Discovery of Polyphenolic Natural Products as SARS-CoV-2 Mpro Inhibitors for COVID-19.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the development of direct-acting antiviral drugs due to the coronavirus disease 2019 (COVID-19) pandemic. The main protease of SARS-CoV-2 is a crucial enzyme that breaks down polyproteins synthesized from the viral RNA, making it a validated target for the development of SARS-CoV-2 therapeutics. New chemical phenotypes are frequently discovered in natural goods. In the current study, we used a fluorogenic assay to test a variety of natural products for their ability to inhibit SARS-CoV-2 Mpro. Several compounds were discovered to inhibit Mpro at low micromolar concentrations. It was possible to crystallize robinetin together with SARS-CoV-2 Mpro, and the X-ray structure revealed covalent interaction with the protease's catalytic Cys145 site. Selected potent molecules also exhibited antiviral properties without cytotoxicity. Some of these powerful inhibitors might be utilized as lead compounds for future COVID-19 research.

COVID-19 therapeutics: Small-molecule drug development targeting SARS-CoV-2 main protease.

The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is the causative factor behind the 2019 global coronavirus pandemic (COVID-19). The main protease, known as Mpro, is encoded by the viral genome and is essential for viral replication. It has also been an effective target for drug development. In this review, we discuss the rationale for inhibitors that specifically target SARS-CoV-2 Mpro. Small molecules and peptidomimetic inhibitors are two types of inhibitor with various modes of action and we focus here on novel inhibitors that were only discovered during the COVID-19 pandemic highlighting their binding modes and structures.

Discovery of Polyphenolic Natural Products as SARS-CoV-2 Mpro Inhibitors for COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the development of direct-acting antiviral drugs due to the coronavirus disease 2019 (COVID-19) pandemic. The main protease of SARS-CoV-2 is a crucial enzyme that breaks down polyproteins synthesized from the viral RNA, making it a validated target for the development of SARS-CoV-2 therapeutics. New chemical phenotypes are frequently discovered in natural goods. In the current study, we used a fluorogenic assay to test a variety of natural products for their ability to inhibit SARS-CoV-2 Mpro. Several compounds were discovered to inhibit Mpro at low micromolar concentrations. It was possible to crystallize robinetin together with SARS-CoV-2 Mpro, and the X-ray structure revealed covalent interaction with the protease's catalytic Cys145 site. Selected potent molecules also exhibited antiviral properties without cytotoxicity. Some of these powerful inhibitors might be utilized as lead compounds for future COVID-19 research.

A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.

Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.

The impact of COVID-19 on right ventricular function in chronic kidney disease patients

Introduction: In chronic kidney disease (CKD) patients, the case fatality rate caused by the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is higher than in the general population [1]. In patients hospitalised with COVID 19, right heart dysfunction is present in 20% of the cases, associated with an increased risk of all-cause death [2]. Purpose: CARDIO-SCARS in CKD is a currently ongoing multi-center observational match controlled trial that aims to assess the cardiovascular (CV) risk in a CKD (stages 3 to 5), dialysis and kidney transplant population, following SARS-CoV-2 infection, by using clinical evaluation, various techniques and novel biomarkers (ClinicalTrials.gov Identifier NCT05125913). We hereby report the main baseline echocardiographic parameters that assess the right ventricular (RV) function. Methods: We conducted a cross-sectional study that included 263 patients with CKD (dialysis, transplantation or eGFR <60 ml/min/1.73 m2). For assessing RV function, 5 parameters were measured: fractional area change (FAC, %), tricuspid annular plane systolic excursion (TAPSE, mm), tricuspid S' wave (S tric, cm/s), Tei index and right ventricular free wall longitudinal strain (RVFWLS, %). Patients in atrial fibrillation, with a permanent pacemaker or with a poor acoustic window were excluded. Results: Our study included 263 patients with CKD, divided in two groups: 168 patients post COVID-19 (94 in dialysis, 38 post kidney transplantation and 36 with CKD) and 95 patients in the control group (57 in dialysis, 30 post kidney transplantation and 8 with CKD).The mean age was 57.3±15.4 years (median 60 years old), 55.2% of the patients were males, 24% were diabetic and 9.5% were smokers. The mean duration of dialysis in the COVID-19 group was 63.8 months vs. 62.6 months in the control group. In the COVID group, the echocardiography was performed at a mean distance of 2.2±2.1 months after testing positive for SARS-CoV-2.All the parameters of RV function were better in the control group (FAC (%): 43.6±11 vs. 41.3±11;TAPSE (mm): 23.2±6.9 vs. 21.4±4.9;S tric (cm/s): 13.4±3.4 vs. 13±3.1;Tei index: 0.5±0.2 vs. 0.6±0.2;RVFWLS (%): −20.1±3.8 vs. −18.6±5.1. After performing a two-sample t-Test, statistical significance was reached only for TAPSE, Tei index and RVFWLS (0.008, 0.0001 and 0.006, respectively). Conclusions: Our study is the first to describe echocardiographic alterations post-COVID in a CKD population. All CKD patients had lower values of RV parameters than those reported in the general population. Still, the CKD COVID group had lower values than CKD control group, with the same magnitude as the changes reported in the general population [3,4]. The evolution of these parameters and their prognostic significance is of interest, regarding long-term CV sequelae of COVID-19. Funding Acknowledgement: Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Ministry of Research and Innovation, CNCS-UEFISCDI

Discovery of Polyphenolic Natural Products as SARS-CoV-2 Mpro Inhibitors for COVID-19 (preprint)

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has forced the development of direct-acting antiviral drugs due to the coronavirus disease 2019 (COVID-19) pandemic. The main protease of SARS-CoV-2 is a crucial enzyme that breaks down polyproteins synthesized from the viral RNA, making it a validated target for the development of SARS-CoV-2 therapeutics. New chemical phenotypes are frequently discovered in natural goods. In the current study, we used a fluorogenic assay to test a variety of natural products for their ability to inhibit SARS-CoV-2 Mpro. Several compounds were discovered to inhibit the Mpro at low micromolar concentrations. It was possible to crystallize robinetin together with SARS-CoV-2 Mpro, and the X-ray structure revealed covalent interaction with the protease's catalytic Cys145 site. Selected potent molecules also exhibited antiviral properties without cytotoxicity. Some of these powerful inhibitors might be utilized as lead compounds for COVID-19 research.

THE EVOLUTION OF INDUSTRY 4.0 AND ITS POTENTIAL IMPACT ON INDUSTRIAL ENGINEERING AND MANAGEMENT EDUCATION

The paper analyses both technical (hardware and software) and managerial elements (management and enterprise culture) of Industry 4.0 related to their potential impact on Industrial Engineering and Management Education in particular, as Industrial Engineering and Management programs are tied up to the industry in a stronger way and are thus more sensitive to innovative changes in the industry. The paper also offers a case study by authors in various European countries, during the restrictions caused by the COVID-19 pandemic, by questioning two professional categories of particular interest to the field of analysis: teachers and students. It also analyzes their position on the inclusion of the Industry 4.0 element in IEM engineering programs in both the technical and management fields, concerning the hardware, software, management and organizational culture elements.

Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination.

The main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target in coronaviruses because of its crucial involvement in viral replication and transcription. Here, we report on the design, synthesis, and structure-activity relationships of novel small-molecule thioesters as SARS-CoV-2 Mpro inhibitors. Compounds 3w and 3x exhibited excellent SARS-CoV-2 Mpro inhibition with kinac/Ki of 58,700 M-1 s-1 (Ki = 0.0141 µM) and 27,200 M-1 s-1 (Ki = 0.0332 µM), respectively. In Calu-3 and Vero76 cells, compounds 3h, 3i, 3l, 3r, 3v, 3w, and 3x displayed antiviral activity in the nanomolar range without host cell toxicity. Co-crystallization of 3w and 3af with SARS-CoV-2 Mpro was accomplished, and the X-ray structures showed covalent binding with the catalytic Cys145 residue of the protease. The potent SARS-CoV-2 Mpro inhibitors also inhibited the Mpro of other beta-coronaviruses, including SARS-CoV-1 and MERS-CoV, indicating that they might be useful to treat a broader range of coronaviral infections.

Definition of factors associated with negative antibody response after COVID-19 vaccination in patients with hematological diseases.

COVID-19 in patients with hematological diseases is associated with a high mortality. Moreover, preventive vaccination demonstrated reduced efficacy and the knowledge on influencing factors is limited. In this single-center study, antibody levels of the SARS-CoV-2 spike protein were measured ≥ 2 weeks after 2nd COVID-19 vaccination with a concentration ≥ 0.8 U/mL considered positive. Between July and October 2021, in a total of 373 patients (median age 64 years, 44% women) with myeloid neoplasms (n = 214, 57%), lymphoid neoplasms (n = 124, n = 33%), and other diseases (n = 35, 10%), vaccination was performed with BNT162b2 (BioNTech), mRNA-1273 (Moderna), ChADOx1 (AstraZeneca), or a combination. A total of 229 patients (61%) were on active therapy within 3 months prior vaccination and 144 patients (39%) were previously treated or treatment naïve. Vaccination-related antibody response was negative in 56/373 patients (15%): in 39/124 patients with lymphoid neoplasms, 13/214 with myeloid neoplasms, and 4/35 with other diseases. Active treatment per se was not correlated with negative response. However, rituximab and BTK inhibitor treatment were correlated significantly with a negative vaccination response, whereas younger age and chronic myeloid leukemia (CML) disease were associated with positive response. In addition, 5 of 6 patients with myeloproliferative neoplasm (MPN) and negative vaccination response were on active treatment with ruxolitinib. In conclusion, a remarkable percentage of patients with hematological diseases had no response after 2nd COVID-19 vaccination. Multivariable analysis revealed important factors associated with response to vaccination. The results may serve as a guide for better protection and surveillance in this vulnerable patient cohort.

ORGANIZATIONAL E-LEARNING IN THE COVID-19 PANDEMIC CONTEXT: A ROMANIAN CASE-STUDY

E-learning concepts gained significant importance in the last decade, tending to be more and more attractive to companies, as skilled employees are the biggest asset of a company. Companies have included e-learning into their business operations. E-learning supports learners with some special capabilities such as interactivity, strong search, immediacy, physical mobility and situating of educational activities, self-organized and self-directed learning, corporate training, personalized learning, and effective technique of delivering lesson and gaining knowledge Because in the last year most companies embraced the “work from home” method, the management needed to take some measures and convert their usual teaching/learning techniques to online trainings. The current paper examines the impact of organizational e-learning on Romanian employees’ productivity, performance, and skills. This study is supported by an innovative online survey from different Romanian public and private organizations and qualitative interviews with some of the participants. The results concluded there is a correlation between e-learning usage and job productivity, performance, and satisfaction. Also, the advantages, the drawbacks of e-learning and the key factors for implementing it successfully were underlined in this paper. © 2021, National Defence University - Carol I Printing House. All rights reserved.

UV-C Light-Based Surface Disinfection: Analysis of Its Virucidal Efficacy Using a Bacteriophage Model.

BACKGROUND: The reprocessing of medical devices has become more complex due to increasing hygiene requirements. Previous studies showed satisfactory bactericidal disinfection effects of UV-C light in rigid and flexible endoscopes. Especially in the context of the current COVID-19 pandemic, virucidal properties are of high importance. In the present study, the virucidal efficacy of UV-C light surface disinfection was analyzed. METHODS: MS-2 bacteriophages were applied to the test samples and irradiated by UV-C light using the UV Smart D25 device; unirradiated test samples were used as controls. A dilution series of the samples was mixed with 1&nbsp;×&nbsp;108&nbsp;Escherichia coli and assayed. RESULTS: 8.6 × 1012 pfu could be harvested from the unprocessed test samples. In the control group without UV-C exposure, a remaining contamination of 1.2 × 1012 pfu was detected, resulting in a procedural baseline reduction rate with a LOG10 reduction factor of 0.72. The LOG10 reduction factor was found to be 3.0 after 25 s of UV-C light exposure. After 50 and 75 s of UV-C radiation LOG10 reduction factors 4.2 and 5.9, respectively, were found, with all reductions being statistically significantly different to baseline. CONCLUSIONS: The tested UV system seems to provide a significant virucidal effect after a relatively short irradiation time.

Collaborative decision-making in software research projects: The innovation challenge

Innovation has the potential to propel organizations to unprecedented levels of performance and to strengthen their competitive advantage. Collaboration plays a significant role in boosting the innovation capabilities and reaching performance goals. Improving collaboration brings substantial overall benefits ranging from faster internal decision making, reduced costs through shared resources, and the development of more innovative products. The COViD-10 outbreak has radically altered traditional collaboration and teamwork patterns, requiring new approaches that would nurture creativity, engagement, and motivation at team level, and that would also streamline decision-making processes. This paper investigates the use of a collaborative platform that can enhance teamwork achievements and decision-making capabilities and presents an analysis of experiments carried out within software research projects. The approach considers key challenges in today's global and fast-changing research and business environments that demand improvements in collaboration among functions ranging from R&D to distribution. The authors explore techniques for improving the effectiveness of teams, capitalizing on the promises of cutting-edge software and the applicability of the Design Thinking methodology and its potential to boost collaboration. This research probes the capacity of technology to support team performance and better decision-making processes. © 2021 The Authors. Published by Elsevier B.V.

Assessment of proarrhythmogenic risk for chloroquine and hydroxychloroquine using the CiPA concept.

Chloroquine and hydroxychloroquine have been proposed recently as therapy for SARS-CoV-2-infected patients, but during 3 months of extensive use concerns were raised related to their clinical effectiveness and arrhythmogenic risk. Therefore, we estimated for these compounds several proarrhythmogenic risk predictors according to the Comprehensive in vitro Proarrhythmia Assay (CiPA) paradigm. Experiments were performed with either CytoPatch™2 automated or manual patch-clamp setups on HEK293T cells stably or transiently transfected with hERG1, hNav1.5, hKir2.1, hKv7.1+hMinK, and on Pluricyte® cardiomyocytes (Ncardia), using physiological solutions. Dose-response plots of hERG1 inhibition fitted with Hill functions yielded IC50 values in the low micromolar range for both compounds. We found hyperpolarizing shifts of tens of mV, larger for chloroquine, in the voltage-dependent activation but not inactivation, as well as a voltage-dependent block of hERG current, larger at positive potentials. We also found inhibitory effects on peak and late INa and on IK1, with IC50 of tens of µM and larger for chloroquine. The two compounds, tested on Pluricyte® cardiomyocytes using the ß-escin-perforated method, inhibited IKr, ICaL, INa peak, but had no effect on If. In current-clamp they caused action potential prolongation. Our data and those from literature for Ito were used to compute proarrhythmogenic risk predictors Bnet (Mistry HB, 2018) and Qnet (Dutta S et al., 2017), with hERG1 blocking/unblocking rates estimated from time constants of fractional block. Although the two antimalarials are successfully used in autoimmune diseases, and chloroquine may be effective in atrial fibrillation, assays place these drugs in the intermediate proarrhythmogenic risk group.

External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories.

This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

Convalescent Plasma in a Patient with Protracted COVID-19 and Secondary Hypogammaglobulinemia Due to Chronic Lymphocytic Leukemia: Buying Time to Develop Immunity?

It is not exactly clear yet which type of immune response prevails to accomplish viral clearance in coronavirus disease 2019 (COVID-19). Studying a patient with chronic lymphocytic leukemia and hypogammaglobulinemia who suffered from COVID-19 provided insight in the immunological responses after treatment with COVID-19 convalescent plasma (CCP). Treatment consisted of oxygen, repeated glucocorticosteroids and multiple dosages of CCP guided by antibody levels. Retrospectively performed humoral and cellular immunity analysis made clear that not every serological test for COVID-19 is appropriate for follow-up of sufficient neutralizing antibodies after CCP. In retrospect, we think that CCP merely bought time for this patient to develop an adequate cellular immune response which led to viral clearance and ultimately clinical recovery.

Increasing diagnostic possibilities using the geneLEAD VIII platform for detection of SARS-CoV-2.

At the time SARS-CoV-2 was identified as the cause of coronavirus disease 2019 (COVID-19) no in vitro diagnostic (IVD) tests were available since it was a new virus. Very shortly after the release of the genomic sequence of SARS-CoV-2, laboratory-developed tests (LDTs) were developed, made available and implemented in several laboratories in the Netherlands and globally. In this study, the performance of an E-gene Sarbeco specific real-time reverse-transcriptase PCR (RT-PCR) was verified on the open modus of the geneLEAD VIII sample-to-answer platform. The results obtained from 134 clinical samples, of which 63 had been tested positive, showed almost complete concordance compared to the same PCR on the routine diagnostic systems and that was validated according to the national reference standard. The only discordant sample tested positive using the routine diagnostic workflow with a cycle threshold (CT) value of 37.7, while the sample tested negative using the geneLEAD VIII workflow. In addition, good performance was achieved in analyzing a blinded SARS-CoV-2 external quality assurance (EQA) panel. Implementation of the geneLEAD VIII platform as routine diagnostic tool resulted in testing 871 clinical samples with 115 positive results. In conclusion, the geneLEAD VIII SARS-CoV-2 workflow presented in this study showed excellent diagnostic performance and with a rapid turnaround time of approximately two hours it proved a valuable option for STAT SARS-CoV-2 testing in the absence of (rapid, CE-IVD) point-of-care testing platforms.

The Bone Marrow as Sanctuary for Plasma Cells and Memory T-Cells: Implications for Adaptive Immunity and Vaccinology.

The bone marrow (BM) is key to protective immunological memory because it harbors a major fraction of the body's plasma cells, memory CD4+ and memory CD8+ T-cells. Despite its paramount significance for the human immune system, many aspects of how the BM enables decade-long immunity against pathogens are still poorly understood. In this review, we discuss the relationship between BM survival niches and long-lasting humoral immunity, how intrinsic and extrinsic factors define memory cell longevity and show that the BM is also capable of adopting many responsibilities of a secondary lymphoid organ. Additionally, with more and more data on the differentiation and maintenance of memory T-cells and plasma cells upon vaccination in humans being reported, we discuss what factors determine the establishment of long-lasting immunological memory in the BM and what we can learn for vaccination technologies and antigen design. Finally, using these insights, we touch on how this holistic understanding of the BM is necessary for the development of modern and efficient vaccines against the pandemic SARS-CoV-2.