to a tether). Feedback traps can do more than trap molecules: they can also subject a target object to forces that are calculated to be the gradient of a desired potential function U(x). If the feedback loop is fast enough, it creates a virtual potential whose dynamics will be very close to those of a particle in an actual potential U(x). But because the dynamics are entirely a result of the feedback loop-absent the feedback, there is only an object diffusing in a fluid-we are free to specify and then manipulate in time an arbitrary potential U(x,t). Here, we review recent applications of feedback traps to studies on the fundamental connections between information and thermodynamics, a topic where feedback plays an even more fundamental role. We discuss how recursive maximum-likelihood techniques allow continuous calibration, to compensate for drifts in experiments that last for days. We consider ways to estimate work and heat, using them to measure fluctuating energies to a precision of ±0.03 kT over these long experiments. Finally, we compare work and heat measurements of the costs of information erasure, the Landauer limit of kT ln 2 per bit of information erased. We argue that, when you want to know the average heat transferred to a bath in a long protocol, you should measure instead the average work and then infer the heat using the first law of thermodynamics.This article is part of the themed issue 'Horizons of cybernetical physics'.
PubMed: 28115614
DOI: 10.1098/rsta.2016.0217 -
Physical Review Letters Sep 2021We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with...
We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with fragment ions, we deduce the molecule's orientation and photoelectron emission direction in the laboratory frame. Thereby, we retrieve a fourfold differential PECD clearly beyond 50%. This strong chiral asymmetry is reproduced by ab initio electronic structure calculations. Providing such a pronounced contrast makes PECD of fixed-in-space chiral molecules an even more sensitive tool for chiral recognition in the gas phase.
PubMed: 34533326
DOI: 10.1103/PhysRevLett.127.103201 -
Journal of Chemical Information and... Aug 2022Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have... (Review)
Review
Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have emerged. Natural language approaches that model each problem as a SMILES-to-SMILES translation lead to a simple end-to-end formulation, reduce the need for data preprocessing, and enable the use of well-optimized machine translation model architectures. However, SMILES representations are not efficient for capturing information about molecular structures, as evidenced by the success of SMILES augmentation to boost empirical performance. Here, we describe a novel Graph2SMILES model that combines the power of Transformer models for text generation with the permutation invariance of molecular graph encoders that mitigates the need for input data augmentation. In our encoder, a directed message passing neural network (D-MPNN) captures local chemical environments, and the global attention encoder allows for long-range and intermolecular interactions, enhanced by graph-aware positional embedding. As an end-to-end architecture, Graph2SMILES can be used as a drop-in replacement for the Transformer in any task involving molecule(s)-to-molecule(s) transformations, which we empirically demonstrate leads to improved performance on existing benchmarks for both retrosynthesis and reaction outcome prediction.
Topics: Molecular Structure; Neural Networks, Computer
PubMed: 35881916
DOI: 10.1021/acs.jcim.2c00321 -
Frontiers in Microbiology 2021Understanding the mechanism behind probiotic action will enable a rational selection of probiotics, increase the chances of success in clinical studies and make it easy... (Review)
Review
Understanding the mechanism behind probiotic action will enable a rational selection of probiotics, increase the chances of success in clinical studies and make it easy to substantiate health claims. However, most probiotic studies over the years have rather focused on the effects of probiotics in health and disease, whereas little is known about the specific molecules that trigger effects in hosts. This makes it difficult to describe the detailed mechanism by which a given probiotic functions. Probiotics communicate with their hosts through molecular signaling. Meanwhile, since the molecules produced by probiotics under conditions may differ from those produced , mechanistic studies would have to be conducted under conditions that mimic gastrointestinal conditions as much as possible. The ideal situation would, however, be to carry out well-designed clinical trials in humans (or the target animal) using adequate quantities of the suspected probiotic molecule(s) or adequate quantities of isogenic knock-out or knock-in probiotic mutants. In this review, we discuss our current knowledge about probiotic bacteria and yeast molecules that are involved in molecular signaling with the host. We also discuss the challenges and future perspectives in the search for probiotic effector molecules.
PubMed: 33746935
DOI: 10.3389/fmicb.2021.655705 -
Microbiology and Molecular Biology... Dec 2015Why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. The... (Review)
Review
Why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. The viral envelope serves several functions, including protecting the RNA or DNA molecule(s), evading recognition by the immune system, and facilitating virus entry. Despite these commonalities, viral envelopes come in a wide variety of shapes and configurations. The evolution of the viral envelope is made more puzzling by the fact that nonenveloped viruses are able to infect a diverse range of hosts across the tree of life. We reviewed the entry, transmission, and exit pathways of all (101) viral families on the 2013 International Committee on Taxonomy of Viruses (ICTV) list. By doing this, we revealed a strong association between the lack of a viral envelope and the presence of a cell wall in the hosts these viruses infect. We were able to propose a new hypothesis for the existence of enveloped and nonenveloped viruses, in which the latter represent an adaptation to cells surrounded by a cell wall, while the former are an adaptation to animal cells where cell walls are absent. In particular, cell walls inhibit viral entry and exit, as well as viral transport within an organism, all of which are critical waypoints for successful infection and spread. Finally, we discuss how this new model for the origin of the viral envelope impacts our overall understanding of virus evolution.
Topics: Animals; Cell Wall; Evolution, Molecular; Virus Internalization; Virus Physiological Phenomena; Virus Release; Viruses
PubMed: 26378223
DOI: 10.1128/MMBR.00017-15 -
Annual Review of Biophysics May 2022Chirality in life has been preserved throughout evolution. It has been assumed that the main function of chirality is its contribution to structural properties. In the... (Review)
Review
Chirality in life has been preserved throughout evolution. It has been assumed that the main function of chirality is its contribution to structural properties. In the past two decades, however, it has been established that chiral molecules possess unique electronic properties. Electrons that pass through chiral molecules, or even charge displacements within a chiral molecule, do so in a manner that depends on the electron's spin and the molecule's enantiomeric form. This effect, referred to as chiral induced spin selectivity (CISS), has several important implications for the properties of biosystems. Among these implications, CISS facilitates long-range electron transfer, enhances bio-affinities and enantioselectivity, and enables efficient and selective multi-electron redox processes. In this article, we review the CISS effect and some of its manifestations in biological systems. We argue that chirality is preserved so persistently in biology not only because of its structural effect, but also because of its important function in spin polarizing electrons.
Topics: Electron Transport; Electrons; Oxidation-Reduction; Stereoisomerism
PubMed: 34932912
DOI: 10.1146/annurev-biophys-083021-070400 -
Journal of Chemical Information and... Mar 2023Cytochrome P450 enzymes aid in the elimination of a preponderance of small molecule drugs, but can generate reactive metabolites that may adversely react with protein...
Cytochrome P450 enzymes aid in the elimination of a preponderance of small molecule drugs, but can generate reactive metabolites that may adversely react with protein and DNA and prompt drug candidate attrition or market withdrawal. Previously developed models help understand how these enzymes modify molecule structure by predicting sites of metabolism or characterizing formation of metabolite-biomolecule adducts. However, the majority of reactive metabolites are formed by multiple metabolic steps, and understanding the progenitor molecule's network-level behavior necessitates an integrative approach that blends multiple site of metabolism and structure inference models. Our previously developed tool, XenoNet 1.0, generates metabolic networks, where nodes are molecules and weighted edges are metabolic transformations. We extend XenoNet with a bidirectional message passing neural network that integrates edge feature information and local network structure using edge-conditioned graph convolutions and jumping knowledge to predict the authenticity of inferred Phase I metabolite structures. Our model significantly outperformed prior work and algorithmic baselines on a data set of 311 networks and 6606 intermediates annotated using a chemically diverse set of 20 736 individual in vitro and in vivo reaction records accounting for 92.3% of all human Phase I metabolism in the Accelrys Metabolite Database. Cross-validated predictions resulted in area under the receiver operating characteristic curves of 88.5% and 87.6% for separating experimentally observed and unobserved metabolites at global and network levels, respectively. Further analysis verified robustness to networks of varying depth and breadth, accurate detection of metabolites, such as d,l-methamphetamine, that are experimentally observed or unobserved in different network contexts, extraction of important metabolic subnetworks, and identification of known bioactivation pathways, such as for nimesulide and terbinafine. By exploiting network structures, our approach accurately suggests unreported metabolites for experimental study and may rationalize modifications for avoiding deleterious pathways antecedent to reactive metabolite formation.
Topics: Humans; Neural Networks, Computer; Molecular Structure; Metabolic Networks and Pathways; Terbinafine
PubMed: 36926871
DOI: 10.1021/acs.jcim.2c01383 -
Biology of Reproduction Aug 2021Recent evidence indicates that niclosamide is an anti-cancer compound that is able to inhibit several signaling pathways. Although niclosamide has previously been...
Recent evidence indicates that niclosamide is an anti-cancer compound that is able to inhibit several signaling pathways. Although niclosamide has previously been identified by high-throughput screening platforms as a potential effective compound against several cancer types, no direct binding interactions with distinct biological molecule(s) has been established. The present study identifies key signal transduction mechanisms altered by niclosamide in ovarian cancer. Using affinity purification with a biotin-modified niclosamide derivative and mass spectrometry analysis, several RNA-binding proteins (RBPs) were identified. We chose the two RBPs, FXR1 and IGF2BP2, for further analysis. A significant correlation exists in which high-expression of FXR1 or IGF2BP2 is associated with reduced survival of ovarian cancer patients. Knockdown of FXR1 or IGF2BP2 in ovarian cancer cells resulted in significantly reduced cell viability, adhesion, and migration. Furthermore, FXR1 or IGF2BP2 deficient ovarian cancer cells exhibited reduced response to most doses of niclosamide showing greater cell viability than those with intact RBPs. These results suggest that FXR1 and IGF2BP2 are direct targets of niclosamide and could have critical activities that drive multiple oncogenic pathways in ovarian cancer.
Topics: Animals; Antineoplastic Agents; Cell Line, Tumor; Female; Humans; Mice; Niclosamide; Ovarian Neoplasms; RNA-Binding Proteins
PubMed: 33855343
DOI: 10.1093/biolre/ioab071