Location, Orientation and Aggregation of Bardoxolone-ME, CDDO-ME, in a Complex Phospholipid Bilayer Membrane.

Bardoxolone methyl (CDDO-Me), a synthetic derivative of the naturally occurring triterpenoid oleanolic acid, displays strong antioxidant, anticancer and anti-inflammatory activities, according to different bibliographical sources. However, the understanding of its molecular mechanism is missing. Furthermore, CDDO-Me has displayed a significant cytotoxicity against various types of cancer cells. CDDO-Me has a noticeable hydrophobic character and several of its effects could be attributed to its ability to be incorporated inside the biological membrane and therefore modify its structure and specifically interact with its components. In this study, we have used full-atom molecular dynamics to determine the location, orientation and interactions of CDDO-Me in phospholipid model membranes. Our results support the location of CDDO-Me in the middle of the membrane, it specifically orients so that the cyano group lean towards the phospholipid interface and it specifically interacts with particular phospholipids. Significantly, in the membrane the CDDO-Me molecules specifically interact with POPE and POPS. Moreover, CDDO-Me does not aggregates in the membrane but it forms a complex conglomerate in solution. The formation of a complex aggregate in solution might hamper its biological activity and therefore it should be taken into account when intended to be used in clinical assays. This work should aid in the development of these molecules opening new avenues for future therapeutic developments.

New Mammalian Target of Rapamycin (mTOR) Modulators Derived from Natural Product Databases and Marine Extracts by Using Molecular Docking Techniques.

Mammalian target of rapamycin (mTOR) is a PI3K-related serine/threonine protein kinase that functions as a master regulator of cellular growth and metabolism, in response to nutrient and hormonal stimuli. mTOR functions in two distinct complexes-mTORC1 is sensitive to rapamycin, while, mTORC2 is insensitive to this drug. Deregulation of mTOR's enzymatic activity has roles in cancer, obesity, and aging. Rapamycin and its chemical derivatives are the only drugs that inhibit the hyperactivity of mTOR, but numerous side effects have been described due to its therapeutic use. The purpose of this study was to identify new compounds of natural origin that can lead to drugs with fewer side effects. We have used computational techniques (molecular docking and calculated ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) parameters) that have enabled the selection of candidate compounds, derived from marine natural products, SuperNatural II, and ZINC natural products, for inhibitors targeting, both, the ATP and the rapamycin binding sites of mTOR. We have shown experimental evidence of the inhibitory activity of eleven selected compounds against mTOR. We have also discovered the inhibitory activity of a new marine extract against this enzyme. The results have been discussed concerning the necessity to identify new molecules for therapeutic use, especially against aging, and with fewer side effects.

Spontaneous membrane insertion of a dengue virus NS2A peptide.

Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly characterized because of its high hydrophobicity. We have previously shown experimentally that NS2A possess a segment, peptide dens25, known to insert into membranes and interact specifically with negatively-charged phospholipids. To characterize its membrane interaction we have used two types of molecular dynamics membrane model systems, a highly mobile membrane mimetic (HMMM) and an endoplasmic reticulum (ER) membrane-like model. Using the HMMM system, we have been able of demonstrating the spontaneous binding of dens25 to the negatively-charged phospholipid 1,2-divaleryl-sn-glycero-3-phosphate containing membrane whereas no binding was observed for the membrane containing the zwitterionic one 1,2-divaleryl-sn-glycero-3-phosphocholine. Using the ER-like membrane model system, we demonstrate the spontaneous insertion of dens25 into the middle of the membrane, it maintained its three-dimensional structure and presented a nearly parallel orientation with respect to the membrane surface. Both charged and hydrophobic amino acids, presenting an interfacial/hydrophobic pattern characteristic of a membrane-proximal segment, are responsible for membrane binding and insertion. Dens25 might control protein/membrane interaction and be involved in membrane rearrangements critical for the viral cycle. These data should help us in the development of inhibitor molecules that target NS2A segments involved in membrane reorganisation.

An Updated Review on Marine Anticancer Compounds: The Use of Virtual Screening for the Discovery of Small-Molecule Cancer Drugs.

Marine secondary metabolites are a promising source of unexploited drugs that have a wide structural diversity and have shown a variety of biological activities. These compounds are produced in response to the harsh and competitive conditions that occur in the marine environment. Invertebrates are considered to be among the groups with the richest biodiversity. To date, a significant number of marine natural products (MNPs) have been established as antineoplastic drugs. This review gives an overview of MNPs, both in research or clinical stages, from diverse organisms that were reported as being active or potentially active in cancer treatment in the past seventeen years (from January 2000 until April 2017) and describes their putative mechanisms of action. The structural diversity of MNPs is also highlighted and compared with the small-molecule anticancer drugs in clinical use. In addition, this review examines the use of virtual screening for MNP-based drug discovery and reveals that classical approaches for the selection of drug candidates based on ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering may miss potential anticancer lead compounds. Finally, we introduce a novel and publically accessible chemical library of MNPs for virtual screening purposes.

Oleuropein aglycone in lipid bilayer membranes. A molecular dynamics study.

Olive oil has been recognized to possess many therapeutic applications. Its beneficial effects arise from many causes, but one of them lies on the presence of oleuropein aglycone (OA). OA presents a plethora of pharmacological beneficial properties. Although there is a great research going on the effect of polyphenols and their derivatives on different aspects of health, much less knowledge is available of the molecular basis of their beneficial effects. Due to the prominent hydrophobic character of OA and its high phospholipid/water partition coefficient, some of its possible effects on biological systems might be related to its capacity to interact with and locate into the membrane. In this work we have aimed to locate the molecule of OA in two membrane model systems, i.e., POPC/Chol and POPC/POPG/Chol. OA locates in between the hydrocarbon acyl chains of the phospholipids but its specific location and molecular interactions differ depending on the lipid system. OA is nearer to the membrane surface in the POPC/Chol system but it is located at a deeper position in the POPC/POPG/Chol system. Furthermore, OA seems to interact stronger with POPG than with POPC, implying the existence of specific interactions with negatively-charged phospholipids. Some of the biological effects of OA could be due to its preferential location in the membrane depending on the membrane lipid composition as well as the existence of specific interactions with specific phospholipids.

The Location of the Protonated and Unprotonated Forms of Arbidol in the Membrane: A Molecular Dynamics Study.

Arbidol is a potent broad-spectrum antiviral molecule for the treatment and prophylaxis of many viral infections. Viruses that can be inhibited by arbidol include enveloped and non-enveloped viruses, RNA and DNA viruses, as well as pH-independent and pH-dependent ones. These differences in viral types highlight the broad spectrum of Arb antiviral activity and, therefore, it must affect a common viral critical step. Arbidol incorporates rapidly into biological membranes, and some of its antiviral effects might be related to its capacity to interact with and locate into the membrane. However, no information is available of the molecular basis of its antiviral mechanism/s. We have aimed to locate the protonated (Arp) and unprotonated (Arb) forms of arbidol in a model membrane system. Both Arb and Arp locate in between the hydrocarbon acyl chains of the phospholipids but its specific location and molecular interactions differ from each other. Whereas both Arb and Arp average location in the membrane palisade is a similar one, Arb tends to be perpendicular to the membrane surface, whereas Arp tends to be parallel to it. Furthermore, Arp, in contrast to Arb, seems to interact stronger with POPG than with POPC, implying the existence of a specific interaction between Arp, the protonated from, with negatively charged phospholipids. This data would suggest that the active molecule of arbidol in the membrane is the protonated one, i.e., the positively charged molecule. The broad antiviral activity of arbidol would be defined by the perturbation it exerts on membrane structure and therefore membrane functioning.

Therapeutic expectancy in physiotherapy.

In health sciences, including physical therapy, communication techniques are a critical part of the success in the therapeutic process. Managing the patient's beliefs, perceptions, and the narrative of their problems, becomes an essential part of the therapeutic process. This is the key to achieving real changes regarding how the patient copes with pain, illness, dysfunction, as well as the ability to develop adequate resources for facing them. We call this "Therapeutic expectancy" a new concept that originates from the well-known Therapeutic alliance and incorporates practices from the field of Motivational interviewing and Strategic dialogue. The Therapeutic expectancy starts from the first interaction with the patient and continues throughout the different stages of the therapeutic process. This article describes the structure of the relationship with the patient and some verbal communication techniques to generate an effective physical therapist-patient interaction, building Therapeutic expectancy, through a "centered on the patient's narrative" strategy. Expectancy constitutes a desirable goal in any patient and in any pathological condition as it pursues a change in an individual's perception of their state of health, thereby enhancing the desire for healing and empowerment.

Performance Overview of the Latest Video Coding Proposals: HEVC, JEM and VVC.

The audiovisual entertainment industry has entered a race to find the video encoder offering the best Rate/Distortion (R/D) performance for high-quality high-definition video content. The challenge consists in providing a moderate to low computational/hardware complexity encoder able to run Ultra High-Definition (UHD) video formats of different flavours (360°, AR/VR, etc.) with state-of-the-art R/D performance results. It is necessary to evaluate not only R/D performance, a highly important feature, but also the complexity of future video encoders. New coding tools offering a small increase in R/D performance at the cost of greater complexity are being advanced with caution. We performed a detailed analysis of two evolutions of High Efficiency Video Coding (HEVC) video standards, Joint Exploration Model (JEM) and Versatile Video Coding (VVC), in terms of both R/D performance and complexity. The results show how VVC, which represents the new direction of future standards, has, for the time being, sacrificed R/D performance in order to significantly reduce overall coding/decoding complexity.

Aggregation of 25-hydroxycholesterol in a complex biomembrane. Differences with cholesterol.

25-Hydroxycholesterol (25HC), one of the most important oxysterol molecules, can be used by cells to fight bacterial and viral infections but the mechanism that defines its biological effects are unknown. Using molecular dynamics, we have aimed to describe the orientation and location of 25HC in the membrane as well as the interactions it might have with lipids. We have studied two complex model membrane systems, one similar to the late endosome membrane and the other one to the plasma membrane. Our results reinforce that 25HC is inserted in the membrane in a relative stable location similar to but not identical to cholesterol. 25HC fluctuates in the membrane to a much greater degree than cholesterol, but the effect of 25HC on the phospholipid order parameters is not significantly different. One of the most notable facts about 25HC is that, unlike cholesterol, this molecule tends to aggregate, forming dimers, trimers and higher-order aggregates. These aggregates are formed spontaneously through the formation of hydrogen bonds between the two 25HC atoms, the formation of hydrogen bonds being independent of the studied system. Remarkably, no contacts or hydrogen bonds are observed between 25HC and cholesterol molecules, as well as between cholesterol molecules themselves at any time. It would be conceivable that 25HC, by forming high order aggregates without significantly altering the membrane properties, would modify the way proteins interact with the membrane and henceforth form a true innate antiviral molecule.

Feasibility study of portable microwave microstrip open-loop resonator for non-invasive blood glucose level sensing: proof of concept.

Self-management of blood glucose level is part and parcel of diabetes treatment, which involves invasive, painful, and uncomfortable methods. A proper non-invasive blood glucose monitor (NIBGM) is therefore desirable to deal better with it. Microwave resonators can potentially be used for such a purpose. Following the positive results from an in vitro previous work, a portable device based upon a microwave resonator was developed and assessed in a multicenter proof of concept. Its electrical response was analyzed when an individual's tongue was placed onto it. The study was performed with 352 individuals during their oral glucose tolerance tests, having four measurements per individual. The findings revealed that the accuracy must be improved before the diabetes community can make real use of the device. However, the relationship between the measuring parameter and the individual's blood glucose level is coherent with that from previous works, although with higher data dispersion. This is reflected in correlation coefficients between glycemia and the measuring magnitude consistently negative, although small, for the different datasets analyzed. Further research is proposed, focused on system improvements, individual calibration, and multitechnology approach. The study of the influence of other blood components different to glucose is also advised. Graphical abstract.

Discovery of nonnucleoside inhibitors of polymerase from infectious pancreatic necrosis virus (IPNV).

INTRODUCTION: Infectious pancreatic necrosis virus (IPNV) causes serious losses in several fish species of commercial interest. IPNV is a non-enveloped double-stranded RNA virus with a genome consisting of two segments A and B. Segment B codes for the VP1 protein, a non-canonical RNA-dependent RNA polymerase that can be found both in its free form and linked to the end of genomic RNA, an essential enzyme for IPNV replication. MATERIALS AND METHODS: We take advantage of the knowledge over the allosteric binding site described on the surface of the thumb domain of Hepatitis C virus (HCV) polymerase to design new non-nucleoside inhibitors against the IPNV VP1 polymerase. RESULTS: Molecular docking techniques have been used to screen a chemical library of 23,760 compounds over a defined cavity in the surface of the thumb domain. Additional ADMET (absorption, distribution, metabolism, excretion, and toxicity) filter criteria has been applied. CONCLUSION: We select two sets of 9 and 50 inhibitor candidates against the polymerases of HCV and IPNV, respectively. Two non-toxic compounds have been tested in vitro with antiviral capacity against IPNV Sp and LWVRT60 strains in the low µM range with different activity depending on the IPNV strain used.

Molecular dynamics study of the membrane interaction of a membranotropic dengue virus C protein-derived peptide.

Dengue virus C protein, essential in the dengue virus life cycle, possesses a segment, peptide PepC, known to bind membranes composed of negatively charged phospholipids. To characterize its interaction with the membrane, we have used the molecular dynamics HMMM membrane model system. This approach is capable of achieving a stable system and sampling the peptide/lipid interactions which determine the orientation and insertion of the peptide upon membrane binding. We have been able to demonstrate spontaneous binding of PepC to the 1,2-divaleryl-sn-glycero-3-phosphate/1,2-divaleryl-sn-glycero-3-phosphocholine membrane model system, whereas no binding was observed at all for the 1,2-divaleryl-sn-glycero-3-phosphocholine one. PepC, adopting an α-helix profile, did not insert into the membrane but did bind to its surface through a charge anchor formed by its three positively charged residues. PepC, maintaining its three-dimensional structure along the whole simulation, presented a nearly parallel orientation with respect to the membrane when bound to it. The positively charged amino acid residues Arg-2, Lys-6, and Arg-16 are mainly responsible for the peptide binding to the membrane stabilizing the structure of the bound peptide. The segment of dengue virus C protein where PepC resides is a fundamental protein-membrane interface which might control protein/membrane interaction, and its positive amino acids are responsible for membrane binding defining its specific location in the bound state. These data should help in our understanding of the molecular mechanism of DENV life cycle as well as making possible the future development of potent inhibitor molecules, which target dengue virus C protein structures involved in membrane binding.

Location of the bioactive pentacyclic triterpene ursolic acid in the membrane. A molecular dynamics study.

Ursolic acid (URS), an ursane-representative bioactive pentacyclic triterpene, is a plant secondary metabolite presenting a great number of pharmacological beneficial properties. Due to the prominent hydrophobic character of URS and its high phospholipid/water partition coefficient, some of its possible effects on biological systems might be related to its capacity to interact with and locate into the membrane as well as interact specifically with its components. In this work, we have studied the location and orientation of URS in the membrane by molecular dynamics simulations. At the end of the simulation, URS locates near the surface in vicinity to the phospholipid headgroups but its orientation depends on lipid composition, its final average orientation being a nearly parallel one in POPC but a nearly perpendicular one in POPC/POPE/POPG/PSM/Chol. Furthermore, in the complex lipid system URS seems to interact specifically with POPE, PSM, and Chol excluding POPG from its surroundings, which could lead to phase separation and domain formation. The different disposition of URS in the membrane and its specific interaction with certain lipid types could lead to a significant perturbation of the membrane structure. The important pharmacological activities of URS would rely on the effects it exerts on the membrane structure in general and the existence of specific interactions with specific lipids in particular.

Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach.

The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds) to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (ΔG <-10.5 kcal/mol) were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo.