Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.

The virally encoded 3C-like protease (3CLpro) is a well-validated drug target for the inhibition of coronaviruses including Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Most inhibitors of 3CLpro are peptidomimetic, with a γ-lactam in place of Gln at the P1 position of the pseudopeptide chain. An effort was pursued to identify a viable alternative to the γ-lactam P1 mimetic which would improve physicochemical properties while retaining affinity for the target. Discovery of a 2-tetrahydrofuran as a suitable P1 replacement that is a potent enzymatic inhibitor of 3CLpro in SARS-CoV-2 virus is described herein.

Feasibility of pain informed movement program for people with knee osteoarthritis.

Objective: To establish the feasibility of an intervention consisting of neuromuscular exercise, mind-body techniques, and pain neuroscience education (PNE), referred to as Pain Informed Movement in people with knee Osteoarthritis (KOA). This program has the potential to improve our understanding of intrinsic pain modulation and its role in the management of chronic pain. Methods: This was a single-arm feasibility trial with a nested qualitative component. Primary outcome: complete follow-up. Inclusion criteria: age ≥40 years, KOA clinical diagnosis or meeting KOA NICE criteria, and pain intensity ≥3/10. The program consisted of 8-week in-person and at-home exercise sessions. PNE and mind-body techniques were provided as videos and integrated into the exercise sessions. Participants completed questionnaires and physical assessments including blood draws at baseline and program completion. Secondary feasibility outcomes: acceptability of the intervention, burden, rates of recruitment, compliance and adherence, and adverse events. A priori success criteria were identified. Participants were invited to an online focus group. Results: 19 participants were enrolled, with a complete follow-up rate of 74% (mean age 63.3 years (SD 10.5), 73% female), indicating modifications were necessary to proceed. All other success criteria were met. The focus groups revealed that the video content pertaining to the mind-body techniques would benefit from on screen demonstrations. Conclusion: The Pain Informed Movement program is deemed feasible, with minor modifications needed to proceed. A pilot two-arm RCT will be conducted to establish the feasibility and explore potential effects of Pain Informed Movement compared to conventional neuromuscular exercise and standard OA education.

Pain Informed Movement for people with knee osteoarthritis: Protocol for a pilot randomized controlled trial.

Objective: Conservative pain management strategies for knee osteoarthritis (KOA) have limited effectiveness and do not employ a pain-mechanism informed approach. Pain Informed Movement is a novel intervention combining mind-body techniques with neuromuscular exercise and pain neuroscience education (PNE), aimed at improving endogenous pain modulation. While the feasibility and acceptability of this program has been previously established, it now requires further evaluation in comparison to standard KOA care. Design: This protocol describes the design of a pilot two-arm randomized controlled trial (RCT) with an embedded qualitative component. The primary outcome is complete follow-up rate. With an allocation ratio of 1:1, 66 participants (33/arm) (age ≥40 years, KOA diagnosis or meeting KOA NICE criteria, and pain intensity ≥3/10), will be randomly allocated to two groups that will both receive 8 weeks of twice weekly in-person exercise sessions. Those randomized to Pain Informed Movement will receive PNE and mind-body technique instruction provided initially as videos and integrated into exercise sessions. The control arm will receive neuromuscular exercise and standard OA education. Assessment will include clinical questionnaires, physical and psychophysical tests, and blood draws at baseline and program completion. Secondary outcomes are program acceptability, burden, rate of recruitment, compliance and adherence, and adverse events. Participants will be invited to an online focus group at program completion. Conclusion: The results of this pilot RCT will serve as the basis for a larger multi-site RCT aimed at determining the program's effectiveness with the primary outcome of assessing the mediating effects of descending modulation on changes in pain.

Multi-disciplinary community-based group intervention for fibromyalgia: a pilot randomized controlled trial.

Fibromyalgia is characterized by widespread pain, fatigue, sleep disturbances, mood disturbances, and cognitive impairment. Most individuals with fibromyalgia experience poorly managed symptoms and increased healthcare service use. Multicomponent therapies, with a focus on nonpharmacological modalities, are increasingly supported in the literature. However, given the limited resources available, implementation in smaller communities remains a challenge. This research tested a community-based multidisciplinary group intervention for individuals diagnosed with FM living in a small urban centre. The primary outcome was perceptions of quality of care and secondary outcomes included disease-related functioning, anxious and depressive symptoms, pain beliefs, and health service utilization. A pilot randomized control trial was conducted in which 60 patients diagnosed with fibromyalgia were randomized into a 10-week community-based multidisciplinary group intervention program or usual care. Treatment components included twice-weekly exercise sessions and weekly education sessions (e.g., pain education, cognitive behavioral strategies for stress, nutrition, peer support). The trial (NCT03270449) was registered September 1 2017. Statistically significant post-intervention improvements were found in the primary outcome, perceived quality of care (Cohen's d = 0.61, 0.66 for follow up care and goal setting, respectively). Secondary outcomes showing statistically significant improvements were disease-related daily functioning (Cohen's d = 0.70), depressive symptoms (Cohen's d = 0.87), and pain beliefs (Cohen's d = 0.61, 0.67, 0.82 for harm, disability and control, respectively). No adverse events were reported. Community-based multidisciplinary group interventions for fibromyalgia show promise for improving satisfaction with quality of care, disease-related functioning, and depression, and fostering more adaptive pain beliefs.

A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer.

Intratumor heterogeneity associates with poor patient outcome. Stromal stiffening also accompanies cancer. Whether cancers demonstrate stiffness heterogeneity, and if this is linked to tumor cell heterogeneity remains unclear. We developed a method to measure the stiffness heterogeneity in human breast tumors that quantifies the stromal stiffness each cell experiences and permits visual registration with biomarkers of tumor progression. We present Spatially Transformed Inferential Force Map (STIFMap) which exploits computer vision to precisely automate atomic force microscopy (AFM) indentation combined with a trained convolutional neural network to predict stromal elasticity with micron-resolution using collagen morphological features and ground truth AFM data. We registered high-elasticity regions within human breast tumors colocalizing with markers of mechanical activation and an epithelial-to-mesenchymal transition (EMT). The findings highlight the utility of STIFMap to assess mechanical heterogeneity of human tumors across length scales from single cells to whole tissues and implicates stromal stiffness in tumor cell heterogeneity.

Novel Bacterial Topoisomerase Inhibitor Gepotidacin Demonstrates Absence of Fluoroquinolone-Like Arthropathy in Juvenile Rats.

Fluoroquinolone use in children is limited due to its potential toxicity and negative effects on skeletal development, but the actual effects/risks of fluoroquinolones on bone growth and the mechanisms behind fluoroquinolone-driven arthropathy remain unknown. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibiotic with a unique mechanism of action that is not anticipated to have the same risks to bone growth as those of fluoroquinolones. Gepotidacin is in phase III clinical development for uncomplicated urinary tract infections (ClinicalTrials.gov identifiers NCT04020341 and NCT04187144) and urogenital gonorrhea (ClinicalTrials.gov identifier NCT04010539) in adults and adolescents ≥12 years of age. To inform arthropathy and other potential toxicity risks of gepotidacin in pediatric studies, this nonclinical study assessed oral gepotidacin toxicity in juvenile rats from postnatal day (PND) 4 to PND 32/35 (approximately equivalent to human ages from newborn to 11 years), using both in-life assessments (tolerability, toxicity, and toxicokinetics) and terminal assessments (necropsy with macroscopic and microscopic skeletal femoral head and/or stifle joint examinations). Gepotidacin doses of ≤300 mg/kg of body weight/day were well tolerated from PND 4 to PND 21, and higher doses of ≤1,250 mg/kg/day were well tolerated from PND 22 when the dose levels were escalated to maintain systemic exposure levels up to PND 35, with no observed treatment-related clinical signs, effects on mean body weight gain, or macroscopic findings on articular surfaces. A dose of 1,000 mg/kg/day was not tolerated during the dosing period from PND 4 to 21, with effects on body weight gain, fecal consistency, and body condition. Microscopic effects on articular surfaces were evaluated after 32 days of gepotidacin treatment at the highest tolerated dose. After 32 days of treatment with the highest tolerated gepotidacin dose of 300/1,250 mg/kg/day (systemic concentrations [area under the curve {AUC} values] of 93.7 µg · h/mL [males] and 121 µg · h/mL [females]), no skeletal effects on articular surfaces of the femoral head or stifle joint were observed. The absence of treatment-related clinical signs and arthropathy in juvenile rats provides evidence to support the potential future use of gepotidacin in children.

Development of a national pain management competency profile to guide entry-level physiotherapy education in Canada.

BACKGROUND: National strategies from North America call for substantive improvements in entry-level pain management education to help reduce the burden of chronic pain. Past work has generated a valuable set of interprofessional pain management competencies to guide the education of future health professionals. However, there has been very limited work that has explored the development of such competencies for individual professions in different regions. Developing profession-specific competencies tailored to the local context is a necessary first step to integrate them within local regulatory systems. Our group is working toward this goal within the context of entry-level physiotherapy (PT) programs across Canada. AIMS: This study aimed to create a consensus-based competency profile for pain management, specific to the Canadian PT context. METHODS: A modified Delphi design was used to achieve consensus across Canadian university-based and clinical pain educators. RESULTS: Representatives from 14 entry-level PT programs (93% of Canadian programs) and six clinical educators were recruited. After two rounds, a total of 15 competencies reached the predetermined endorsement threshold (75%). Most participants (85%) reported being "very satisfied" with the process. CONCLUSIONS: This process achieved consensus on a novel pain management competency profile specific to the Canadian PT context. The resulting profile delineates the necessary abilities required by physiotherapists to manage pain upon entry to practice. Participants were very satisfied with the process. This study also contributes to the emerging literature on integrated research in pain management by profiling research methodology that can be used to inform related work in other health professions and regions.

Contexte: Contexte: Les stratégies nationales nord-américaines préconisent des améliorations sensibles à la formation de base en matiére de prise en charge de la douleur afin de contribuer à la réduction du fardeau de la douleur chronique. Des travaux antérieurs ont généré un ensemble de compétences interprofessionnelles utile en matiére de prise en charge de la douleur afin de guider la formation des futurs professionnels de la santé. Cependant, trés peu de travaux ont porté sur l'acquisition de telles compétences pour des professions individuelles dans différentes régions. L'uisition de compétences spécifiques à une profession adaptées au contexte local est une première étape nécessaire pour leur intégration dans les systèmes réglementaires locaux. Notre groupe travaille à cet objectif dans le cadre de programmes de formation de base en physiothèrapie partout au Canada.Objectifs: Cette étude visait à créer un profil de compétences consensuel pour la prise en charge de la douleur, propre au contexte canadien de la physiothérapie.Méthodes: Un devis Delphi modifié a étè utilisé pour parvenir à un consensus parmi des formateurs en milieu universitaire et clinique en matière de douleur en milieu universitaire et clinique.Résultats: Des représentants de 14 programmes de formation de base en physiothérapie (93 % des programmes canadiens) et de six formateurs en milieu clinique ont été recrutés. Après deux tours, 15 compétences ont atteint le seuil d'approbation prédéterminé (75 %). La plupart des participants (85 %) ont déclaré être « très satisfaits ¼du processus.Conclusions: Ce processus a permis de dégager un consensus sur un nouveau profil de compétences en matiére de prise en charge de la douleur propre au contexte canadien de la physiothérapie. Ce profil délimite les habiletés requises des physiothérapeutes pour prendre en charge la douleur en début de pratique. Les participants ont été très satisfaits du processus. Cette étude contribue également à la littérature émergente sur la recherche intégrée en matière de prise en charge de la douleur en définissant une méthodologie de recherche qui peut être utilisée pour éclairer des travaux similaires dans d'autres professions de la santé et dans d'autres régions.

White Paper: Yoga Therapy and Pain-How Yoga Therapy Serves in Comprehensive Integrative Pain Management, and How It Can Do More.

This paper examines the role of yoga therapy in comprehensive integrative pain management (CIPM). The pain crisis is described, and how yoga therapists can contribute to its solution is explained. Yoga therapy can be an essential component of the multidisciplinary undertaking that will be required to improve patient outcomes and alter the trajectory of the global public health crisis constituted by an epidemic of poorly understood and inadequately addressed pain. Additional context and evidence are presented to document the effectiveness of yoga therapy interventions to support people living with pain. The white paper concludes by listing recommendations to providers, consumers, payers, and legislators, who together can address systemic and structural barriers to CIPM, as well as suggestions for enabling the yoga therapy profession to more fully participate in these solutions.

TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability.

SUMMARY: We present software to characterize and rank potential therapeutic (drug) targets with data from public databases and present it in a user-friendly format. By understanding potential obstacles to drug development through the gathering and understanding of this information, combined with robust approaches to target validation to generate therapeutic hypotheses, this approach may provide high quality targets, leading the process of drug development to become more efficient and cost-effective. AVAILABILITY AND IMPLEMENTATION: The information we gather on potential targets concerns small-molecule druggability (ligandability), suitability for large-molecule approaches (e.g. antibodies) or new modalities (e.g. antisense oligonucleotides, siRNA or PROTAC), feasibility (availability of resources such as assays and biological knowledge) and potential safety risks (adverse tissue-wise expression, deleterious phenotypes). This information can be termed 'tractability'. We provide visualization tools to understand its components. TractaViewer is available from https://github.com/NeilPearson-Lilly/TractaViewer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Retromer Controls Planar Polarity Protein Levels and Asymmetric Localization at Intercellular Junctions.

The coordinated polarization of cells in the plane of a tissue, termed planar polarity, is a characteristic feature of epithelial tissues [1]. In the fly wing, trichome positioning is dependent on the core planar polarity proteins adopting asymmetric subcellular localizations at apical junctions, where they form intercellular complexes that link neighboring cells [1-3]. Specifically, the seven-pass transmembrane protein Frizzled and the cytoplasmic proteins Dishevelled and Diego localize to distal cell ends, the four-pass transmembrane protein Strabismus and the cytoplasmic protein Prickle localize proximally, and the seven-pass transmembrane spanning atypical cadherin Flamingo localizes both proximally and distally. To establish asymmetry, these core proteins are sorted from an initially uniform distribution; however, the mechanisms underlying this polarized trafficking remain poorly understood. Here, we describe the identification of retromer, a master controller of endosomal recycling [4-6], as a key component regulating core planar polarity protein localization in Drosophila. Through generation of mutants, we verify that loss of the retromer-associated Snx27 cargo adaptor, but notably not components of the Wash complex, reduces junctional levels of the core proteins Flamingo and Strabismus in the developing wing. We establish that Snx27 directly associates with Flamingo via its C-terminal PDZ binding motif, and we show that Snx27 is essential for normal Flamingo trafficking. We conclude that Wash-independent retromer function and the Snx27 cargo adaptor are important components in the endosomal recycling of Flamingo and Strabismus back to the plasma membrane and thus contribute to the establishment and maintenance of planar polarization.

Sorting nexin-21 is a scaffold for the endosomal recruitment of huntingtin.

The endo-lysosomal network serves an essential role in determining the fate of endocytosed transmembrane proteins and their associated proteins and lipids. Sorting nexins (SNXs) play a central role in the functional organisation of this network. Comprising over 30 proteins in humans, SNXs are classified into sub-groups based on the presence of additional functional domains. Sorting nexin-20 (SNX20) and sorting nexin-21 (SNX21) comprise the SNX-PXB proteins. The presence of a predicted protein-protein interaction domain, termed the PX-associated B (PXB) domain, has led to the proposal that they function as endosome-associated scaffolds. Here, we used unbiased quantitative proteomics to define the SNX21 interactome. We reveal that the N-terminal extension of SNX21 interacts with huntingtin (Htt) whereas the PXB domain appears to associate with septins, a family of cytoskeletal- and membrane-associated proteins. In establishing that these interactions are sufficient for SNX21 to recruit Htt and septins on to an endosomal population, we reveal a scaffolding function for this sorting nexin. Our work paves the way for a more-detailed mechanistic analysis of the role(s) of the SNX-PXB proteins in endosomal biology.

Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.

Following endocytosis into the endosomal network, integral membrane proteins undergo sorting for lysosomal degradation or are retrieved and recycled back to the cell surface. Here we describe the discovery of an ancient and conserved multiprotein complex that orchestrates cargo retrieval and recycling and, importantly, is biochemically and functionally distinct from the established retromer pathway. We have called this complex 'retriever'; it is a heterotrimer composed of DSCR3, C16orf62 and VPS29, and bears striking similarity to retromer. We establish that retriever associates with the cargo adaptor sorting nexin 17 (SNX17) and couples to CCC (CCDC93, CCDC22, COMMD) and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5ß1 integrin. Through quantitative proteomic analysis, we identify over 120 cell surface proteins, including numerous integrins, signalling receptors and solute transporters, that require SNX17-retriever to maintain their surface levels. Our identification of retriever establishes a major endosomal retrieval and recycling pathway.

Reconciling movement and exercise with pain neuroscience education: A case for consistent education.

This article will introduce a conceptual framework of kinesthetic education that is consistent with and reinforces pain neuroscience education. This article will also provide some specific guidance for integrating pain neuroscience education with exercise and movement in a more congruent manner. Our belief is that this will enhance the effectiveness of specific movement approaches such as graded exposure techniques. Over the past decade, a new paradigm of pain education has been explored in an effort to improve patient outcomes. Using advances in pain neuroscience, patients are educated in the biological and physiological processes involved in their pain experience. Growing evidence supports the ability of pain neuroscience education (PNE) to positively impact a person's pain ratings, disability, pain catastrophization, and movement limitations. What is often overlooked, however, is the consistency between the messages of PNE and those of other therapeutic interventions, including movement therapies. This article proposes the following: education provided in isolation will be limited in its impact, the addition of guided purposeful movement performed in a manner consistent with PNE may be vital to the desired behavioral changes, and when inconsistent messages are delivered between education and movement interventions, outcomes may be adversely impacted.

Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases.

During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties.

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops.

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.

Novel hydroxyl tricyclics (e.g., GSK966587) as potent inhibitors of bacterial type IIA topoisomerases.

During the course of our research to find novel mode of action antibacterials, we discovered a series of hydroxyl tricyclic compounds that showed good potency against Gram-positive and Gram-negative pathogens. These compounds inhibit bacterial type IIA topoisomerases. Herein we will discuss structure-activity relationships in this series and report advanced studies on compound 1 (GSK966587) which demonstrates good PK and in vivo efficacy properties. X-ray crystallographic studies were used to provide insight into the structural basis for the difference in antibacterial potency between enantiomers.

Novel amino-piperidines as potent antibacterials targeting bacterial type IIA topoisomerases.

We have identified a series of amino-piperidine antibacterials with a good broad spectrum potency. We report the investigation of various subunits in this series and advanced studies on compound 8. Compound 8 possesses good pharmacokinetics, broad spectrum antibacterial activity and demonstrates oral efficacy in a rat lung infection model.

Novel cyclohexyl-amides as potent antibacterials targeting bacterial type IIA topoisomerases.

As part of our wider efforts to exploit novel mode of action antibacterials, we have discovered a series of cyclohexyl-amide compounds that has good Gram positive and Gram negative potency. The mechanism of action is via inhibition of bacterial topoisomerases II and IV. We have investigated various subunits in this series and report advanced studies on compound 7 which demonstrates good PK and in vivo efficacy properties.

Type IIA topoisomerase inhibition by a new class of antibacterial agents.

Despite the success of genomics in identifying new essential bacterial genes, there is a lack of sustainable leads in antibacterial drug discovery to address increasing multidrug resistance. Type IIA topoisomerases cleave and religate DNA to regulate DNA topology and are a major class of antibacterial and anticancer drug targets, yet there is no well developed structural basis for understanding drug action. Here we report the 2.1 A crystal structure of a potent, new class, broad-spectrum antibacterial agent in complex with Staphylococcus aureus DNA gyrase and DNA, showing a new mode of inhibition that circumvents fluoroquinolone resistance in this clinically important drug target. The inhibitor 'bridges' the DNA and a transient non-catalytic pocket on the two-fold axis at the GyrA dimer interface, and is close to the active sites and fluoroquinolone binding sites. In the inhibitor complex the active site seems poised to cleave the DNA, with a single metal ion observed between the TOPRIM (topoisomerase/primase) domain and the scissile phosphate. This work provides new insights into the mechanism of topoisomerase action and a platform for structure-based drug design of a new class of antibacterial agents against a clinically proven, but conformationally flexible, enzyme class.