Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.

Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC₅₀ values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.

Quinolinonyl Non-Diketo Acid Derivatives as Inhibitors of HIV-1 Ribonuclease H and Polymerase Functions of Reverse Transcriptase

Novel anti-HIV agents are still needed to overcome resistance issues, in particular inhibitors acting against novel viral targets. The ribonuclease H (RNase H) function of the reverse transcriptase (RT) represents a validated and promising target, and no inhibitor has reached the clinical pipeline yet. Here, we present rationally designed non-diketo acid selective RNase H inhibitors (RHIs) based on the quinolinone scaffold starting from former dual integrase (IN)/RNase H quinolinonyl diketo acids. Several derivatives were synthesized and tested against RNase H and viral replication and found active at micromolar concentrations. Docking studies within the RNase H catalytic site, coupled with site-directed mutagenesis, and Mg²⁺ titration experiments demonstrated that our compounds coordinate the Mg²⁺ cofactor and interact with amino acids of the RNase H domain that are highly conserved among naïve and treatment-experienced patients. In general, the new inhibitors influenced also the polymerase activity of RT but were selective against RNase H vs the IN enzyme.

Cardiac implantable electronic devices replacements in patients followed by remote monitoring during COVID-19 lockdown

Aims 

Following coronavirus disease (COVID-19) outbreak, the Italian government adopted strict rules of lockdown and social distancing. The aim of our study was to assess the admission rate for cardiac implantable electronic devices (CIEDs) replacement procedures in Campania, the 3rd-most-populous region of Italy, during COVID-19 lockdown.

Methods and results 

Data were sourced from 16 referral hospitals in Campania from 10 March to 4 May 2020 (lockdown period) and during the same period in 2019. We retrospectively evaluated consecutive patients hospitalized for CIEDs replacement procedures during the two observational periods. The number and type of CIEDs replacement procedures among patients followed by remote monitoring (RM), the admission rate, and the type of hospital admission between the two observational periods were compared. In total, 270 consecutive patients were hospitalized for CIEDs replacement procedures over the two observation periods. Overall CIEDs replacement procedures showed a reduction rate of 41.2% during COVID-19 lockdown. Patients were equally distributed for sex (P = 0.581), and both age [median 76 years (IQR: 68–83) vs. 79 years (IQR: 68–83); P = 0.497]. Cardiac implantable electronic devices replacement procedures in patients followed by RM significantly increased (IR: +211%; P < 0.001), mainly driven by the remarkable increase rate trend of both PM (IR: +475%; P < 0.001) and implantable cardiac defibrillator replacement procedures (IR: +67%, P = 0.01), during COVID-19 lockdown compared with 2019 timeframe.

Conclusions 

We showed a significant increase trend rate of replacement procedures among CIEDs patients followed by RM, suggesting the hypothesis of its increased use to closely monitoring and to optimize the hospital admission time during COVID-19 lockdown.

Identification of differential DNA methylation associated with multiple sclerosis: A family-based study

Multiple Sclerosis (MS) is caused by a still unknown interplay between genetic and environmental factors. Epigenetics, including DNA methylation, represents a model for environmental factors to influence MS risk. Twenty-six affected and 26 unaffected relatives from 8 MS multiplex families were analysed in a multicentric Italian study using MeDIP-Seq, followed by technical validation and biological replication in two additional families of differentially methylated regions (DMRs) using SeqCap Epi Choice Enrichment kit (Roche®). Associations from MeDIP-Seq across families were combined with aggregation statistics, yielding 162 DMRs at FDR ≤ 0.1. Technical validation and biological replication led to 2 hypo-methylated regions, which point to NTM and BAI3 genes, and to 2 hyper-methylated regions in PIK3R1 and CAPN13. These 4 novel regions contain genes of potential interest that need to be tested in larger cohorts of patients.

Periodic Bedrock Ridges at the ExoMars 2022 Landing Site: Evidence for a Changing Wind Regime

Wind-formed features are abundant in Oxia Planum (Mars), the landing site of the 2022 ExoMars mission, which shows geological evidence for a past wet environment. Studies of aeolian bedforms at the landing site were focused on assessing the risk for rover trafficability, however their potential in recording climatic fluctuations has not been explored. Here we show that the landing site experienced multiple climatic changes in the Amazonian, which are recorded by an intriguing set of ridges that we interpret as Periodic Bedrock Ridges (PBRs). Clues for a PBR origin result from ridge regularity, defect terminations, and the presence of preserved megaripples detaching from the PBRs. PBR orientation differs from superimposed transverse aeolian ridges pointing toward a major change in wind regime. Our results provide constrains on PBR formation mechanisms and offer indications on paleo winds that will be crucial for understanding the landing site geology.

Hypervirulent and hypermucoviscous extended-spectrum β-lactamase-producing Klebsiella pneumoniae and Klebsiella variicola in Chile

Convergence of virulence and antibiotic-resistance has been reported in Klebsiella pneumoniae, but not in Klebsiella variicola. We, hereby, report the detection and genomic characterization of hypervirulent and hypermucoviscous K. pneumoniae and K.variicola recovered in Chile from health-care associated infections, which displayed resistance to broad-spectrum cephalosporins. One hundred forty-six K. pneumoniae complex isolates were screened by hypermucoviscosity by the “string test.” Two hypermucoid isolates, one hypermucoviscous K. pneumoniae (hmKp) and one K. variicola (hmKv), were further investigated by whole-genome sequencing. In vivo virulence was analyzed by the Galleria mellonella killing assay. In silico analysis of hmKp UCO-494 and hmKv UCO-495 revealed the presence of multiple antibiotic-resistance genes, such as bla_CTX-M-1, bla_DHA-1 and bla_LEN-25 among others clinically relevant resistance determinants, including mutations in a two-component regulatory system related to colistin resistance. These genetic features confer a multidrug-resistant (MDR) phenotype in both strains. Moreover, virulome in silico analysis confirmed the presence of the aerobactin gene iutA, in addition to yersiniabactin and/or colicin V encoding genes, which are normally associated to high virulence in humans. Furthermore, both isolates were able to kill G. mellonella and displayed higher virulence in comparison with the control strain. In summary, the convergence of virulence and the MDR-phenotype in K. pneumoniae complex members is reported for the first time in Chile, denoting a clinical problem that deserves special attention and continuous surveillance in South America.

Scaffold hopping and optimisation of 3',4'-dihydroxyphenyl- containing thienopyrimidinones: synthesis of quinazolinone derivatives as novel allosteric inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H

Bioisosteric replacement and scaffold hopping are powerful strategies in drug design useful for rationally modifying a hit compound towards novel lead therapeutic agents. Recently, we reported a series of thienopyrimidinones that compromise dynamics at the p66/p51 HIV-1 reverse transcriptase (RT)-associated Ribonuclease H (RNase H) dimer interface, thereby allosterically interrupting catalysis by altering the active site geometry. Although they exhibited good submicromolar activity, the isosteric replacement of the thiophene ring, a potential toxicophore, is warranted. Thus, in this article, the most active 2-(3,4-dihydroxyphenyl)-5,6-dimethylthieno[2,3-d]pyrimidin-4(3H)-one 1 was selected as the hit scaffold and several isosteric substitutions of the thiophene ring were performed. A novel series of highly active RNase H allosteric quinazolinone inhibitors was thus obtained. To determine their target selectivity, they were tested against RT-associated RNA-dependent DNA polymerase (RDDP) and integrase (IN). Interestingly, none of the compounds were particularly active on (RDDP) but many displayed micromolar to submicromolar activity against IN.

Use of dual layered stents in endovascular treatment of extracranial stenosis of the internal carotid artery: one year results of a patient-based meta-analysis of 4 clinical studies

Background

Small sized clinical studies evaluating one year outcomes of CAS performed with two available DLS, Roadsaver® (RS) and CGuard® (CG), have been published.

Purpose

To evaluate one year safety and efficacy of dual layered mesh covered carotid stent systems (DLS) for carotid artery stenting (CAS).

Methods

We performed an individual patient-level meta-analysis including studies enrolling more than 100 CAS with DLS. Primary endpoint was the death and stroke rate; secondary endpoints were restenosis and in-stent thrombosis rates at one year.

Results

Patients were divided in two groups according to DLS (RS N=250; CG N=306). At one year, 11 patients died (1.97%), 7 patients in the group RS (2.8%) and 4 patients in the CG one (1.31%), 10 strokes occurred, 4 in the group RS (1.6%) and 6 in the CG one (1.96%). Overall death and stroke rate was 3.77% (N=21), 11 events in the group RS (4.4%) and 10 in the CG group (3.27%). Symptomatic status was the only predictor of death and or stroke.

At one year restenosis occurred in 12 patients (2.1%), 10 in the group RS (4%) and 2 in the CG one (0.65%) (p=0.007). In stent thrombosis occurred in 1 patient (0.18%) of the group CG (0.32%). RS use was the only independent restenosis predictor.

Conclusions

This study suggests that DLS use for CAS is associated to a low one year death and stroke rate and specific DLS stent use could affect restenosis rate.

Funding Acknowledgement

Type of funding source: None

Development of a Raltegravir-based Photoaffinity-Labeled Probe for Human Immunodeficiency Virus-1 Integrase Capture

Photoaffinity labeling (PAL) is one of the upcoming and powerful tools in the field of molecular recognition. It includes the determination of dynamic parameters, such as the identification and localization of the target protein and the site of drug binding. In this study, a photoaffinity-labeled probe for full-length human immunodeficiency virus-1 integrase (HIV-1 IN) capture was designed and synthesized, following the structure of the FDA-approved drug Raltegravir. This photoprobe was found to retain the HIV IN inhibitory potential in comparison with its parent molecule and demonstrates the ability to label the HIV-1 IN protein. Putative photoprobe/inhibitor binding sites near the catalytic site were then identified after protein digestion coupled to mass and molecular modeling analyses.

Colon sparing resection versus extended colectomy for left-sided obstructing colon cancer with caecal ischaemia or perforation: a nationwide study from the French Surgical Association

AIM

It is not known whether patients with obstructive left colon cancer (OLCC) with caecal ischaemia or diastatic perforation (defined as a blowout of the caecal wall related to colonic overdistension) should undergo a (sub)total colectomy (STC) or an ileo-caecal resection with double-barrelled ileo-colostomy. We aimed to compare the results of these two strategies.

METHOD

From 2000 to 2015, 1220 patients with OLCC underwent surgery by clinicians who were members of the French Surgical Association. Of these cases, 201 (16%) were found to have caecal ischaemia or diastatic perforation intra-operatively: 174 patients (87%) underwent a STC (extended colectomy group) and 27 (13%) an ileo-caecal resection with double-end stoma (colon-sparing group). Outcomes were compared retrospectively.

RESULTS

In the extended colectomy group, 95 patients (55%) had primary anastomosis and 79 (45%) had a STC with an end ileostomy. In the colon-sparing group, 10 patients (37%) had simultaneous resection of their primary tumour with segmental colectomy and an anastomosis which was protected by a double-barrelled ileo-colostomy. The demographic data for the two groups were comparable. Median operative time was longer in the STC group (P = 0.0044). There was a decrease in postoperative mortality (7% vs 12%, P = 0.75) and overall morbidity (56% vs 67%, P = 0.37) including surgical (30% vs 40%, P = 0.29) and severe complications (17% vs 27%, P = 0.29) in the colon-sparing group, although these differences did not reach statistical significance. Cumulative morbidity included all surgical stages and the rate of permanent stoma was 66% and 37%, respectively, with no significant difference between the two groups. Overall survival and disease-free survival were similar between the two groups.

CONCLUSION

The colon-sparing strategy may represent a valid and safe alternative to STC in OLCC patients with caecal ischaemia or diastatic perforation.

HILIC-UPLC-MS for high throughput and isomeric N-glycan separation and characterization in Congenital Disorders Glycosylation and human diseases

N-glycan analyses may serve uncovering disease-associated biomarkers, as well as for profiling distinctive changes supporting diagnosis of genetic disorders of glycan biosynthesis named congenital disorders of glycosylation (CDG). Strategies based on liquid chromatography (LC) preferentially coupled to electrospray ionization (ESI) - mass spectrometry (MS) have emerged as powerful analytical methods for N-glycan identification and characterization. To enhance detection sensitivity, glycans are commonly labelled with a functional tag prior to LC-MS analysis. Since most derivatization techniques are notoriously time-consuming, some commercial analytical kits have been developed to speed up N-deglycosylation and N-glycan labelling of glycoproteins of pharmaceutical and biological interest such as monoclonal antibodies (mAbs). We exploited the analytical capabilities of RapiFluor-MS (RFMS) to perform, by a slightly modified protocol, a detailed N-glycan characterization of total serum and single serum glycoproteins from specific patients with CDG (MAN1B1-CDG, ALG12-CDG, MOGS-CDG, TMEM199-CDG). This strategy, accomplished by Hydrophilic Interaction Chromatography (HILIC)-UPLC-ESI-MS separation of the RFMS derivatized N-glycans, allowed us to uncover structural details of patients serum released N-glycans, thus extending the current knowledge on glycan profiles in these individual glycosylation diseases. The applied methodology enabled to differentiate in some cases either structural isomers and isomers differing in the linkage type. All the here reported applications demonstrated that RFMS method, coupled to HILIC-UPLC-ESI-MS, represents a sensitive high throughput approach for serum N-glycome analysis and a valuable option for glycan detection and separation particularly for isomeric species.

Concordance between child’s and parents’- reported Health-related quality of life and overweight

Background

Health-related quality of life (HRQoL) of children is an important health outcome which has frequently been investigated regarding children's chronicle illnesses using parents proxy-reported HRQoL. Obesity is an increasingly frequent condition in children, for which the evidence about perceived quality of life is lacking. The aim of our study is to examine the concordance between child's and parents'- reported HRQoL according to children's weight status.

Methods

A cross-sectional study was conducted in 2019 among 128 children, aged 6-10, recruited in a primary school of Imola (Italy). Children were divided in Group1 (G1: normal-underweight) and Group2 (G2: overweight-obese) using the International Obesity Task Force cut points. HRQoL was assessed using the Italian version 4.0 of Paediatric Quality of Life (PedsQL) questionnaire. We obtained self-reported children's HRQoL total score and the parents' perceived children's HRQoL total score. Each score had two subscales: one for physical health and one for emotional, social and school functioning.

Results

In G1 there were 86 children and in G2 42. The correlation between the children's and parents' HRQoL scores is low in G1 (physical health: 0.24; emotional, social and school functioning: 0.15). Children in G2 and their and parents' perception of physical health are poorly correlated (r=-0.09) and those of emotional, social and school functioning are well correlated (r = 0.43).We observed that in case of discordant HRQoL results, parents usually overestimate their children's HRQoL.

Conclusions

Correlation between the children's and parents' HRQoL scores is low in G1. In G2 children's and parents' perception are concordant for emotional, social and school functioning and unrelated for physical health. It would be useful to investigate whether these results depend from lack of communication between parents and children or lack of parents' awareness of health-related problems with obesity.

Key messages

Parents and children have a discordant perception of physical health quality of life. Further studies should investigate the reasons why these results are discordant.

Scientific literature response in Pubmed for the novel Coronavirus outbreak: a literature analysis

Background

Recent events highlight how emerging and re-emerging pathogens are actually becoming global challenges for public health. In December 2019, a novel coronavirus (SARS-CoV-2) has emerged. This has suddenly turned out into a global health concern which has led to a very high number of papers published in the scientific literature. Aim of this research is to focus on the bibliometric aspects in order to give researchers a glimpse on what is published in the first 30-days of a global epidemic outbreak.

Methods

We searched MEDLINE (PubMed) electronic database in order to find all relevant studies in the first 30-days from the first publication (which appeared on Pubmed at 14/01/2020), meaning the period 15/01/2020-13/02/2020. We used the following search string: coronavirus* OR Pneumonia of Unknown Etiology OR Covid-19 OR nCoV. We placed a language restriction for English, but no publication status or study design limit was put in place for our search.

Results

From the initial 462 identified articles, 234 articles were found as pertinent and read in extenso in order to classify them. The vast majority of papers come from China, UK and USA. 66.2% of the papers were Editorials, comments, letters or other kind of mainly reported data. 10.7% of papers were secondary literature papers (mainly narrative reviews). The remaining 23.1% were original primary studies. Only 17.5% of the sources used data which were directly collected on the field.

Conclusions

Almost all of data came from China. Even if some preferential channels were guaranteed for publishing those results in the most important journals, it appears that the vast majority of publication in scientific literature in the first 30-days of an epidemic outbreak is based more on reported data and comments, and only a small fraction of the papers have primary data collected in the field. Nevertheless the whole international literature depends on that type of data sources in the early days of the epidemic.

Key messages

This is the first bibliometric research in Pubmed Database on the first 30 days of publications regarding the novel Coronavirus (2019-nCoV) outbreak of 2019.

The vast majority of publication in the first 30-days of an epidemic outbreak are reported data or comments, and only a small fraction of the papers has directly collected data.

Comparison between health-related quality of life in normal-weight and overweight-obese children

Background

In Italy 32% of 6-10 aged children were overweight in 2017-2018. Measures of Health-Related Quality of Life (HRQoL) assess important aspects of health daily activities, physical symptoms, social interactions and emotional well-being. It is suggested that HRQoL is influenced by children's weight status. The aim of the study is to compare HRQoL among normal-underweight and overweight-obese children in an Italian sample.

Methods

A cross-sectional study was conducted in 2019 among 144 children, aged 6-10, recruited in a primary school in Bologna (Italy). Children were divided in Group1 (G1: normal-underweight) and Group2 (G2: overweight-obese) using the International Obesity Task Force cut points. HRQoL was assessed using 4.0 Italian version of PedsQL questionnaire. We obtained summary scores for children's total HRQoL and two subscales: one for physical health and one for emotional, social and school functioning.

Results

Of 144 children, 98 (68%) and 46 (32%) were respectively in G1 and G2. HRQoL total scores were 73.10±1.30 in G1 and 69.28±1.96 in G2 (p = 0.051). We analysed separately children in Grade 1 and Grade 3-4. In Grade 1, there were 68 children: 48 (71%) in G1 and 20 (29%) in G2. In grade 3-4 there were 76 children: 50 (66%) in G1 and 26 (34%) in G2. HRQoL total scores in grade 3-4 were: 73.28±1.63 in G1 and 72.66±2.32 in G2 (p = 0.41). In Grade 1, HRQoL total scores were 72.92±2.05 in G1 and 64.89±3.15 in G2 (p = 0.02); at subscale levels, means for physical health were 77.73±1.92 in G1 and 72.5±3.58 in G2 (p = 0.08) and means for emotional, social and school functioning were 70.35±2.48 in G1 and 60.83±4.04 in G2 (p = 0.02).

Conclusions

The effects of child overweight and obesity on health-related QOL was more evident in children aged 6-7, especially regarding emotional, social and school functioning. Prevention of childhood overweight and obesity is important not only to avoid health consequences of weight but also to improve children' quality of life.

Key messages

Overweight is a public health problem in Italy not only among adults, but even among children. Overweight has a negative impact on quality of life, therefore a healthy lifestyle should be promoted.