Molecular Dynamics Simulations for Genetic Interpretation in Protein Coding Regions: Where we Are, Where to Go and When

The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants

F4-Neuroprostane Effects on Human Sperm

Swim-up selected human sperm were incubated with 7 ng F4-neuroprostanes (F4-NeuroPs) for 2 and 4 h. Sperm motility and membrane mitochondrial potential (MMP) were evaluated. The percentage of reacted acrosome was assessed by pisum sativum agglutinin (PSA). Chromatin integrity was detected using the acridine orange (AO) assay and localization of the ryanodine receptor was performed by immunofluorescence analysis. Sperm progressive motility (p = 0.02) and the percentage of sperm showing a strong MMP signal (p = 0.012) significantly increased after 2 h F4-NeuroP incubation compared to control samples. The AO assay did not show differences in the percentage of sperm with dsDNA between treated or control samples. Meanwhile, a significantly higher number of sperm with reacted acrosomes was highlighted by PSA localization after 4 h F4-NeuroP incubation. Finally, using an anti-ryanodine antibody, the immunofluorescence signal was differentially distributed at 2 and 4 h: a strong signal was evident in the midpiece and postacrosomal sheath (70% of sperm) at 2 h, whereas a dotted one appeared at 4 h (53% of sperm). A defined concentration of F4-NeuroPs in seminal fluid may induce sperm capacitation via channel ions present in sperm cells, representing an aid during in vitro sperm preparation that may increase the positive outcome of assisted fertilization

Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton’s method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers

Design, synthesis and structure-activity evaluation of novel 2-pyridone-based inhibitors of a-synuclein aggregation with potentially improved BBB permeability

The treatment of Parkinson''s disease (PD), the second most common neurodegenerative human disorder, continues to be symptomatic. Development of drugs able to stop or at least slowdown PD progression would benefit several million people worldwide. SynuClean-D is a low molecular weight 2-pyridone-based promising drug candidate that inhibits the aggregation of a-synuclein in human cultured cells and prevents degeneration of dopaminergic neurons in a Caenorhabditis elegans model of PD. Improving SynuClean-D pharmacokinetic/pharmacodynamic properties, performing structure/activity studies and testing its efficacy in mammalian models of PD requires the use of gr-amounts of the compound. However, not enough compound is on sale, and no synthetic route has been reported until now, which hampers the molecule progress towards clinical trials. To circumvent those problems, we describe here an efficient and economical route that enables the synthesis of SynuClean-D with good yields as well as the synthesis of SynuClean-D derivatives. Structure-activity comparison of the new compounds with SynuClean-D reveals the functional groups of the molecule that can be disposed of without activity loss and those that are crucial to interfere with a-synuclein aggregation. Several of the derivatives obtained retain the parent''s compound excellent in vitro anti-aggregative activity, without compromising its low toxicity. Computational predictions and preliminary testing indicate that the blood brain barrier (BBB) permeability of SynuClean-D is low. Importantly, several of the newly designed and obtained active derivatives are predicted to display good BBB permeability. The synthetic route developed here will facilitate their synthesis for BBB permeability determination and for efficacy testing in mammalian models of PD. © 2021 The Author

Nonenzymatic lipid mediators, neuroprostanes, exert the antiarrhythmic properties of docosahexaenoic acid

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Shape oscillations of an oil drop rising in water: effect of surface contamination

Inertial shape oscillations of heptane drops rising in water are investigated experimentally. Diameters from 0.59 to 3.52 mm are considered, corresponding to a regime where the rising motion should not affect shape oscillations for pure immiscible fluids. The interface, however, turns out to be contaminated. The drag coefficient is considerably increased compared to that of a clean drop due to the well-known. Marangoni effect resulting from a gradient of surfactant concentration generated by the fluid motion along the interface. Thanks to the decomposition of the shape into spherical harmonics, the eigenfrequencies and the damping rates of oscillation modes n = 2, 3, 4 and 5 have been measured. Frequencies are not affected by contamination, while damping rates are increased by a considerable amount that depends neither on drop instantaneous velocity nor on diameter. This augmentation, however, depends on the mode number: it is maximum for mode two (multiplied by 2.4) and then relaxes towards the value of a clean drop as n increases. A previous similar investigation of a drop attached to a capillary has not revealed such an increase of the damping rates, indicating that the coupling between rising motion and surface contamination is responsible for this effect

Proba-3: ESA’s Small Satellites Precise Formation Flying Mission to Study the Sun’s Inner Corona as Never Before

This paper showcases ESA’s Proba-3 mission as a demonstration of how small satellites, in combination with formation flying technology, can achieve relevant scientific goals and perform scientific measurements not possible otherwise, all within a tight cost and programmatic context. The study of the Sun inner corona down to 1.1 solar radius can only be performed by creating in space artificial eclipses with a large distance between a Coronograph instrument and an occulting disk, much bigger than the size of any spacecraft that can fit within a launcher. Proba-3 will achieve these enhanced scientific observations by controlling two small satellites (~1.5 m cubes in the 200-300kg range) as a 150 m long ‘large virtually rigid structure’ by maintaining millimetre and arc second relative precision. In effect the paired satellites will fly as a giant virtual satellite creating an ‘externally occulted’ coronagraph, in which a satellite imager is shielded from glaring sunlight by an occulting disk on the other satellite, forming an artificial eclipse. Precise station keeping for Coronagraphy will be kept for 6 consecutive hours within each 20 hour orbit for a minimum total of 1000 hours of scientific observations over the 2 years of mission lifetime. This will be achieved autonomously, without relying on the ground for active control of the formation. In addition, Proba-3 will practically demonstrate formation flying technologies enabling other future science missions: station-keeping at different relative distances (from 25 m up to 250 m); approaching and separating in precise formation without losing millimetre precision; the capability to repoint the formation as a virtual rigid body away from the Sun and the combination of station keeping, resizing and re-targeting manoeuvres. Proba-3 is at full speed in the assembly, integration and verification phase, with the aim of launching Proba-3 in two years’ time. The paper describes the overall Proba-3 mission concept and detailed design, the different challenges that were overcome in spacecraft design, formation flying metrology and control, and the need to implement novel verification and operation approaches to achieve the world’s first precise formation flying mission

Identification of Novel F2-Isoprostane Metabolites by Specific UDP-Glucuronosyltransferases

UDP-glucuronosyltransferases (UGTs) catalyze the conjugation of glucuronic acid with endogenous and exogenous lipophilic small molecules to facilitate their inactivation and excretion from the body. This represents approximately 35 % of all phase II metabolic transformations. Fatty acids and their oxidized eicosanoid derivatives can be metabolized by UGTs. F2-isoprostanes (F2-IsoPs) are eicosanoids formed from the free radical oxidation of arachidonic acid. These molecules are potent vasoconstrictors and are widely used as biomarkers of endogenous oxidative damage. An increasing body of evidence demonstrates the efficacy of measuring the β-oxidation metabolites of F2-IsoPs rather than the unmetabolized F2-IsoPs to quantify oxidative damage in certain settings. Yet, the metabolism of F2-IsoPs is incompletely understood. This study sought to identify and characterize novel phase II metabolites of 15-F2t-IsoP and 5-epi-5-F2t-IsoP, two abundantly produced F2-IsoPs, in human liver microsomes (HLM). Utilizing liquid chromatography-mass spectrometry, we demonstrated that glucuronide conjugates are the major metabolites of these F2-IsoPs in HLM. Further, we showed that these molecules are metabolized by specific UGT isoforms. 15-F2t-IsoP is metabolized by UGT1A3, 1A9, and 2B7, while 5-epi-5-F2t-IsoP is metabolized by UGT1A7, 1A9, and 2B7. We identified, for the first time, the formation of intact glucuronide F2-IsoPs in human urine and showed that F2-IsoP glucuronidation is reduced in people supplemented with eicosapentaenoic and docosahexaenoic acids for 12 weeks. These studies demonstrate that endogenous F2-IsoP levels can be modified by factors other than redox mechanisms

Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase

Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ¿¿Gb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme. © 2022 by the authors. Licensee MDPI, Basel, Switzerland