Binding of Inhibitors to Nuclear Localization Signal Peptide from Venezuelan Equine Encephalitis Virus Capsid Protein Explored with All-Atom Replica Exchange Molecular Dynamics.

Several small molecule inhibitors have been designed to block binding of the Venezuelan equine encephalitis virus (VEEV) nuclear localization signal (NLS) sequence to the importin-α nuclear transport protein. To probe the inhibition mechanism on a molecular level, we used all-atom explicit water replica exchange molecular dynamics to study the binding of two inhibitors, I1 and I2, to the coreNLS peptide, representing the core fragment of the VEEV NLS sequence. Our objective was to evaluate the possibility of masking wherein binding of these inhibitors to the coreNLS occurs prior to its binding to importin-α.

Competitive Binding of Viral Nuclear Localization Signal Peptide and Inhibitor Ligands to Importin-α Nuclear Transport Protein.

Venezuelan equine encephalitis virus (VEEV) is a highly virulent pathogen whose nuclear localization signal (NLS) sequence from capsid protein binds to the host importin-α transport protein and blocks nuclear import. We studied the molecular mechanisms by which two small ligands, termed I1 and I2, interfere with the binding of VEEV's NLS peptide to importin-α protein. To this end, we performed all-atom replica exchange molecular dynamics simulations probing the competitive binding of the VEEV coreNLS peptide and I1 or I2 ligand to the importin-α major NLS binding site.

Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein.

Using all-atom replica-exchange molecular dynamics simulations, we mapped the mechanisms of binding of the nuclear localization signal (NLS) sequence from Venezuelan equine encephalitis virus (VEEV) capsid protein to importin-α (impα) transport protein. Our objective was to identify the VEEV NLS sequence fragment that confers native, experimentally resolved binding to impα as well as to study associated binding energetics and conformational ensembles. The two selected VEEV NLS peptide fragments, KKPK and KKPKKE, show strikingly different binding mechanisms.

Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?

Free energy perturbation coupled with replica exchange with solute tempering (FEP/REST) offers a rigorous approach to compute relative free energy changes for ligands. To determine the applicability of FEP/REST for the ligands with distributed binding poses, we considered two alchemical transformations involving three putative inhibitors I0, I1, and I2 of the Venezuelan equine encephalitis virus nuclear localization signal sequence binding to the importin-α (impα) transporter protein. I0 → I1 and I0 → I2 transformations, respectively, increase or decrease the polarity of the parent molecule.

Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-α Receptors Explored with All-Atom Replica Exchange Molecular Dynamics.

Although Venezuelan equine encephalitis virus (VEEV) is a life-threatening pathogen with a capacity for epidemic outbreaks, there are no FDA-approved VEEV antivirals for humans. VEEV cytotoxicity is partially attributed to the formation of a tetrameric complex between the VEEV capsid protein, the nuclear import proteins importin-α and importin-β, and the nuclear export protein CRM1, which together block trafficking through the nuclear pore complex. Experimental studies have identified small molecules from the CL6662 scaffold as potential inhibitors of the viral nuclear localization signal (NLS) sequence binding to importin-α.

Testing Precision and Accuracy of an Upper Extremity Proprioceptive Targeting Task Assessment.

Objective: To develop and test an assessment measuring extended physiological proprioception (EPP). EPP is a learned skill that allows one to extend proprioception to an external tool, which is important for controlling prosthetic devices. The current study examines the ability of this assessment to measure EPP in a nonamputee population for translation into the affected population.

Substrate-dependent modulation of the leukotriene A hydrolase aminopeptidase activity and effect in a murine model of acute lung inflammation.

The aminopeptidase activity (AP) of the leukotriene A hydrolase (LTAH) enzyme has emerged as a therapeutic target to modulate host immunity. Initial reports focused on the benefits of augmenting the LTAH AP activity and clearing its putative pro-inflammatory substrate Pro-Gly-Pro (PGP). However, recent reports have introduced substantial complexity disconnecting the LTAH modulator 4-methoxydiphenylmethane (4MDM) from PGP as follows: (1) 4MDM inhibits PGP hydrolysis and subsequently inhibition of LTAH AP activity, and (2) 4MDM activates the same enzyme target in the presence of alternative substrates.

Changes in Step Characteristics Over a Known Outdoor Surface Transition: The Effect of Parkinson Disease.

The factors that contribute to the difficulties persons with Parkinson Disease (PwPD) have when negotiating transitions in walking surfaces are not completely known. The authors investigated if PwPD adjusted their step characteristics when negotiating a familiar outdoor surface transition between synthetic concrete and synthetic turf. Force plate and motion capture data were collected for 10 participants with mild to moderate Parkinson disease and 5 healthy older control participants ambulating bidirectionally across the transition between synthetic concrete and synthetic turf.

Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase.

β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition.

Ankle strength, muscle size, and adipose content following unilateral tibiotalar arthrodesis.

Tibiotalar arthrodesis is commonly used to treat end-stage ankle osteoarthritis. Post-operative impairments are often attributed to limited ankle motion. However, whether muscular deficits also exist, thereby potentially contributing to impairments, is unknown.

Target-Directed Self-Assembly of Homodimeric Drugs Against β-Tryptase.

Tryptase, a serine protease released from mast cells, is implicated in many allergic and inflammatory disorders. Human tryptase is a donut-shaped tetramer with the active sites facing inward forming a central pore. Bivalent ligands spanning two active sites potently inhibit this configuration, but these large compounds have poor drug-like properties.

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers.

Permeable reactive barriers (PRBs) remove nitrogen from groundwater by enhancing microbial denitrification. The PRBs consist of woodchips that provide carbon for denitrifiers, but these woodchips also support other anaerobic microbes, including sulfate-reducing bacteria. Some of these anaerobes have the ability to methylate inorganic mercury present in groundwater.

Quadriceps weakness preferentially predicts detrimental gait compensations among common impairments after total knee arthroplasty.

Patients with total knee arthroplasty (TKA) have large deficits in physical performance in comparison to their healthy age-matched peers. Limb asymmetry stemming from less relative load borne by the surgical limb during daily mobility is associated with diminished performance and worsens with greater mobility demands. How common targets of postoperative care, such as muscle weakness, lower limb extension power, residual knee pain, and poor balance confidence can influence asymmetrical limb loading remains unclear.

A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands.

Empirical data has shown that bivalent inhibitors can bind a given target protein significantly better than their monomeric counterparts. However, predicting the corresponding theoretical fold improvements has been challenging. The current work builds off the reacted-site probability approach to provide a straightforward baseline reference model for predicting fold-improvements in effective affinity of dimerized ligands over their monomeric counterparts.

Morphometry of the lower lumbar intervertebral discs and endplates: comparative analyses of new MRI data with previous findings.

Purpose: Variability of the human lower lumbar geometry is related to complications of disc arthroplasty surgery. Accurate morphometric descriptions are essential for the design of artificial intervertebral discs to ensure good prothesis-vertebra contact and better load distribution, and can improve spinal biomechanics. Unfortunately, current knowledge of the lower lumbar geometry is limited either in the representativeness of sample populations or the accuracy and comprehensiveness of measurements.

Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions.

Permeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers.

Reversible linkage of two distinct small molecule inhibitors of Myc generates a dimeric inhibitor with improved potency that is active in myc over-expressing cancer cell lines.

We describe the successful application of a novel approach for generating dimeric Myc inhibitors by modifying and reversibly linking two previously described small molecules. We synthesized two directed libraries of monomers, each comprised of a ligand, a connector, and a bioorthogonal linker element, to identify the optimal dimer configuration required to inhibit Myc. We identified combinations of monomers, termed self-assembling dimeric inhibitors, which displayed synergistic inhibition of Myc-dependent cell growth.

Prediction models for the erector spinae muscle cross-sectional area.

Accurate and reliable "individualized" low back erector spinae muscle (ESM) data are of importance to estimate its force producing capacity. Knowing the force producing capacity, along with spinal loading, enhances the understanding of low back injury mechanisms. The objective of this study was to build regression models to estimate the ESM cross-sectional area (CSA).

C-terminal domain of SMYD3 serves as a unique HSP90-regulated motif in oncogenesis.

The SMYD3 histone methyl transferase (HMTase) and the nuclear chaperone, HSP90, have been independently implicated as proto-oncogenes in several human malignancies. We show that a degenerate tetratricopeptide repeat (TPR)-like domain encoded in the SMYD3 C-terminal domain (CTD) mediates physical interaction with HSP90. We further demonstrate that the CTD of SMYD3 is essential for its basal HMTase activity and that the TPR-like structure is required for HSP90-enhanced enzyme activity.

Discovery of novel insulin-like growth factor-1 receptor inhibitors with unique time-dependent binding kinetics.

This letter describes a series of small molecule inhibitors of IGF-1R with unique time-dependent binding kinetics and slow off-rates. Structure-activity and structure-kinetic relationships were elucidated and guided further optimizations within the series, culminating in compound 2. With an IGF-1R dissociative half-life (t 1/2) of >100 h, compound 2 demonstrated significant and extended PD effects in conjunction with tumor growth inhibition in xenograft models at a remarkably low and intermittent dose, which correlated with the observed in vitro slow off-rate properties.

Predictors of gait speeds and the relationship of gait speeds to falls in men and women with Parkinson disease.

Gait difficulties and falls are commonly reported in people with Parkinson disease (PD). Reduction in gait speed is a major characteristic of Parkinsonian gait, yet little is known about its underlying determinants, its ability to reflect an internal reservation about walking, or its relationship to falls. To study these issues, we selected age, disease severity, and nonmotor factors (i.

Structural and functional profiling of the human histone methyltransferase SMYD3.

The SET and MYND Domain (SMYD) proteins comprise a unique family of multi-domain SET histone methyltransferases that are implicated in human cancer progression. Here we report an analysis of the crystal structure of the full length human SMYD3 in a complex with an analog of the S-adenosyl methionine (SAM) methyl donor cofactor. The structure revealed an overall compact architecture in which the "split-SET" domain adopts a canonical SET domain fold and closely assembles with a Zn-binding MYND domain and a C-terminal superhelical 9 α-helical bundle similar to that observed for the mouse SMYD1 structure.

Potent and selective cyclohexyl-derived imidazopyrazine insulin-like growth factor 1 receptor inhibitors with in vivo efficacy.

Preclinical and emerging clinical evidence suggests that inhibiting insulin-like growth factor 1 receptor (IGF-1R) signaling may offer a promising therapeutic strategy for the treatment of several types of cancer. This Letter describes the medicinal chemistry effort towards a series of 8-amino-imidazo[1,5-a]pyrazine derived inhibitors of IGF-1R which features a substituted quinoline moiety at the C1 position and a cyclohexyl linking moiety at the C3 position. Lead optimization efforts which included the optimization of structure-activity relationships and drug metabolism and pharmacokinetic properties led to the identification of compound 9m, a potent, selective and orally bioavailable inhibitor of IGF-1R with in vivo efficacy in an IGF-driven mouse xenograft model.