Dess-Martin periodinane-mediated oxidation of the primary alcohol of cytidine into a carboxylic acid.

Herein the first example of conversion of alcohols into carboxylic acids by use of the Dess-Martin Periodinane (DMP), which is otherwise routinely employed for the conversion to aldehydes, is reported. This methodology will have significant potential utility in the synthesis of cytidine analogues and other related biologically important molecules.

Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase.

Malaria remains a significant public health challenge, with Plasmodium vivax being the species responsible for the most prevalent form of the disease. Given the limited therapeutic options available, the search for new antimalarials against P. vivax is urgent. This study aims to identify new inhibitors for P. vivax N-myristoyltransferase (PvNMT), an essential drug target against malaria. Through a validated virtual screening campaign, we prioritized 23 candidates for further testing. In the yeast NMT system, seven compounds exhibit a potential inhibitor phenotype. In vitro antimalarial phenotypic assays confirmed the activity of four candidates while demonstrating an absence of cytotoxicity. Enzymatic assays reveal LabMol-394 as the most promising inhibitor, displaying selectivity against the parasite and a strong correlation within the yeast system. Furthermore, molecular dynamics simulations shed some light into its binding mode. This study constitutes a substantial contribution to the exploration of a selective quinoline scaffold and provides valuable insights into the development of new antimalarial candidates.

Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase.

Inositol-requiring enzyme 1 (IRE1) is a transmembrane sensor that is part of a trio of sensors responsible for controlling the unfolded protein response within the endoplasmic reticulum (ER). Upon the accumulation of unfolded or misfolded proteins in the ER, IRE1 becomes activated and initiates the cleavage of a 26-nucleotide intron from human X-box-containing protein 1 (XBP1). The cleavage is mediated by the RtcB ligase enzyme, which splices together two exons, resulting in the formation of the spliced isoform XBP1s. The XBP1s isoform activates the transcription of genes involved in ER-associated degradation to maintain cellular homeostasis. The catalytic activity of RtcB is controlled by the phosphorylation and dephosphorylation of three tyrosine residues (Y306, Y316, and Y475), which are regulated by the ABL1 tyrosine kinase and PTP1B phosphatase, respectively. This study focuses on investigating the mechanism by which the PTP1B phosphatase activates the RtcB ligase using a range of advanced in silico methods. Protein-protein docking identified key interacting residues between RtcB and PTP1B. Notably, the phosphorylated Tyr306 formed hydrogen bonds and salt bridge interactions with the "gatekeeper" residues Arg47 and Lys120 of the inactive PTP1B. Classical molecular dynamics simulation emphasized the crucial role of Asp181 in the activation of PTP1B, driving the conformational change from an open to a closed state of the WPD-loop. Furthermore, QM/MM-MD simulations provided insights into the free energy landscape of the dephosphorylation reaction mechanism of RtcB, which is mediated by the PTP1B phosphatase.

Exploring women's interpretations of survey questions on pregnancy and pregnancy outcomes: cognitive interviews in Iganga Mayuge, Uganda.

BACKGROUND: In 2021, Uganda's neonatal mortality rate was approximately 19 deaths per 1000 live births, with an estimated stillbirth rate of 15.1 per 1000 total births. Data are critical for indicating areas where deaths occur and why, hence driving improvements. Many countries rely on surveys like Demographic and Health Surveys (DHS), which face challenges with respondents' misinterpretation of questions. However, little is documented about this in Uganda. Cognitive interviews aim to improve questionnaires and assess participants' comprehension of items. Through cognitive interviews we explored women's interpretations of questions on pregnancy and pregnancy outcomes. METHODS: In November 2021, we conducted cognitive interviews with 20 women in Iganga Mayuge health and demographic surveillance system site in eastern Uganda. We adapted the reproductive section of the DHS VIII women's questionnaire, purposively selected questions and used concurrent verbal probing. Participants had secondary school education and were English speaking. Cognition was measured through comparing instructions in the DHS interviewers' manual to participants' responses and researcher's knowledge. A qualitative descriptive approach to analysis was undertaken. RESULTS: We report findings under the cognitive aspect of comprehension. Some questions were correctly understood, especially those with less technical terms or without multiple sections. Most participants struggled with questions asking whether the woman has her living biological children residing with her or not. Indeed, some thought it referred to how many living children they had. There were comprehension difficulties with long questions like 210 that asks about miscarriages, newborn deaths, and stillbirths together. Participants had varying meanings for miscarriages, while many misinterpreted stillbirth, not linking it to gestational age. Furthermore, even amongst educated women some survey questions were misunderstood. CONCLUSIONS: Population surveys may misclassify, over or under report events around pregnancy and pregnancy outcomes. Interviewers should begin with a standard definition of key terms and ensure respondents understand these. Questions can be simplified through breaking up long sentences, while interviewer training should be modified to ensure they thoroughly understand key terms. We recommend cognitive interviews while developing survey tools, beyond basic pre-testing. Improving respondents' comprehension and thus response accuracy will increase reporting and data quality.

Different binding modalities of quercetin to inositol-requiring enzyme 1 of S. cerevisiae and human lead to opposite regulation.

The flavonoid Quercetin (Qe) was identified as an activator of Inositol-requiring enzyme 1 (IRE1) in S. cerevisiae (scIre1p), but its impact on human IRE1 (hIRE1) remains controversial due to the absence of a conserved Qe binding site. We have explored the binding modes and effect of Qe on both scIre1p and hIRE1 dimers using in silico and in vitro approaches. The activation site in scIre1p stably accommodates both Qe and its derivative Quercitrin (Qi), thus enhancing the stability of the RNase pocket. However, the corresponding region in hIRE1 does not bind any of the two molecules. Instead, we show that both Qe and Qi block the RNase activity of hIRE1 in vitro, with sub-micromolar IC50 values. Our results provide a rationale for why Qe is an activator in scIre1p but a potent inhibitor in hIRE1. The identification of a new allosteric site in hIRE1 opens a promising window for drug development and UPR modulation.

Discovery of novel inhibitors for Pseudomonas aeruginosa lipase enzyme from in silico and in vitro studies.

Pseudomonas aeruginosa is an opportunistic pathogen prone to developing drug-resistance and is a major cause of infection for burn patients and patients suffering from cystic fibrosis or are hospitalized in intensive care units. One of the virulence factors of this bacterium is the lipase enzyme that degrades the extracellular matrix of the host tissue and promotes invasion. Bromhexine is a mucolytic drug and has recently been reported to function as a competitive inhibitor of lipase with an IC50 value of 49 µM. In the present study, an attempt was made to identify stronger inhibitors from the ChEMBL database of bioactive compounds, as compared to the reference compound Bromhexine. Following docking and MD simulations, four hit compounds (N1-N4) were selected that showed promising binding modes and low RMSD values indicative of stable protein-ligand complexes. From subsequent binding pose metadynamics (BPMD) simulations, two of these (N2 and N4) stood out as more potent than Bromhexine, displaying stable interactions with residues in the catalytic site of the enzyme. Biological investigations were performed for all four compounds. Among them, the same two hit compounds were found to be the most effective binders with IC50 values of 22.1 and 27.5 µM, respectively; i.e. roughly twice as efficient as the reference Bromhexine. Taken together, our results show that these hits can be promising new candidates to use as leads for the development of drugs targeting the P. aeruginosa lipase enzyme.Communicated by Ramaswamy H. Sarma.

UFMylation: a ubiquitin-like modification.

Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein-protein interactions, protein stability, and thus the functions of their protein targets. Here, we focus on the most recently identified UBL, ubiquitin-fold modifier 1 (UFM1), and the machinery responsible for its transfer to substrates (UFMylation) or its removal (deUFMylation). We first highlight the biochemical peculiarities of these processes, then we develop on how UFMylation and its machinery control various intertwined cellular processes and we highlight some of the outstanding research questions in this emerging field.

Insights into the structure and function of the RNA ligase RtcB.

To be functional, some RNAs require a processing step involving splicing events. Each splicing event necessitates an RNA ligation step. RNA ligation is a process that can be achieved with various intermediaries such as self-catalysing RNAs, 5'-3' and 3'-5' RNA ligases. While several types of RNA ligation mechanisms occur in human, RtcB is the only 3'-5' RNA ligase identified in human cells to date. RtcB RNA ligation activity is well known to be essential for the splicing of XBP1, an essential transcription factor of the unfolded protein response; as well as for the maturation of specific intron-containing tRNAs. As such, RtcB is a core factor in protein synthesis and homeostasis. Taking advantage of the high homology between RtcB orthologues in archaea, bacteria and eukaryotes, this review will provide an introduction to the structure of RtcB and the mechanism of 3'-5' RNA ligation. This analysis is followed by a description of the mechanisms regulating RtcB activity and localisation, its known partners and its various functions from bacteria to human with a specific focus on human cancer.

Psychosocial effects of adverse pregnancy outcomes and their influence on reporting pregnancy loss during surveys and surveillance: narratives from Uganda.

BACKGROUND: In 2021, Uganda had an estimated 25,855 stillbirths and 32,037 newborn deaths. Many Adverse Pregnancy Outcomes (APOs) go unreported despite causing profound grief and other mental health effects. This study explored psychosocial effects of APOs and their influence on reporting these events during surveys and surveillance settings in Uganda. METHODS: A qualitative cross-sectional study was conducted in September 2021 in Iganga Mayuge health and demographic surveillance system site, eastern Uganda. Narratives were held with 44 women who had experienced an APO (miscarriage, stillbirth or neonatal death) and 7 men whose spouses had undergone the same. Respondents were purposively selected and the sample size premised on the need for diverse respondents. Reflexive thematic analysis was undertaken, supported by NVivo software. RESULTS: 60.8% of respondents had experienced neonatal deaths, 27.4% stillbirths, 11.8% miscarriages and almost half had multiple APOs. Theme one on psychosocial effects showed that both women and men suffered disbelief, depression, shame and thoughts of self-harm. In theme two on reactions to interviews, most respondents were reminded about their loss. Indeed, some women cried and a few requested termination of the interview. However, many said they eventually felt better, especially where interviewers comforted and advised them. In theme three about why people consent to such interviews, it was due to the respondents' need for sensitization on causes of pregnancy loss and danger signs, plus the expectation that the interview would lead to improved health services. Theme four on suggestions for improving interviews highlighted respondents' requests for a comforting and encouraging approach by interviewers. CONCLUSION: Psychosocial effects of APOs may influence respondents' interest and ability to effectively engage in an interview. Findings suggest that a multi-pronged approach, including interviewer training in identifying and dealing responsively with grieving respondents, and meeting needs for health information and professional counselling could improve reporting of APOs in surveys and surveillance settings. More so, participants need to understand the purpose of the interview and have realistic expectations.

Binding Analysis and Structure-Based Design of Tricyclic Coumarin-Derived MTHFD2 Inhibitors as Anticancer Agents: Insights from Computational Modeling.

Unfolded protein response (UPR)-dependent metabolic reprogramming diverts metabolites from glycolysis to mitochondrial 1C metabolism, highlighting pharmacological resistance to folate drugs and overexpression of certain enzymes. Methylenetetrahydrofolate dehydrogenase (MTHFD2) is a mitochondrial enzyme that plays a key role in 1C metabolism in purine and thymidine synthesis and is exclusively overexpressed in cancer cells but absent in most healthy adult human tissues. To the best of our knowledge, tricyclic coumarin-based compounds (substrate site binders) and xanthine derivatives (allosteric site binders) are the only selective inhibitors of MTHFD2 reported until the present date. The current study aims at the investigation of the available structural data of MTHFD2 in complex with potent and selective inhibitors that occupy the substrate binding site, further providing insights into binding mode, key protein-ligand interactions, and conformational dynamics, that correspond to the experimental binding affinities and biological activities. In addition, we carried out structure-based drug design on the substrate binding site of MTHFD2, by exploiting the cocrystal structure of MTHFD2 with the tricyclic coumarin-based inhibitor. The structure-based drug design campaign involves R-group enumeration, bioisostere replacement, molecular docking, ADME prediction, MM-GBSA binding free energy calculations, and molecular dynamics simulations, that led to a small library of new and potential compounds, capable of selectively inhibiting MTHFD2. The results reported herein are expected to benefit medicinal chemists working on the development of selective MTHFD2 inhibitors for cancer treatment, although experimental validation by biochemical and/or pharmacokinetic assays is required to substantiate the outcomes of the study.

Binding Modes of Xanthine-Derived Selective Allosteric Site Inhibitors of MTHFD2.

Methylenetetrahydrofolate dehydrogenase (MTHFD2) is a mitochondrial enzyme involved in 1 C metabolism that is upregulated in various cancer cells, but absent in normal proliferating cells. Xanthine derivatives are the first selective inhibitors of MTHFD2 which bind to its allosteric site. Xanthine derivatives (including the co-crystallized inhibitors) were herein interrogated by molecular/induced-fit docking, MM-GBSA binding free energy calculations and molecular dynamics simulations in both MTHFD2 and MTHFD1 (a close homolog expressed in healthy cells). The gained insights from our in silico protocol allowed us to study binding mode, key protein-ligand interactions and dynamic movement of the allosteric inhibitors, correlating with their experimental binding affinities, biological activities and selectivity for MTHFD2. The reported conformational changes with MTHFD2 upon binding of xanthine derivatives were furthermore evaluated and confirmed by RMSF analyses of the MD simulation trajectories. The results reported herein are expected to benefit in the rational design of selective MTHFD2 allosteric inhibitors.

A novel IRE1 kinase inhibitor for adjuvant glioblastoma treatment.

Inositol-requiring enzyme 1 (IRE1) is a major mediator of the unfolded protein response (UPR), which is activated upon endoplasmic reticulum (ER) stress. Tumor cells experience ER stress due to adverse microenvironmental cues, a stress overcome by relying on IRE1 signaling as an adaptive mechanism. Herein, we report the discovery of structurally new IRE1 inhibitors identified through the structural exploration of its kinase domain. Characterization in in vitro and in cellular models showed that they inhibit IRE1 signaling and sensitize glioblastoma (GB) cells to the standard chemotherapeutic, temozolomide (TMZ). Finally, we demonstrate that one of these inhibitors, Z4P, permeates the blood-brain barrier (BBB), inhibits GB growth, and prevents relapse in vivo when administered together with TMZ. The hit compound disclosed herein satisfies an unmet need for targeted, non-toxic IRE1 inhibitors and our results support the attractiveness of IRE1 as an adjuvant therapeutic target in GB.

A facilitated social innovation: stakeholder groups using Plan-Do-Study-Act cycles for perinatal health across levels of the health system in Cao Bang province, Vietnam.

BACKGROUND: Universal coverage of evidence-based interventions for perinatal health, often part of evidence-based guidelines, could prevent most perinatal deaths, particularly if entire communities were engaged in the implementation. Social innovations may provide creative solutions to the implementation of evidence-based guidelines, but successful use of social innovations relies on the engagement of communities and health system actors. This proof-of-concept study aimed to assess whether an earlier successful social innovation for improved neonatal survival that employed regular facilitated Plan-Do-Study-Act meetings on the commune level was feasible and acceptable when implemented on multiple levels of the health system (52 health units) and resulted in actions with plausibly favourable effects on perinatal health and survival in Cao Bang province, northern Vietnam. METHODS: The Integrated Promoting Action on Research Implementation in Health Services (i-PARIHS) framework guided the implementation and evaluation of the Perinatal Knowledge-Into-Practice (PeriKIP) project. Data collection included facilitators' diaries, health workers' knowledge on perinatal care, structured observations of antenatal care, focus group discussions with facilitators, their mentors and representatives of different actors of the initiated stakeholder groups and an individual interview with the Reproductive Health Centre director. Clinical experts assessed the relevance of the identified problems and actions taken based on facilitators' diaries. Descriptive statistics included proportions, means, and t-tests for the knowledge assessment and observations. Qualitative data were analysed by content analysis. RESULTS: The social innovation resulted in the identification of about 500 relevant problems. Also, 75% of planned actions to overcome prioritised problems were undertaken, results presented and a plan for new actions to achieve the group's goals to enhance perinatal health. The facilitators had significant roles, ensuring that the stakeholder groups were established based on principles of mutual respect. Overall, the knowledge of perinatal health and performance of antenatal care improved over the intervention period. CONCLUSIONS: The establishment of facilitated local stakeholder groups can remedy the need for tailored interventions and grassroots involvement in perinatal health and provide a scalable structure for focused efforts to reduce preventable deaths and promote health and well-being.

Structural Insights into Pseudomonas aeruginosa Exotoxin A-Elongation Factor 2 Interactions: A Molecular Dynamics Study.

Exotoxin A (ETA) is an extracellular secreted toxin and a single-chain polypeptide with A and B fragments that is produced by Pseudomonas aeruginosa. It catalyzes the ADP-ribosylation of a post-translationally modified histidine (diphthamide) on eukaryotic elongation factor 2 (eEF2), which results in the inactivation of the latter and the inhibition of protein biosynthesis. Studies show that the imidazole ring of diphthamide plays an important role in the ADP-ribosylation catalyzed by the toxin. In this work, we employ different in silico molecular dynamics (MD) simulation approaches to understand the role of diphthamide versus unmodified histidine in eEF2 on the interaction with ETA. Crystal structures of the eEF2-ETA complexes with three different ligands NAD+, ADP-ribose, and ßTAD were selected and compared in the diphthamide and histidine containing systems. The study shows that NAD+ bound to ETA remains very stable in comparison with other ligands, enabling the transfer of ADP-ribose to the N3 atom of the diphthamide imidazole ring in eEF2 during ribosylation. We also show that unmodified histidine in eEF2 has a negative impact on ETA binding and is not a suitable target for the attachment of ADP-ribose. Analyzing of radius of gyration and COM distances for NAD+, ßTAD, and ADP-ribose complexes revealed that unmodified His affects the structure and destabilizes the complex with all different ligands throughout the MD simulations.

Training and support for the role of facilitator in implementation of innovations in health and community care: a scoping review protocol.

BACKGROUND: Implementing and sustaining innovations in clinical practice, such as evidence-based practices, programmes, and policies, is frequently described as challenging. Facilitation as a strategy for supporting implementation requires a facilitator, i.e. an individual with a designated role to support the implementation process. A growing number of studies report that facilitation can help tackle the challenges in implementation efforts. To optimise the potential contribution of facilitation as a strategy to improve the implementation of new practices, there is a need to enhance understanding about what training and support is required for individuals in the facilitator role. The objective of this scoping review is to map how facilitators have been trained for, and supported in, the facilitator role in implementation studies in health and community care. Specifically, the review aims to examine what is reported on training and support of facilitators in terms of learning outcomes, content, dose, mode of delivery, learning activities, and qualifications of the trainers and how the facilitators perceive training and support. METHODS: This scoping review will follow the guidance of the Joanna Briggs Institute and the PRISMA Extension for Scoping Review checklist. We will include articles in which (a) facilitation is deployed as an implementation strategy, with identified facilitator roles targeting staff and managers, to support the implementation of specified innovations in health or community care, and (b) training and/or support of facilitators is reported. We will exclude articles where facilitation is directed to education or training in specific clinical procedures or if facilitation supports the implementation of general quality improvement systems. All types of peer-reviewed studies and study protocols published in English will be included. A systematic search will be performed in MEDLINE (Ovid), Embase (embase.com), Web of Science Core Collection, and CINAHL (Ebsco). DISCUSSION: The proposed scoping review will provide a systematic mapping of the literature on the training and support of implementation facilitators and contribute useful knowledge within the field of implementation science to inform future facilitation initiatives. SYSTEMATIC REVIEW REGISTRATION: Registered at Open Science Framework (registration https://doi.org/10.17605/OSF.IO/M6NPQ ).

In silico and in vitro studies confirm Ondansetron as a novel acetylcholinesterase and butyrylcholinesterase inhibitor.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is growing rapidly among the elderly population around the world. Studies show that a lack of acetylcholine and butyrylcholine due to the overexpression of enzymes Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) may lead to reduced communication between neuron cells. As a result, seeking novel inhibitors targeting these enzymes might be vital for the future treatment of AD. Ondansetron is used to prevent nausea and vomiting caused by chemotherapy or radiation treatments and is herein shown to be a potent inhibitor of cholinesterase. Comparison is made between Ondansetron and FDA-approved cholinesterase inhibitors Rivastigmine and Tacrine. Molecular docking demonstrates that interactions between the studied ligand and aromatic residues in the peripheral region of the active site are important in binding. Molecular dynamics simulations and binding pose metadynamics show that Ondansetron is highly potent against both enzymes and far better than Rivastigmine. Inhibitor activities evaluated by in vitro studies confirm that the drug inhibits AChE and BChE by non-competitive and mixed inhibition, respectively, with IC50 values 33 µM (AChE) and 2.5 µM (BChE). Based on the findings, we propose that Ondansetron may have therapeutic applications in inhibiting cholinesterase, especially for BChE.

Gene Editing Corrects In Vitro a G > A GLB1 Transition from a GM1 Gangliosidosis Patient.

Ganglioside-monosialic acid (GM1) gangliosidosis, a rare autosomal recessive disorder, is frequently caused by deleterious single nucleotide variants (SNVs) in GLB1 gene. These variants result in reduced ß-galactosidase (ß-gal) activity, leading to neurodegeneration associated with premature death. Currently, no effective therapy for GM1 gangliosidosis is available. Three ongoing clinical trials aim to deliver a functional copy of the GLB1 gene to stop disease progression. In this study, we show that 41% of GLB1 pathogenic SNVs can be replaced by adenine base editors (ABEs). Our results demonstrate that ABE efficiently corrects the pathogenic allele in patient-derived fibroblasts, restoring therapeutic levels of ß-gal activity. Off-target DNA analysis did not detect off-target editing activity in treated patient's cells, except a bystander edit without consequences on ß-gal activity based on 3D structure bioinformatics predictions. Altogether, our results suggest that gene editing might be an alternative strategy to cure GM1 gangliosidosis.

Metalloprotease-mediated cleavage of CD95 ligand.

CD95 is a member of the TNF receptor superfamily that is ubiquitously expressed in healthy and pathological tissues. Stimulation of CD95 by its physiological ligand CD95L induces its oligomerization leading in turn to the transduction of either apoptotic or nonapoptotic signals. CD95L can exist as both membrane-anchored and soluble forms (sCD95L), the latter resulting from the proteolytic cleavage of the former. Candidate proteases able to achieve CD95L cleavage were identified as matrix metalloproteases (MMP) due to their demonstrated ability to cleave other TNF superfamily ligands. The main goal of this study was to systematically identify the MMP family members capable of cleaving CD95L and subsequently determine the corresponding cleavage sites. By using different orthogonal biochemical approaches and combining them with molecular modelling, we confirmed data from the literature regarding CD95L cleavage by MMP-3 and MMP-7. Moreover, we found that MMP-2 and MMP-12 can cleave CD95L and characterized their resulting cleavage sites. This study provides a systematic approach to analyse the cleavage of CD95L, which until now had only been poorly described.

High-resolution structure of a fish aquaporin reveals a novel extracellular fold.

Aquaporins are protein channels embedded in the lipid bilayer in cells from all organisms on earth that are crucial for water homeostasis. In fish, aquaporins are believed to be important for osmoregulation; however, the molecular mechanism behind this is poorly understood. Here, we present the first structural and functional characterization of a fish aquaporin; cpAQP1aa from the fresh water fish climbing perch (<i>Anabas testudineus</i>), a species that is of high osmoregulatory interest because of its ability to spend time in seawater and on land. These studies show that cpAQP1aa is a water-specific aquaporin with a unique fold on the extracellular side that results in a constriction region. Functional analysis combined with molecular dynamic simulations suggests that phosphorylation at two sites causes structural perturbations in this region that may have implications for channel gating from the extracellular side.