Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity.

Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.

Perspectives on the role of nutrition in influencing academy soccer player development and performance: A qualitative case study of key stakeholders from an English category one soccer academy.

This study aimed to explore player and stakeholder perceptions of the role of nutrition in influencing the development of male academy soccer players. Semi-structured interviews (28 ± 13 mins in length) were conducted with 31 participants from an English category one academy, including players (Youth Development Phase, YDP: n = 6; Professional Development Phase, PDP: n = 4), parents/guardians (n = 10), coaches (n = 3), sport scientists (n = 3), physiotherapists (n = 3), and catering (n = 2). Via reflexive thematic analysis, data demonstrate an apparent lack of understanding and awareness on the role of nutrition in influencing player development, especially in relation to growth, maturation and reducing injury risk. Players highlighted the influence of their parents on their dietary behaviours, whilst parents also called for education to better support their sons. Notably, players and stakeholders perceived that the daily schedule of an academy soccer player presents as "too busy to eat", especially in relation to before school, and before and after training. The results demonstrate the necessity for the co-creation of player and stakeholder specific nutrition education programmes as an initial step towards positively impacting the nutrition culture associated with the academy soccer environment.

Coherent Scattering of Low Mass Dark Matter from Optically Trapped Sensors.

We propose a search for low mass dark matter particles through momentum recoils caused by their scattering from trapped, nanometer-scale objects. Our projections show that even with a modest array of femtogram-mass sensors, parameter space beyond the reach of existing experiments can be explored. The case of smaller, attogram-mass sensors is also analyzed-where dark matter can coherently scatter from the entire sensor-enabling a large enhancement in the scattering cross-section relative to interactions with single nuclei. Large arrays of such sensors have the potential to investigate new parameter space down to dark matter masses as low as 10 keV. If recoils from dark matter are detected by such sensors, their inherent directional sensitivity would allow an unambiguous identification of a dark matter signal.

Trapped Electrons and Ions as Particle Detectors.

Electrons and ions trapped with electromagnetic fields have long served as important high-precision metrological instruments, and more recently have also been proposed as a platform for quantum information processing. Here we point out that these systems can also be used as highly sensitive detectors of passing charged particles, due to the combination of their extreme charge-to-mass ratio and low-noise quantum readout and control. In particular, these systems can be used to detect energy depositions many orders of magnitude below typical ionization scales. As illustrations, we suggest some applications in particle physics. We outline a nondestructive time-of-flight measurement capable of sub-eV energy resolution for slowly moving, collimated particles. We also show that current devices can be used to provide competitive sensitivity to models where ambient dark matter particles carry small electric millicharges ≪e. Our calculations may also be useful in the characterization of noise in quantum computers coming from backgrounds of charged particles.

Novel High-Throughput Strategy for the Aqueous Solubility Assessment of Peptides and Proteins Exhibiting a Propensity for Gelation: Application to the Discovery of Novel Antibacterial Teixobactin Analogues.

A novel high-throughput aqueous solubility assay was developed for peptides and proteins exhibiting a high gelling propensity (in this case, antibacterial teixobactin analogues). By integrating the assessment of gel formation, as indicated by an increase in the solution viscosity, into the peptide equilibrium solubility screening assay, we were able to estimate the "free-flowing solubility", which is defined as the concentration at which the peptide solution not only is fully dissolved but also is a liquid exhibiting ideal flowing characteristics. In this workflow, peptide solutions passing the turbidity assessment were further screened by viscosity measurements based on nanobead-assisted dynamic light scattering analysis in a 96-well plate. The method is able to effectively detect the initiation of peptide gelation and facilitate compound ranking based on their aqueous solubility. The application of such an approach helped confirm that the substitution of Ser3 in teixobactin led to desired physicochemical improvements and provided a focal point for further chemistry structure-activity relationship exploration.

Prioritizing Injury Prevention: Cause of Injury Text Analysis.

BACKGROUND: Motor vehicle (MVCs) and motorcycle crashes (MCCs) continue to be among the most prevalent mechanisms of trauma injury and mortality. We sought to identify specific populations and factors associated with MVCs and MCCs for local injury prevention efforts. A novel, yet easily performed, research method was utilized-a qualitative content analysis of text narratives describing each patient's cause of injury. OBJECTIVE: To determine target populations for local MVC and MCC injury prevention. METHODS: A retrospective descriptive analysis was performed using registry data from a Level I trauma center. The registry was queried for all trauma patients presenting with MVC or MCC injuries between June 8, 2014, and June 7, 2019. Cases were then reviewed via their respective text narratives of injury causation. Common themes were identified, coded by independent raters, and assessed for interrater reliability using Cohen's κ. Frequencies and proportions are reported for each preventable factor and patient characteristic. RESULTS: There were a total of 2,861 cases studied, of which 2,330 (81.4%) were MVC and 531 (18.6%) were MCC. Demographics varied by mechanism of injury. Driver drug or alcohol use was involved in 97 (3.4%), protective devices were not used in 776 (27.1%), distracted driving was involved in 30 (1%), excessive speeding was involved in 152 (5.3%), and driver sleeping/syncope/medical condition was present in 113 (3.9%) cases. CONCLUSIONS: Content analysis of cause of injury text narratives can detect target populations and preventable factors to direct injury prevention efforts specific to the local population.

Dissecting the Binding Interactions of Teixobactin with the Bacterial Cell-Wall Precursor Lipid†II.

The prevalence of life-threatening, drug-resistant microbial infections has challenged researchers to consider alternatives to currently available antibiotics. Teixobactin is a recently discovered "resistance-proof" antimicrobial peptide that targets the bacterial cell wall precursor lipid II. In doing so, teixobactin exhibits potent antimicrobial activity against a wide range of Gram-positive organisms. Herein we demonstrate that teixobactin and several structural analogues are capable of binding lipid II from both Gram-positive and Gram-negative bacteria. Furthermore, we show that when combined with known outer membrane-disrupting peptides, teixobactin is active against Gram-negative organisms.

Search for Composite Dark Matter with Optically Levitated Sensors.

Results are reported from a search for a class of composite dark matter models with feeble long-range interactions with normal matter. We search for impulses arising from passing dark matter particles by monitoring the mechanical motion of an optically levitated nanogram mass over the course of several days. Assuming such particles constitute the dominant component of dark matter, this search places upper limits on their interaction with neutrons of α_{n}≤1.2×10^{-7} at 95% confidence for dark matter masses between 1 and 10 TeV and mediator masses m_{ϕ}≤0.1 eV. Because of the large enhancement of the cross section for dark matter to coherently scatter from a nanogram mass (∼10^{29} times that for a single neutron) and the ability to detect momentum transfers as small as ∼200 MeV/c, these results provide sensitivity to certain classes of composite dark matter models that substantially exceeds existing searches, including those employing kilogram- or ton-scale targets. Extensions of these techniques can enable directionally sensitive searches for a broad class of previously inaccessible heavy dark matter candidates.

Cross-sectional comparison of body composition and resting metabolic rate in Premier League academy soccer players: Implications for growth and maturation.

For the first time we aimed to: (1) assess fat-free mass (FFM) and RMR in youth soccer players, (2) compare measured RMR to estimated RMR using previously published prediction equations, and (3) develop a novel population-specific prediction equation. In a cross-sectional design, 99 males from a Premier League academy underwent assessments of body composition (DXA) and RMR (indirect-calorimetry). Measured RMR was compared to estimated values from five prediction equations. A novel RMR prediction equation was developed using stepwise multiple regression. FFM increased (P<0.05) between U12 (31.6±4.2 kg) and U16 (56.3±5.3 kg) after which no further increases occurred (P>0.05). RMR in the U12s (1655±195 kcal.day-1), U13s (1720±205 kcal.day-1) and U14s (1846±218kcal.day-1) was significantly lower than the U15s (1957±128 kcal.day-1), U16s (2042±155 kcal.day-1), U18s (1875±180 kcal.day-1) and U23s (1941±197 kcal.day-1) squads (P>0.05). FFM was the single best predictor of RMR (r2=0.43; P<0.01) and was subsequently included in the novel prediction equation: RMR (kcal.day-1) = 1315 + (11.1 x FFM in kg). Both FFM and RMR increase from 12-16 years old, thus highlighting the requirement to adjust daily energy intake to support growth and maturation. The novel prediction RMR equation developed may help to inform daily energy requirements.

Ultrapotent vinblastines in which added molecular complexity further disrupts the target tubulin dimer-dimer interface.

Approaches to improving the biological properties of natural products typically strive to modify their structures to identify the essential pharmacophore, or make functional group changes to improve biological target affinity or functional activity, change physical properties, enhance stability, or introduce conformational constraints. Aside from accessible semisynthetic modifications of existing functional groups, rarely does one consider using chemical synthesis to add molecular complexity to the natural product. In part, this may be attributed to the added challenge intrinsic in the synthesis of an even more complex compound. Herein, we report synthetically derived, structurally more complex vinblastines inaccessible from the natural product itself that are a stunning 100-fold more active (IC50 values, 50-75 pM vs. 7 nM; HCT116), and that are now accessible because of advances in the total synthesis of the natural product. The newly discovered ultrapotent vinblastines, which may look highly unusual upon first inspection, bind tubulin with much higher affinity and likely further disrupt the tubulin head-to-tail α/ß dimer-dimer interaction by virtue of the strategic placement of an added conformationally well-defined, rigid, and extended C20' urea along the adjacent continuing protein-protein interface. In this case, the added molecular complexity was used to markedly enhance target binding and functional biological activity (100-fold), and likely represents a general approach to improving the properties of other natural products targeting a protein-protein interaction.

Refractometric Sensing with Periodic Nano-Indented Arrays: Effect of Structural Dimensions.

Fabrication and sensor application of a simple plasmonic structure is described in this paper. The sensor element consists of nano-patterned gold film brought about from two-dimensional periodic photoresist templates created by holographic laser interference lithography. Reflectance spectroscopy revealed that the sensor exhibits significant refractive index sensitivity. A linear relationship between shifts in plasmonic resonances and changes in the refractive index were demonstrated. The sensor has a bulk sensitivity (SB) of 880 nm/refractive index unit and work under normal incidence conditions. This sensitivity exceeded that of many common types of plasmonic sensors with more intricate structures. A modeled spectral response was used to study the effect of its geometrical dimensions on plasmonic behavior. A qualitative agreement between the experimental spectra and modeled ones was obtained.

Infrared Quantum Information.

We discuss information-theoretic properties of low-energy photons and gravitons in the S matrix. Given an incoming n-particle momentum eigenstate, we demonstrate that unobserved soft photons decohere nearly all outgoing momentum superpositions of charged particles, while the universality of gravity implies that soft gravitons decohere nearly all outgoing momentum superpositions of all the hard particles. Using this decoherence, we compute the entanglement entropy of the soft bosons and show that it is infrared-finite when the leading divergences are resummed in the manner of Bloch and Nordsieck.

Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.

Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein-substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.

Examination of a Structural Model of Peptidomimicry by Cyclic Acyldepsipeptide Antibiotics in Their Interaction with the ClpP Peptidase.

The cyclic acyldepsipeptide (ADEP) antibiotics act by binding the ClpP peptidase and dysregulating its activity. Their exocyclic N-acylphenylalanine is thought to structurally mimic the ClpP-binding, (I/L)GF tripeptide loop of the peptidase's accessory ATPases. We found that ADEP analogues with exocyclic N-acyl tripeptides or dipeptides resembling the (I/L)GF motif were weak ClpP activators and had no bioactivity. In contrast, ADEP analogues possessing difluorophenylalanine N-capped with methyl-branched acyl groups-like the side chains of residues in the (I/L)GF motifs-were superior to the parent ADEP with respect to both ClpP activation and bioactivity. We contend that the ADEP's N-acylphenylalanine moiety is not simply a stand-in for the ATPases' (I/L)GF motif; it likely has physicochemical properties that are better suited for ClpP binding. Further, our finding that the methyl-branching on the acyl group of the ADEPs improves activity opens new avenues for optimization.

Restriction of the conformational dynamics of the cyclic acyldepsipeptide antibiotics improves their antibacterial activity.

The cyclic acyldepsipeptide (ADEP) antibiotics are a new class of antibacterial agents that kill bacteria via a mechanism that is distinct from all clinically used drugs. These molecules bind and dysregulate the activity of the ClpP peptidase. The potential of these antibiotics as antibacterial drugs has been enhanced by the elimination of pharmacological liabilities through medicinal chemistry efforts. Here, we demonstrate that the ADEP conformation observed in the ADEP-ClpP crystal structure is fortified by transannular hydrogen bonding and can be further stabilized by judicious replacement of constituent amino acids within the peptidolactone core structure with more conformationally constrained counterparts. Evidence supporting constraint of the molecule into the bioactive conformer was obtained by measurements of deuterium-exchange kinetics of hydrogens that were proposed to be engaged in transannular hydrogen bonds. We show that the rigidified ADEP analogs bind and activate ClpP at lower concentrations in vitro. Remarkably, these compounds have up to 1200-fold enhanced antibacterial activity when compared to those with the peptidolactone core structure common to two ADEP natural products. This study compellingly demonstrates how rational modulation of conformational dynamics may be used to improve the bioactivities of natural products.

A simple fragment of cyclic acyldepsipeptides is necessary and sufficient for ClpP activation and antibacterial activity.

The development of new antibacterial agents, particularly those with unique biological targets, is essential to keep pace with the inevitable emergence of drug resistance in pathogenic bacteria. We identified the minimal structural component of the cyclic acyldepsipeptide (ADEP) antibiotics that exhibits antibacterial activity. We found that N-acyldifluorophenylalanine fragments function via the same mechanism of action as ADEPs, as evidenced by the requirement of ClpP for the fragments' antibacterial activity, the ability of fragments to activate Bacillus subtilis ClpP in vitro, and the capacity of an N-acyldifluorophenylalanine affinity matrix to capture ClpP from B. subtilis cell lysates. N-acyldifluorophenylalanine fragments are much simpler in structure than the full ADEPs and are also highly amenable to structural diversification. Thus, the stage has been set for the development of non-peptide activators of ClpP that can be used as antibacterial agents.

Structural optimization of a retrograde trafficking inhibitor that protects cells from infections by human polyoma- and papillomaviruses.

Human polyoma- and papillomaviruses are non-enveloped DNA viruses that cause severe pathologies and mortalities. Under circumstances of immunosuppression, JC polyomavirus causes a fatal demyelinating disease called progressive multifocal leukoencephalopathy (PML) and the BK polyomavirus is the etiological agent of polyomavirus-induced nephropathy and hemorrhagic cystitis. Human papillomavirus type 16, another non-enveloped DNA virus, is associated with the development of cancers in tissues like the uterine cervix and oropharynx. Currently, there are no approved drugs or vaccines to treat or prevent polyomavirus infections. We recently discovered that the small molecule Retro-2(cycl), an inhibitor of host retrograde trafficking, blocked infection by several human and monkey polyomaviruses. Here, we report diversity-oriented syntheses of Retro-2(cycl) and evaluation of the resulting analogs using an assay of human cell infections by JC polyomavirus. We defined structure-activity relationships and also discovered analogs with significantly improved potency as suppressors of human polyoma- and papillomavirus infection in vitro. Our findings represent an advance in the development of drug candidates that can broadly protect humans from non-enveloped DNA viruses and toxins that exploit retrograde trafficking as a means for cell entry.

Synthetic Approaches to the New Drugs Approved During 2022.

In 2022, 23 new small molecule chemical entities were approved as drugs by the United States FDA, European Union EMA, Japan PMDA, and China NMPA. This review describes the synthetic approach demonstrated on largest scale for each new drug based on patent or primary literature. The synthetic routes highlight practical methods to construct molecules, sometimes on the manufacturing scale, to access the new drugs. Ten additional drugs approved in 2021 and one approved in 2020 are included that were not covered in the previous year's review.

Design and Discovery of a Potent and Selective Inhibitor of Integrin αvß1.

Selective inhibition of the RGD (Arg-Gly-Asp) integrin αvß1 has been recently identified as an attractive therapeutic approach for the treatment of liver fibrosis given its function, target expression, and safety profile. Our identification of a non-RGD small molecule lead followed by focused, systematic changes to the core structure utilizing a crystal structure, in silico modeling, and a tractable synthetic approach resulted in the identification of a potent small molecule exhibiting a remarkable affinity for αvß1 relative to several other integrin isoforms measured. Azabenzimidazolone 25 demonstrated antifibrotic efficacy in an in vivo rat liver fibrosis model and represents a tool compound capable of further exploring the biological consequences of selective αvß1 inhibition.

Creating a Patient and Family Advisory Council at a level 1 trauma center.

Partnering with patients and families through a Patient and Family Advisory Council (PFAC) provides the opportunities to improve health care quality and safety. PFAC is a well-defined group of patients, families, and staff members who meet on a regular basis to ensure that patient's experiences, points of view, and recommendations are identified and shared with the organization. In fall 2010, at our level 1 trauma center, Trauma Services collaborated with the trauma nursing staff to formulate our first trauma-related PFAC.