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The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments., (© 2023 The Authors. Molecular Informatics published by Wiley-VCH GmbH.)

The cytoplasmic steps of peptidoglycan synthesis represent an important targeted pathway for development of new antibiotics. Herein, we report the synthesis of novel 3-oxopyrazolidin-4-carboxamide derivatives with variable amide side chains as potential antibacterial agents targeting MurA enzyme, the first committed enzyme in these cytosolic steps. Compounds 15 (isoindoline-1,3-dione-5-yl), 16 (4-(1H-pyrazol-4-yl)phenyl), 20 (5-cyanothiazol-2-yl), 21 and 31 (5-nitrothiazol-2-yl derivatives) exhibited the most potent MurA inhibition, with IC 50 values of 9.8-12.2 μM. Compounds 15, 16 and 21 showed equipotent inhibition of the C115D MurA mutant developed by fosfomycin-resistant Escherichia coli. NMR binding studies revealed that some of the MurA residues targeted by 15 also interacted with fosfomycin, but not all, indicating an overlapping but not identical binding site. The antibacterial activity of the compounds against E. coli ΔtolC suggests that inhibition of MurA accounts for the observed effect on bacterial growth, considering that a few potent MurA inhibitors could not penetrate the bacterial outer membrane and were therefore inactive as proven by the bacterial cell uptake assay. The most promising compounds were also evaluated against a panel of Gram-positive bacteria. Remarkably, compounds 21 and 31 (MurA IC 50  = 9.8 and 10.2 μM respectively) exhibited a potent activity against Clostridioides difficile strains with MIC values ranging from 0.125 to 1 μg/mL, and were also shown to be bactericidal with MBC values between 0.25 and 1 μg/mL. Furthermore, both compounds were shown to have a limited activity against human normal intestinal flora and showed high safety towards human colon cells (Caco-2) in vitro. The thiolactone derivative (compound 5) exhibited an interesting broad spectrum antibacterial activity despite its weak MurA inhibition. Altogether, the presented series provides a promising class of antibiotics that merits further investigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Acyl carrier proteins (ACPs) are universally conserved proteins amongst different species and are involved in fatty acid synthesis. Bacteria utilize ACPs as acyl carriers and donors for the synthesis of products such as endotoxins or acyl homoserine lactones (AHLs), which are used in quorum sensing mechanisms. In this study, wehave expressed isotopically labeled holo-ACP from Burkholderia mallei in Escherichia coli to assign 100% of non-proline backbone amide (HN) resonances, 95.5% of aliphatic carbon resonances and 98.6% of aliphatic hydrogen sidechain resonances., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Context: Does lower baseline cognitive function predispose athletes to ACL injury risk, especially when performing unplanned or dual-task movements?, Objective: To evaluate the association between cognitive function and biomechanics related to ACL injuries during cognitively challenging sports movements., Data Sources: PubMed (MEDLINE), Web of Science, Scopus, and SciELO databases were searched; additional hand searching was also conducted., Study Selection: The following inclusion criteria had to be met: participants completed (1) a neurocognitive test, (2) a cognitively challenging sport-related task involving lower limbs, and (3) a biomechanical analysis. The following criteria determined exclusion from the review: studies involving participants with (1) recent or current musculoskeletal injuries; (2) recent or current concussion; (3) ACL surgical reconstruction, reviews of the literature, commentary or opinion articles, and case studies., Study Design: Systematic review using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P) statement and registered at the International Prospective Register of Systematic Reviews (PROSPERO)., Level of Evidence: Level 3., Data Extraction: Two of authors independently extracted data and assessed the methodological quality of the articles with the Downs and Black and ROBINS-I checklists, to assess methodological quality and risk of bias, respectively., Results: Six studies with different methodologies and confounding factors were included in this review. Of these 6 studies, 3 were ranked as high-quality, 3 demonstrated a low risk of bias, 2 a moderate risk, and 1 a severe risk. Five studies found a cognitive-motor relationship, with worse cognitive performance associated with increased injury risk, with 1 study reporting the opposite directionality for 1 variable. One study did not identify any interaction between cognitive function and biomechanical outcomes., Conclusion: Worse cognitive performance is associated with an increased injury risk profile during cognitively challenging movements., Competing Interests: The authors report no potential conflicts of interest in the development and publication of this article.

An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum information guidelines define the fundamental complement of data that can support an unambiguous conclusion based on experimental observations. We present the Minimum Information About Disorder Experiments (MIADE) guidelines to define the parameters required for the wider scientific community to understand the findings of an experiment studying the structural properties of intrinsically disordered regions (IDRs). MIADE guidelines provide recommendations for data producers to describe the results of their experiments at source, for curators to annotate experimental data to community resources and for database developers maintaining community resources to disseminate the data. The MIADE guidelines will improve the interpretability of experimental results for data consumers, facilitate direct data submission, simplify data curation, improve data exchange among repositories and standardize the dissemination of the key metadata on an IDR experiment by IDR data sources., (© 2023. Springer Nature America, Inc.)

Background: Physical fatigue and cognitive performance have been suggested as risk factors for an anterior cruciate ligament (ACL) injury, and fatigue has also been demonstrated to reduce cognitive processing. The combined effects of fatigue and lower cognitive function during cognitive-challenging movements may increase knee mechanics associated with the ACL injury risk., Hypotheses: We hypothesized that (1) knee mechanics would be detrimentally affected by fatigue and associated with baseline cognitive function and (2) fatigue-induced deleterious changes in cognitive performance and knee mechanics would be correlated., Study Design: Descriptive laboratory study., Methods: A total of 22 athletes completed baseline cognitive testing. After performing maximal vertical jumps, they performed a jump-land-jump task based on unanticipated visual cues. Then, they completed a fatigue protocol including countermovement jumps, among other tasks, until the jump height decreased below 90% of their assessed maximum. Immediately after reaching the first fatigue point, they performed another set of jump-landing tasks, followed by repeating the fatigue protocol until the jump height decreased below 85% of their assessed maximum. After reaching the second fatigue point, they performed a final set of jump-landing tasks and repeated the initial cognitive assessment battery., Results: Mixed-effects models revealed that knee flexion decreased through the fatigue protocol (baseline: 61.8°; midpoint: 61.1°; final: 60.1°; P = .003). Stepwise regression showed that fatigue-worsened attentional control corresponded to smaller knee abduction angles ( R 2 adjusted = 51.68%; β standardized = 1.16; P = .001), and worse reaction time after fatigue correlated with increased knee abduction angles (β standardized = 0.85; P = .006) after accounting for the role of attentional control., Conclusion: Fatigue induced incremental modifications in sagittal-plane knee mechanics during an unanticipated sports movement. In addition, fatigue induced changes in cognitive function related to ACL injury-relevant knee mechanics., Clinical Relevance: The novel findings regarding fatigue-dependent changes in injury-relevant biomechanics during cognitively challenging movements represent an extension of recent developments in understanding the role of cognition in the ACL injury risk.

Lactate is abundant in rapidly dividing cells owing to the requirement for elevated glucose catabolism to support proliferation 1-6 . However, it is not known whether accumulated lactate affects the proliferative state. Here we use a systematic approach to determine lactate-dependent regulation of proteins across the human proteome. From these data, we identify a mechanism of cell cycle regulation whereby accumulated lactate remodels the anaphase promoting complex (APC/C). Remodelling of APC/C in this way is caused by direct inhibition of the SUMO protease SENP1 by lactate. We find that accumulated lactate binds and inhibits SENP1 by forming a complex with zinc in the SENP1 active site. SENP1 inhibition by lactate stabilizes SUMOylation of two residues on APC4, which drives UBE2C binding to APC/C. This direct regulation of APC/C by lactate stimulates timed degradation of cell cycle proteins, and efficient mitotic exit in proliferative human cells. This mechanism is initiated upon mitotic entry when lactate abundance reaches its apex. In this way, accumulation of lactate communicates the consequences of a nutrient-replete growth phase to stimulate timed opening of APC/C, cell division and proliferation. Conversely, persistent accumulation of lactate drives aberrant APC/C remodelling and can overcome anti-mitotic pharmacology via mitotic slippage. In sum, we define a biochemical mechanism through which lactate directly regulates protein function to control the cell cycle and proliferation., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Acyl-homoserine lactone synthases make specific AHL quorum sensing signals to aid virulence in Gram-negative bacteria. Here, we use solution NMR spectroscopy to demonstrate that the carrier protein-enzyme interface accurately reveals substrate recognition mechanisms in two quorum signal synthases.

To develop novel antibiotics, targeting the early steps of cell wall peptidoglycan biosynthesis seems to be a promising strategy that is still underutilized. MurA, the first enzyme in this pathway, is targeted by the clinically used irreversible inhibitor fosfomycin. However, mutations in its binding site can cause bacterial resistance. We herein report a series of novel reversible pyrrolidinedione-based MurA inhibitors that equally inhibit wild type (WT) MurA and the fosfomycin-resistant MurA C115D mutant, showing an additive effect with fosfomycin for the inhibition of WT MurA. For the most potent inhibitor 46 (IC 50 = 4.5 μM), the mode of inhibition was analyzed using native mass spectrometry and protein NMR spectroscopy. The compound class was nontoxic against human cells and highly stable in human S9 fraction, human plasma, and bacterial cell lysate. Taken together, this novel compound class might be further developed toward antibiotic drug candidates that inhibit cell wall synthesis.

Cognitive function plays a role in understanding noncontact anterior cruciate ligament injuries, but the research into how cognitive function influences sport-specific movements is underdeveloped. The purpose of this study was to determine how various cognitive tasks influenced dual-task jump-landing performance along with how individuals' baseline cognitive ability mediated these relationships. Forty female recreational soccer and basketball players completed baseline cognitive function assessments and dual-task jump landings. The baseline cognitive assessments quantified individual processing speed, multitasking, attentional control, and primary memory ability. Dual-task conditions for the jump landing included unanticipated and anticipated jump performance, with and without concurrent working memory and captured visual attention tasks. Knee kinematics and kinetics were acquired through motion capture and ground reaction force data. Jumping conditions that directed visual attention away from the landing, whether anticipated or unanticipated, were associated with decreased peak knee flexion angle (P < .001). No interactions between cognitive function measures and jump-landing conditions were observed for any of the biomechanical variables, suggesting that injury-relevant cognitive-motor relationships may be specific to secondary task demands and movement requirements. This work provides insight into group- and subject-specific effects of established anticipatory and novel working memory dual-task paradigms on the neuromuscular control of a sport-specific movement.

The eukaryotic translation initiation factor 4E (eIF4E) is the master regulator of cap-dependent protein synthesis. Overexpression of eIF4E is implicated in diseases such as cancer, where dysregulation of oncogenic protein translation is frequently observed. eIF4E has been an attractive target for cancer treatment. Here we report a high-resolution X-ray crystal structure of eIF4E in complex with a novel inhibitor (i4EG-BiP) that targets an internal binding site, in contrast to the previously described inhibitor, 4EGI-1, which binds to the surface. We demonstrate that i4EG-BiP is able to displace the scaffold protein eIF4G and inhibit the proliferation of cancer cells. We provide insights into how i4EG-BiP is able to inhibit cap-dependent translation by increasing the eIF4E-4E-BP1 interaction while diminishing the interaction of eIF4E with eIF4G. Leveraging structural details, we designed proteolysis targeted chimeras (PROTACs) derived from 4EGI-1 and i4EG-BiP and characterized these on biochemical and cellular levels. We were able to design PROTACs capable of binding eIF4E and successfully engaging Cereblon, which targets proteins for proteolysis. However, these initial PROTACs did not successfully stimulate degradation of eIF4E, possibly due to competitive effects from 4E-BP1 binding. Our results highlight challenges of targeted proteasomal degradation of eIF4E that must be addressed by future efforts., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: E. S. F. is a founder, science advisory board member and equity holder in Civetta, Jengu (board member) and Neomorph, an equity holder in C4, and a consultant to Astellas, Novartis, Deerfield, RA Capital and EcoR1. The Fischer lab receives or has received research funding from Novartis, Astellas, Ajax and Deerfield. G.W. is co-founder of PIC Therapeutics, Cellmig biolabs, Skinap therapeutics and Virtual Discovery. H.A. is an equity holder in PIC Therapeutics. The research described here is scientifically and financially independent of the efforts in any of the above-mentioned companies., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and the inclusion of experimental constraints. Here, we add support of PLANTS to VirtualFlow (VirtualFlow Ants), which adds a valuable method for primary virtual screenings and rescoring procedures. Furthermore, we have added support of ligand libraries in the MOL2 format, as well as on the fly conversion of ligand libraries which are in the PDBQT format to the MOL2 format to endow VirtualFlow Ants with an increased flexibility regarding the ligand libraries. The on the fly conversion is carried out with Open Babel and the program SPORES. We applied VirtualFlow Ants to a test system involving KEAP1 on the Google Cloud up to 128,000 CPUs, and the observed scaling behavior is approximately linear. Furthermore, we have adjusted several central docking parameters of PLANTS (such as the speed parameter or the number of ants) and screened 10 million compounds for each of the 10 resulting docking scenarios. We analyzed their docking scores and average docking times, which are key factors in virtual screenings. The possibility of carrying out ultra-large virtual screening with PLANTS via VirtualFlow Ants opens new avenues in computational drug discovery.

The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions., Competing Interests: M.C. and V.D. report working for Innophore. C.C.G. reports being a shareholder and CEO of Innophore, an enzyme and drug discovery company. G.W. and C.G. report being co-founders of the company Virtual Discovery, Inc., which provides virtual screening services. G.W. reports serving as the director of this company. G.W. reports being a co-founder of PIC Therapeutics, Cellmig Biolabs, and Skinap Therapeutics. H.A. reports being an equity holder in PIC Therapeutics. I.I. and D.R. report working for Enamine, a company that is involved in the synthesis and distribution of chemical building blocks, fragments, and screening compounds. Y.M. reports being a scientific advisor for Enamine. Y.M., O.T., and A.P. report working for Chemspace, a company that is involved in the distribution of chemical building blocks, fragments, and screening compounds. I.D. reports working for UkrOrgSyntez Ltd. (UORSY), a company that is involved in the synthesis of chemical building blocks, fragments, and screening compounds. G.T., S.P., A.S., M.G., N.L., C.H., E.Y., R.L., R.Y., D.P., and J.K. report working for Google, a company that also provides cloud computing services. The research described here is scientifically and financially independent of the efforts in any of the above mentioned companies., (© 2020 The Author(s).)

On average, an approved drug currently costs US$2-3 billion and takes more than 10 years to develop 1 . In part, this is due to expensive and time-consuming wet-laboratory experiments, poor initial hit compounds and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening has the potential to mitigate these problems. With structure-based virtual screening, the quality of the hits improves with the number of compounds screened 2 . However, despite the fact that large databases of compounds exist, the ability to carry out large-scale structure-based virtual screening on computer clusters in an accessible, efficient and flexible manner has remained difficult. Here we describe VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we prepared one of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened more than 1 billion compounds and identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. One of the lead inhibitors (iKeap1) engages KEAP1 with nanomolar affinity (dissociation constant (K d ) = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify molecules that bind with high affinity to target proteins.

BACKGROUND Pneumomediastinum is an uncommon clinical condition that usually occurs spontaneously, or is caused by blunt thoracic or abdominal trauma. This report is of a rare case of pneumomediastinum caused by blunt neck trauma in an adult and describes the clinical and radiological features and the principles of clinical management. CASE REPORT A 23-year-old man presented with increased neck swelling, dysphonia and pain on swallowing (odynophagia) after blunt neck trauma during a rugby game. Chest X-ray and computed tomography (CT) showed features that were consistent with pneumomediastinum, including extensive subcutaneous emphysema. The patient was intubated and monitored in the intensive care unit (ICU) and managed with early stabilization of the airway and with conservative methods. He had no complications on clinical follow-up following hospital discharge. CONCLUSIONS Although pneumomediastinum is an uncommon condition, the complications can be fatal. This case highlights the importance of thoroughly investigating cases of subcutaneous emphysema and the importance of early stabilization of the airway.

Muraymycins are a subclass of antimicrobially active uridine-derived natural products. Biological data on several muraymycin analogues have been reported, including some inhibitory in vitro activities toward their target protein, the bacterial membrane enzyme MraY. However, a structure-activity relationship (SAR) study on naturally occurring muraymycins based on such in vitro data has been missing so far. In this work, we report a detailed SAR investigation on representatives of the four muraymycin subgroups A-D using a fluorescence-based in vitro MraY assay. For some muraymycins, inhibition of MraY with IC 50 values in the low-picomolar range was observed. These inhibitory potencies were compared with antibacterial activities and were correlated to modelling data derived from a previously reported X-ray crystal structure of MraY in complex with a muraymycin inhibitor. Overall, these results will pave the way for the development of muraymycin analogues with optimized properties as antibacterial drug candidates., (© 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The Cavitron ultrasonic surgical aspirator has been successfully used in general surgery and neurosurgery. We have explored its use in the dissection of small-diameter blood vessels and nerves (1-2 mm) in a rat model. Our results seem to indicate that this technique may be useful in isolating blood vessels surrounded by fatty tissue without damage to the vessel itself. In this study, however, high-frequency ultrasound did cause significant damage to peripheral nerves.