Improving the preclinical and clinical success rates of LMW drugs depends on radical revisions to the status quo scientific foundations of medicinal chemistry: a case study on COVID Mpro inhibition

The poor preclinical and clinical success rates of low molecular weight compounds is partially attributable to the inherent trial-and-error nature of pharmaceutical research, which is limited largely to retrospective data-driven, rather than prospective prediction-driven workflows stemming from: 1) inadequate scientific understanding of structure-activity, structure-property, and structure-free energy relationships; 2) disconnects between empirical models derived from in vitro equilibrium data (e.g., Hill and Michaelis-Menten models) vis-a-vis the native non-equilibrium cellular setting (where the pertinent metrics consist of rates, rather than equilibrium state distributions); and 3) inadequate understanding of the non-linear dynamic (NLD) basis of cellular function and disease. We argue that the limit of understanding of cellular function/dysfunction and pharmacology based on empirical principles (observation/inference) has been reached, and that further progress depends on understanding these phenomena at the first principles theoretical level. Toward that end, we are developing and applying a theory on the mechanisms by which: 1) cellular functions are conveyed by dynamic multi-molecular/-ionic (multi-flux) systems operating in the NLD regime; 2) cellular dysfunction results from molecular dysfunction; 3) molecular structure and function are powered by covalent/non-covalent forms of free energy; and 4) cellular dysfunction is corrected pharmacologically. Our theory represents a radical departure from the status quo empirical science and reduction to practice thereof, replacing: 1) the interatomic contact model of structure-free energy and structure-property relationships with a solvation free energy model; 2) equilibrium drug-target occupancy models with dynamic models accounting for time-dependent drug and target/off-target binding site buildup and decay; and 3) linear models of molecular structure-function and multi-molecular/-ionic systems conveying cellular function and dysfunction with NLD models that more realistically capture the emergent behaviors of such systems. Here, we apply our theory to COVID Mpro inhibition and overview its implications for a holistic, in vivo relevant approach to drug design.

Increased use of birth interventions during the COVID-19 pandemic?: An exploratory qualitative study.

Context: Since the onset of the COVID-19 pandemic policies have been implemented to limit disease transmission and manage patient flow in clinical settings, including perinatal healthcare settings. Emergent literature indicates increased medicalization of childbirth during the pandemic, however experiences of pregnancy and birth remain unexplored. Understanding the impact of pandemic policies on healthcare practices is important for planning better care in future. Objective: To examine how people in Canada who gave birth during the COVID-19 pandemic were affected by pandemic-related policies, especially policies aimed at limiting interpersonal contact to reduce SARS-CoV-2 transmission. Study Design: exploratory qualitative descriptive study. Dataset: Semi-structured telephone interviews. Population studied: 67 participants were recruited. Study inclusion was extended to anyone aged 18 years or more who was located in Canada and was pregnant or had given birth during the COVID-19 pandemic. Intervention/Instrument (for interventional studies): N/A. Outcome Measures: N/A. Results: Findings suggest that the pandemic has resulted in an overall scaling back of perinatal care alongside the heavy use of interventions (e.g., induction of labour, cesarean section) in response to pandemic stresses and uncertainties on the part of both healthcare providers and pregnant people themselves. Some participants pushed for non-medically necessary interventions as a means of averting the possibility that their partner would be banned from attending the birth (e.g. if the partner contracted COVID-19). Some participants reported being offered interventions as a means of controlling patient flow and in response to clinicians' fears of healthcare system collapse in the event of escalating infection rates. Conclusions: For some people in Canada, giving birth during the COVID-19 pandemic entails medicalization and implementation of non-medically necessary interventions. If healthcare systems are increasing intervention use at the same time that the "safety net" intended to catch the complications from those interventions is reduced, then birthing people are being exposed to extra risk precisely when it is most important to minimize it. Continuity of care throughout pregnancy and postpartum, labour support persons, and non-medical forms of care are all essential components of safe maternal healthcare, however pandemic perinatal care demonstrates that they are not viewed as such.

Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction

IntroductionTools to detect SARS-Coronavirus-2 variants of concern and track the ongoing evolution of the virus are necessary to support public health efforts and the design and evaluation of novel COVID-19 therapeutics and vaccines. Although next-generation sequencing (NGS) has been adopted as the gold standard method for discriminating SARS-CoV-2 lineages, alternative methods may be required when processing samples with low viral loads or low RNA quality. MethodsAn allele-specific probe polymerase chain reaction (ASP-PCR) targeting lineage-specific single nucleotide polymorphisms (SNPs) was developed and used to screen 1,082 samples from two clinical trials in the United Kingdom and Brazil. Probit regression models were developed to compare ASP-PCR performance against 1,771 NGS results for the same cohorts. ResultsIndividual SNPs were shown to readily identify specific variants of concern. ASP-PCR was shown to discriminate SARS-CoV-2 lineages with a higher likelihood than NGS over a wide range of viral loads. Comparative advantage for ASP-PCR over NGS was most pronounced in samples with Ct values between 26-30 and in samples that showed evidence of degradation. Results for samples screened by ASP-PCR and NGS showed 99% concordant results. DiscussionASP-PCR is well-suited to augment but not replace NGS. The method can differentiate SARS-COV-2 lineages with high accuracy and would be best deployed to screen samples with lower viral loads or that may suffer from degradation. Future work should investigate further destabilization from primer:target base mismatch through altered oligonucleotide chemistry or chemical additives.

Virological and serological characterization of critically ill patient with COVID-19 in the UK: a special focus on variant detection

BackgroundTreatment of COVID-19 patients with convalescent plasma containing neutralising antibody to SARS-CoV-2 is under investigation as a means of reducing viral loads, ameliorating disease outcomes, and reducing mortality. However, its efficacy might be reduced in those infected with the emerging B.1.1.7 SARS-CoV-2 variant. Here, we report the diverse virological characteristics of UK patients enrolled in the Immunoglobulin Domain of the REMAP-CAP randomised controlled trial. MethodsSARS-CoV-2 viral RNA was detected and quantified by real-time PCR in nasopharyngeal swabs obtained from study subjects within 48 hours of admission to intensive care unit. Antibody status was determined by spike-protein ELISA. B.1.1.7 strain was differentiated from other SARS-CoV-2 strains by two novel typing methods detecting the B.1.1.7-associated D1118H mutation with allele-specific probes and by restriction site polymorphism (SfcI). FindingsOf 1260 subjects, 90% were PCR-positive with viral loads in nasopharyngeal swabs ranging from 72 international units [IUs]/ml to 1.7x1011 IU/ml. Median viral loads were 45-fold higher in those who were seronegative for IgG antibodies (n=314; 28%) compared to seropositives (n=804; 72%), reflecting in part the latter groups possible later disease stage on enrolment. Frequencies of B.1.1.7 infection increased from early November (<1%) to December 2020 (>60%). Anti-SARS-CoV-2 seronegative individuals infected with wild-type SARS-CoV-2 had significantly higher viral loads than seropositives (medians of 1.2x106 and 3.4 x104 IU/ml respectively; p=2x10-9). However, viral load distributions were elevated in both seropositive and seronegative subjects infected with B.1.1.7 (13.4x106 and 7.6x106 IU/ml; p=0.18). InterpretationHigh viral loads in seropositive B.1.1.7-infected subjects are consistent with increased replication capacity and/or less effective clearance by innate or adaptive immune response of B.1.1.7 strain than wild-type. As viral genotype was associated with diverse virological and immunological phenotypes, metrics of viral load, antibody status and infecting strain should be used to define subgroups for analysis of treatment efficacy.

Seven-month kinetics of SARS-CoV-2 antibodies and protective role of pre-existing antibodies to seasonal human coronaviruses on COVID-19

Unraveling the long-term kinetics of antibodies to SARS-CoV-2 and its determinants, including the impact of pre-existing antibodies to human coronaviruses causing common cold (HCoVs), is essential to understand protective immunity to COVID-19 and devise effective surveillance strategies. IgM, IgA and IgG levels against six SARS-CoV-2 and four HCoV antigens were quantified by Luminex, and antibody neutralization capacity was assessed by flow cytometry, in a cohort of health care workers followed-up for 6 months. Seroprevalence increased over time from 13.5% (month 0) and 15.6% (month 1) to 16.4% (month 6). Levels of antibodies, including those with neutralizing capacity, were stable over time, except IgG to nucleocapsid antigen and IgM levels that waned. After the peak response, anti-spike antibody levels increased from [~]150 days post-symptom onset in all individuals (73% for IgG), in the absence of any evidence of re-exposure. Pre-existing antibodies to alpha-HCoV were lower in individuals who subsequently seroconverted for SARS-CoV-2. IgG and IgA to HCoV were significantly higher in asymptomatic than symptomatic seropositive individuals. Thus, pre-existing cross-reactive HCoVs antibodies could have a protective effect against SARS-CoV-2 infection and COVID-19 disease.

SARS-CoV-2 infections and antibody responses among health care workers in a Spanish hospital after a month of follow-up

BackgroundAt the peak of the COVID-19 pandemic in Spain, cumulative prevalence of SARS-CoV-2 infection in a cohort of 578 randomly selected health care workers (HCW) from Hospital Clinic de Barcelona was 11.2%. MethodsA follow-up survey one month after the baseline (April-May 2020) measured SARS-CoV-2 infection by real time reverse-transcriptase polymerase chain reaction (rRT-PCR) and IgM, IgA, IgG and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein by Luminex. Prevalence of infection was defined by a positive SARS-CoV-2 rRT-PCR and/or antibody seropositivity. ResultsThe cumulative prevalence of infection at month 1 was 14.9% (84/565) and the seroprevalence 14.5% (82/565) for IgM and/or IgG and/or IgA. We found 25 (5%) new infections in participants without previous evidence of infection at baseline (501) and two participants seroreverted for IgM and/or IgG and/or IgA. Among seropositive participants at baseline, IgM and IgA levels generally declined at month 1 (antibody decay rates of 0.49 (95% CI, 0.40-0.60) and 0.34 (95% CI, 0.26-0.44)), respectively. Eight percent of the participants seroreverted for IgM and 11% for IgA. Subjects reporting COVID-19-like symptoms and laboratory and other technicians had higher risk of infection. The most frequent subclass responses were IgG1 and IgG2, followed by IgG3, with higher levels of IgG1, and only IgA1 but no IgA2 was detected. ConclusionsOur findings highlight the importance of a continuous and improved surveillance of SARS-CoV-2 infections in HCW, particularly in high risk groups. The decay of IgA and IgM levels have implications for seroprevalence studies using these isotypes.

The operational impact of deploying SARS-CoV-2 vaccines in countries of the WHO African Region

BackgroundAfter SARS-CoV-2 vaccines become available, they will be deployed to many countries with limited immunization systems. MethodsWe conducted a cold chain capacity assessment of a simulated country in the WHO African Region. We combined region-specific data regarding immunization, population, healthcare workforce, and cold storage capacity (upper and lower range and quartile values for national and subnational levels). We used seasonal influenza vaccines as proxies for SARS-CoV-2 vaccines. We evaluated the increase in vaccine doses to be administered, doses administered per vaccinator, and cold storage volumes for SARS-CoV-2 campaigns targeting risk groups compared to routine immunization baselines. FindingsCompared to routine immunization, a SARS-CoV-2 vaccination campaign would increase monthly doses administered when targeting risk groups: [≥]65 years (29.9%), chronic diseases patients (101.5%), and healthcare workers (1.2%). SARS-CoV-2 vaccination campaigns would increase doses administered per vaccinator for risk groups: [≥]65 years (32.5%), chronic diseases patients (110.4%), or healthcare workers (1.4%). Routine vaccine volumes already exceed national level storage capacity for at least 75% of African Region countries, but subnational levels would have sufficient storage capacity for SARS-CoV-2 vaccines in all but the lower 25% of African Region countries. InterpretationSARS-CoV-2 vaccination campaigns would substantially increase doses per vaccinator and cold chain capacity requirements over routine immunization baselines. Pandemic vaccination campaigns would add volume to national level stores already at their limits, but substantial capacity exists at subnational levels for SARS-CoV-2 vaccines. Immediate attention to strengthening delivery systems is essential to support pandemic vaccine responses in the African Region. FundingNone

Seroprevalence of antibodies against SARS-CoV-2 among health care workers in a large Spanish reference hospital

BackgroundHealth care workers (HCW) are a high-risk population to acquire SARS-CoV-2 infection from patients or other fellow HCW. At the same time, they can be contagious to highly vulnerable individuals seeking health care. This study aims at estimating the seroprevalence of antibodies against SARS-CoV-2 and associated factors in HCW from a large referral hospital in Barcelona, Spain, one of the countries hardest hit by COVID-19 in the world. MethodsFrom 28 March to 9 April 2020, we recruited a random sample of 578 HCW from the human resources database of Hospital Clinic in Barcelona. We collected a nasopharyngeal swab for direct SARS-CoV-2 detection through real time reverse-transcriptase polymerase chain reaction (rRT-PCR), as well as blood for plasma antibody quantification. IgM, IgG and IgA antibodies to the receptor-binding domain of the spike protein were measured by Luminex. The cumulative prevalence of infection (past or current) was defined by a positive SARS-CoV-2 rRT-PCR and/or antibody seropositivity. ResultsOf the 578 total participants, 39 (6.7%, 95% CI: 4.8-9.1) had been previously diagnosed with COVID-19 by rRT-PCR, 14 (2.4%, 95% CI: 1.4-4.3) had a positive rRT-PCR at recruitment, and 54 (9.3%, 95% CI: 7.2-12.0) were seropositive for IgM and/or IgG and/or IgA against SARS-CoV-2. Of the 54 seropositive HCW, 21 (38.9%) had not been previously diagnosed with COVID-19, although 10 of them (47.6%) reported past COVID-19-compatible symptoms. The cumulative prevalence of SARS-CoV-2 infection was 11.2% (65/578, 95% CI: 8.9-14.1). Among those with evidence of past or current infection, 40.0% (26/65) had not been previously diagnosed with COVID-19, of which 46.2% (12/26) had history of COVID-19-compatible symptoms. The odds of being seropositive was higher in participants who reported any COVID-19 symptom (OR: 8.84, 95% CI: 4.41-17.73). IgM levels positively correlated with age (rho=0.36, p-value=0.031) and were higher in participants with more than 10 days since onset of symptoms (p-value=0.022), and IgA levels were higher in symptomatic than asymptomatic subjects (p-value=0.041). ConclusionsThe seroprevalence of antibodies against SARS-CoV-2 among HCW was lower than expected. Thus, being a high-risk population, we anticipate these estimates to be an upper limit to the seroprevalence of the general population. Forty per cent of those with past or present infection had not been previously diagnosed with COVID-19, which calls for active periodic rRT-PCR testing among all HCW to minimize potential risk of hospital-acquired SARS-CoV-2 infections.

Preparing Leaders in Maternal-Child Health Nursing.

OBJECTIVE: To describe leadership and patient outcomes from an international leadership development program undertaken by a nursing organization (Sigma Theta Tau International Honor Society of Nursing) in partnership with Johnson & Johnson Corporate Contributions to strengthen the leadership base of maternal-child bedside nurses. DESIGN: Pretest/posttest design with no control group program evaluation. SETTING: Health care facilities, academic institutions, and public health clinics. PARTICIPANTS: Mentor/fellow dyads (N = 100) of the Maternal-Child Health Nurse Leadership Academy (MCHNLA). INTERVENTION/MEASUREMENTS: The MCHNLA engaged participants in an 18-month mentored leadership experience within the context of an interdisciplinary team project. Each mentor/fellow dyad was paired with a faculty member during the program. RESULTS: One hundred dyads have participated and conducted projects to improve health care for childbearing women and children up to age 5 years during the past decade. For the two cohorts for which consistent data were obtained, mentors and fellows enhanced leadership knowledge, skills, and behaviors. Review of 2010 to 2011 cohort project reports revealed they had the potential to influence more than 1000 students, 4000 nurses, and 1300 other health care students or professionals during the project period. CONCLUSIONS: This leadership development model is replicable in other areas of nursing and other professions.

Family child care providers' compliance with state physical activity regulations, Delaware Child Care Provider Survey, 2011.

INTRODUCTION: Delaware is one state that has implemented comprehensive child care regulations to foster healthy dietary and physical activity behaviors of young children. This study describes the Delaware family child care environment and providers' knowledge of and compliance with physical activity regulations. We analyzed the data to determine characteristics associated with predictors of knowledge of and compliance with these regulations. METHODS: A random stratified sample of 663 licensed Delaware family child care providers was mailed a survey on family child care characteristics and providers' awareness and practices of the child care regulations. Three logistic regression models were used to explore the association between provider characteristics and their knowledge of and compliance with the regulations. RESULTS: Ultimately, 313 of the 663 eligible family child care providers participated in the survey (47.2% response rate). Controlling for covariates, we found that family child care providers' education level was significantly associated with knowledge of the physical activity regulation. Another model showed that family child care providers with larger amounts of outdoor space were more likely to report compliance with the recommendation for unstructured physical activity than those without this described space (odds ratio, 2.45). A third model showed a significant association between available indoor space for all activities including running and reported greater compliance with the recommendation for structured physical activity than was reported by caregivers with less indoor space (odds ratio, 11.2). CONCLUSION: To provide the recommended levels of physical activity for children in child care, the available physical space environment is an important area of focus for advocates of physical activity recommendations within the family child care environment.