Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

What are the mental health changes associated with the COVID-19 pandemic in people with medical conditions? An international survey.

OBJECTIVES: The COVID-19 pandemic has negatively impacted mental health worldwide but there is paucity of knowledge regarding the level of change in mental health in people with a medical condition (physical/psychiatric). The objectives of this study were (1) to compare the change in mental health in people with and without medical conditions, (2) to assess the change in various types of medical conditions, (3) to evaluate the association between change in mental health and number of comorbidities, and (4) to investigate the influence of receiving treatment and activity limitation imposed by the medical condition(s). DESIGN: Cross-sectional. SETTING: Online international survey. PARTICIPANT: English-speaking adults (age ≥18) were included in the study, with no exclusions based on sex/gender or location. 1276 participants (mean age 30.4, 77.7% female) were included. PRIMARY AND SECONDARY OUTCOME MEASURES: Pre and during COVID-19 pandemic symptoms of anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-9) were assessed. The Self-Administered Comorbidity Questionnaire was used to collect data regarding medical conditions.Repeated-measures analysis of covariance (objectives 1, 2 and 4) and Pearson's correlation coefficient (objective 3). RESULTS: 50.1% of participants had a medical condition. During the COVID-19 pandemic, compared with people with no medical condition, people with both psychiatric and physical conditions experienced significantly higher symptoms of anxiety (12%, p=0.009) and depression (9.4%, p<0.001). Although not statistically significant, the increase in anxiety and depression occurred across seven major categories of conditions. An association was found between having a higher number of medical conditions with higher anxiety and depression symptoms (r=0.16 anxiety, r=0.14 depression, p<0.001). Receiving treatment and being functionally limited by the disease did not have a significant impact on the amount of change (p>0.05). CONCLUSIONS: During the COVID-19 pandemic, people who had a combination of psychiatric and physical conditions experienced greater symptoms of anxiety and depression. Patients with chronic diseases may need extra support to address their mental health as a result of the pandemic.

An intersectional approach to identifying factors associated with anxiety and depression following the COVID-19 pandemic.

The COVID-19 pandemic is impacting mental health, with some populations bearing a greater burden. In this cross-sectional online study, we examined the personal and intersectional factors associated with increased symptoms of anxiety and depression following the COVID-19 pandemic. We assessed pre- and post-pandemic levels of anxiety and depressive symptoms using the Generalized Anxiety Disorder-2 (GAD-2) and Patient Health Questionnaire-9 (PHQ-9) scales, respectively. The study included 1847 participants, with an age range of 18 to 79 years and representing 43 countries. Variables with significance (p < 0.05) in predicting post-pandemic GAD-2 and PHQ-9 scores were pre-pandemic scores on the same scales, an interaction between increasing age and non-man gender, and an interaction between non-man gender and having children. Health practitioners, psychiatrists, and policy makers need to be aware and respond to the mental health burden of the pandemic on women and other gendered individuals, especially those who care for children.

The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.

The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.

COVID-19 attributed Changes of Home and Family Responsibilities among Single Mothers

Lockdown measures during COVID-19 have presented increased challenges in the home and family responsibilities. Single mothers may face unique challenges as they may be isolated from external family supports. Changes on a 19-item home and family work role survey pre- and post-COVID were tested with a paired t-test and sign test;the impact of age and people in the home was assessed using linear regression. There was a significant increase (p < 0.05) in 6/19 post-COVID-19 family responsibilities. In comparison to pre-COVID-19, post-COVID-19 single mothers reported a statistically significant median increase in family responsibilities (Mdn = .0000), p < .041. Each additional person living in the home was associated with a decrease in family responsibilities (B = -13.1, 95% CI [-21.943, -4.247]). Changes in the home and family responsibilities confirm that COVID-19 led to increased unpaid work to fulfill home and family responsibilities among single mothers.

Understanding the unpaid work roles amongst households, during COVID-19.

Background: Worldwide, the COVID-19 pandemic has had a rapid disruption on work, social activities and family life. Pre-pandemic norms suggested that women spend more time in unpaid work roles and with childcare, while men spend more time in paid work roles. This study aims to understand: 1) the distribution of unpaid work roles within households, and 2) if there are certain factors that explain the unpaid work roles within a household during the pandemic. Methods: This study used a cross-sectional survey of people across the globe, during the pandemic. The survey, administered through a virtual platform of Qualtrics, consisted of the following sections: (a) consent, (b) location and job description (c) marital status and household numbers (d) age, sex, and gender (e) unpaid work roles and family responsibilities. Descriptive statistics and percentages were reported for all the data regarding the study variables. A multivariable regression model was used to understand which factors may explain the changes in unpaid work roles recalling before and during the pandemic. Results: This survey was completed by 1847 participants. The mean age was 30 years old (standard deviation of 13.3). The majority of participants identified themselves as women (76.0%) and single (62.1%). The multivariable linear regression indicated that marital status (single, common-law, married, divorced), higher number of household members (1-8,12), older age, higher number of dependent children, and gender (female) were positive and significant predictors of baseline changes in unpaid work role scores, explaining 50% of the variance (R2 = 0.50). Discussion: All households experienced a significant increase in the amount of unpaid work roles during the pandemic. However, older women who were in a relationship and experienced additional household members such as dependent children or sick older adults, were faced with more changes in unpaid work roles during COVID-19, than other individuals.

What Are Work-Related Predictors of Post-COVID-19 Home and Family Work Roles? A Cross-Sectional Survey.

OBJECTIVE: To determine the extent to which pre-and post-COVID-19 work-related factors can explain post-COVID-19 home and family work roles. METHODS: This study was a cross-sectional survey. The primary outcome measure was the Home and Family Work Roles Questionnaire. Descriptive statistical methods and multiple regression analyses were run. The significant predictors were further probed in a one-way analysis of covariance (ANCOVA) model with a Tukey posthoc correction. RESULTS: In our sample of 1447 participants, the two significant predictors of post-COVID-19 home and family work roles were pre-pandemic paid job status (F [3, 1401] = 5.66, P < 0.001), and pre-COVID-19 home and family work roles (F [1, 1401] = 2509.26, P < 0.001). CONCLUSION: Greater pre-pandemic home and family role responsibilities, full-time and part-time employment pre-COVID-19 were associated with greater post-COVID-19 home and family responsibilities.

The role of sex and gender in the changing levels of anxiety and depression during the COVID-19 pandemic: A cross-sectional study.

BACKGROUND: Several studies have assessed the impact of the COVID-19 pandemic on anxiety and depression, but have not focused on the role of sex and gender. This study compared changes in the levels of anxiety and depression (pre- and post-COVID) experienced by individuals of various sexes and genders. METHODS: We used a cross-sectional online survey that assessed pre- and post-COVID symptoms of anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-9). General linear modeling (fixed model factorial analysis of variance) was used to evaluate changes in anxiety and depression between pre- and post-pandemic periods and explore differential effects of sex and gender on those changes. RESULTS: Our study included 1847 participants from 43 countries and demonstrated a percentage increase of 57.1% and 74.2% in anxiety and depression, respectively. For the Generalized Anxiety Disorder-2 scale (maximum score 6), there was a mean increase in anxiety by sex for male, female, and other of 1.0, 1.2, and 1.4, respectively; and by gender for man, woman, and others of 0.9, 1.3, and 1.6, respectively. For the Patient Health Questionnaire-9 (maximum score 27), there was a mean increase in depressive symptoms by sex for male, female, and other of 3.6, 4.7, and 5.5 respectively; and by gender for man, woman, and others of 3.3, 4.8, and 6.5, respectively. CONCLUSION: During COVID-19, there was an increase in anxiety and depressive symptoms for all sexes and genders, with the greatest increases reported by those identifying as non-male and non-men.

Behind the mask: extended use of surgical masks is not associated with increased risk of surgical site infection.

PURPOSE: COVID-19 has prompted significant policy change, with critical attention to the conservation of personal protective equipment (PPE). An extended surgical mask use policy was implemented at our institution, allowing use of one disposable mask per each individual, per day, for all the cases. We investigate the clinical impact of this policy change and its effect on the rate of 30-day surgical site infection (SSI). METHODS: A single-institution retrospective review was performed for all the elective pediatric general surgery cases performed pre-COVID from August 2019 to October 2019 and under the extended mask use policy from August 2020 to October 2020. Procedure type, SSI within 30 days, and postoperative interventions were recorded. RESULTS: Four hundred and eighty-eight cases were reviewed: 240 in the pre-COVID-19 cohort and 248 in the extended surgical mask use cohort. Three SSIs were identified in the 2019 cohort, and two in the 2020 cohort. All postoperative infections were superficial and resolved within 1 month of diagnosis with oral antibiotics. There were no deep space infections, readmissions, or infections requiring re-operation. CONCLUSION: Extended surgical mask use was not associated with increased SSI in this series of pediatric general surgery cases and may be considered an effective and safe strategy for resource conservation with minimal clinical impact.

Learning lessons from the paediatric critical care response to the SARS-CoV-2 pandemic in England and Wales: a qualitative study.

OBJECTIVES: To explore the experiences of clinical leads in paediatric critical care units (PCCUs) in England and Wales during the reorganisation of services in the initial surge of the SARS-CoV-2 pandemic and to learn lessons for future surges and service planning. METHODS: A qualitative study design using semistructured interviews via virtual conferencing was conducted with consultant clinical leads and lead nurses covering 21 PCCUs. Interviews were conducted over a period of 2 weeks, 2 months after the initial SARS-CoV-2 surge. Interview notes underwent thematic analysis. RESULTS: Thematic analysis revealed six themes: leadership, management and planning; communication; workforce development and training; innovation; workforce experience; and infection prevention and control. Leadership was facilitated through clinician-led local autonomy for decision-making and services were better delivered when the workforce was empowered to be flexible in their response. Communication was preferred through collaborative management structures. Further lessons include recognising workforce competencies in surge preparations, the use of virtual technology in facilitating training and meetings, the importance of supporting the well-being of the workforce and the secondary consequences of personal protective equipment use. CONCLUSIONS: During the 2020 SARS-CoV-2 pandemic, an agile response to a rapidly changing situation was enabled through effective clinical leadership and an adaptive workforce. Open systems of communication across senior clinical and management teams facilitated service planning. Support for all members of the workforce through implementation of appropriate and innovative education and well-being solutions was vital in sustaining resilience. This learning supports planning for future surge capacity across paediatric critical care locally and nationally.

Discovery of allosteric binding sites by crystallographic fragment screening.

Understanding allosteric regulation of proteins is fundamental to our study of protein structure and function. Moreover, allosteric binding pockets have become a major target of drug discovery efforts in recent years. However, even though the function of almost every protein can be influenced by allostery, it remains a challenge to discover, rationalise and validate putative allosteric binding pockets. This review examines how the discovery and analysis of putative allosteric binding sites have been influenced by the availability of centralised facilities for crystallographic fragment screening, along with newly developed computational methods for modelling low occupancy features. We discuss the experimental parameters required for success, and how new methods could influence the field in the future. Finally, we reflect on the general problem of how to translate these findings into actual ligand development programs.

Caring for critically ill adults in paediatric intensive care units in England during the COVID-19 pandemic: planning, implementation and lessons for the future.

OBJECTIVE: To describe the experience of paediatric intensive care units (PICUs) in England that repurposed their units, equipment and staff to care for critically ill adults during the first wave of the COVID-19 pandemic. DESIGN: Descriptive study. SETTING: Seven PICUs in England. MAIN OUTCOME MEASURES: (1) Modelling using historical Paediatric Intensive Care Audit Network data; (2) space, staff, equipment, clinical care, communication and governance considerations during repurposing of PICUs; (3) characteristics, interventions and outcomes of adults cared for in repurposed PICUs. RESULTS: Seven English PICUs, accounting for 137 beds, repurposed their space, staff and equipment to admit critically ill adults. Neighbouring PICUs increased their bed capacity to maintain overall bed numbers for children, which was informed by historical data modelling (median 280-307 PICU beds were required in England from March to June). A total of 145 adult patients (median age 50-62 years) were cared for in repurposed PICUs (1553 bed-days). The vast majority of patients had COVID-19 (109/145, 75%); the majority required invasive ventilation (91/109, 85%). Nearly, a third of patients (42/145, 29%) underwent a tracheostomy. Renal replacement therapy was provided in 20/145 (14%) patients. Twenty adults died in PICU (14%). CONCLUSION: In a rapid and unprecedented effort during the first wave of the COVID-19 pandemic, seven PICUs in England were repurposed to care for adult patients. The success of this effort was underpinned by extensive local preparation, close collaboration with adult intensivists and careful national planning to safeguard paediatric critical care capacity.