Combined drug repurposing and virtual screening strategies with molecular dynamics simulation identified potent inhibitors for SARS-CoV-2 main protease (3CLpro)

The current coronavirus (SARS-COV-2) pandemic and phenomenal spread to every nook and cranny of the world has raised major apprehensions about the modern public health care system. So far as a result of this epidemic, 4,434,653 confirmed cases and 302,169 deaths are reported. The growing infection rate and death toll demand the use of all possible approaches to design novel drugs and vaccines to curb this disease. In this study, we combined drugs repurposing and virtual drug screening strategies to target 3CLpro, which has an essential role in viral maturation and replication. A total of 31 FDA approved anti-HIV drugs, and Traditional Chinese medicines (TCM) database were screened to find potential inhibitors. As a result, Saquinavir, and five drugs (TCM5280805, TCM5280445, TCM5280343, TCM5280863, and TCM5458190) from the TCM database were found as promising hits. Furthermore, results from molecular dynamics simulation and total binding free energy revealed that Saquinavir and TCM5280805 target the catalytic dyad (His41 and Cys145) and possess stable dynamics behavior. Thus, we suggest that these compounds should be tested experimentally against the SARS-COV-2 as Saquinavir has been reported to inhibit HIV protease experimentally. Considering the intensity of coronavirus dissemination, the present research is in line with the idea of discovering the latest inhibitors against the coronavirus essential pathways to accelerate the drug development cycle.Communicated by Ramaswamy H. Sarma.

Degradation of ribonucleic acid in mouse fibroblasts treated with actinomycin

The cellular RNA content of mouse fibroblasts incubated with actinomycin decreases at a rate of about 1 to 1.5 per cent per hour, while DNA and protein content remain unchanged. This degradation affects nuclear and cytoplasmic RNA, ribosomal and soluble RNA. The breakdown products appear quantitatively in the acid-soluble fraction of the cells and the medium. Polynucleotides synthesized a short period (120 minutes) prior to exposure to actinomycin are degraded before those synthesized 8 to 12 hours previously.

An international comparison of retinopathy of prematurity grading performance within the Benefits of Oxygen Saturation Targeting II trials

Purpose

To investigate whether the observed international differences in retinopathy of prematurity (ROP) treatment rates within the Benefits of Oxygen Saturation Targeting (BOOST) II trials might have been caused by international variation in ROP disease grading.

Methods

Groups of BOOST II trial ophthalmologists in UK, Australia, and New Zealand (ANZ), and an international reference group (INT) used a web based system to grade a selection of RetCam images of ROP acquired during the BOOST II UK trial. Rates of decisions to treat, plus disease grading, ROP stage grading, ROP zone grading, inter-observer variation within groups and intra-observer variation within groups were measured.

Results

Forty-two eye examinations were graded. UK ophthalmologists diagnosed treat-requiring ROP more frequently than ANZ ophthalmologists, 13.9 (3.49) compared to 9.4 (4.46) eye examinations, P=0.038. UK ophthalmologists diagnosed plus disease more frequently than ANZ ophthalmologists, 14.1 (6.23) compared to 8.5 (3.24) eye examinations, P=0.021. ANZ ophthalmologists diagnosed stage 2 ROP more frequently than UK ophthalmologists, 20.2 (5.8) compared to 12.7 (7.1) eye examinations, P=0.026. There were no other significant differences in the grading of ROP stage or zone. Inter-observer variation was higher within the UK group than within the ANZ group. Intra-observer variation was low in both groups.

Conclusions

We have found evidence of international variation in the diagnosis of treatment-requiring ROP. Improved standardisation of the diagnosis of treatment-requiring ROP is required. Measures might include improved training in the grading of ROP, using an international approach, and further development of ROP image analysis software.

Interventions for infantile esotropia

BACKGROUND

Various aspects of the clinical management of infantile esotropia (IE) are unclear - mainly, the most effective type of intervention and the age at intervention.

OBJECTIVES

The objective of this review was to assess the effectiveness of various surgical and non-surgical interventions for IE and to determine the significance of age at treatment with respect to outcome.

SEARCH STRATEGY

Trials were identified from the Cochrane Central Register of Controlled Trials - CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) in The Cochrane Library (Issue 3 2004), MEDLINE (1966 to July 2004), EMBASE (1980 to August 2004) and LILACS (July 2004). We manually searched the conference proceedings of the European Strabismological Association (ESA) (1975-1997, 1999-2002), International Strabismological Association (ISA) (1994) and American Academy of Paediatric Ophthalmology and Strabismus meeting (AAPOS) (1995-2003). Efforts were made to contact researchers who are active in the field for information about further published or unpublished studies.

SELECTION CRITERIA

Randomised trials comparing any surgical or non-surgical intervention for infantile esotropia.

DATA COLLECTION AND ANALYSIS

Each reviewer independently assessed study abstracts identified from the electronic and manual searches.

MAIN RESULTS

No studies were found that met our selection criteria and therefore none were included for analysis.

AUTHORS' CONCLUSIONS

The main body of literature on interventions for IE are either retrospective studies or prospective cohort studies. It has not been possible through this review to resolve the controversies regarding type of surgery, non-surgical intervention and age of intervention. There is clearly a need for good quality trials to be conducted in these areas to improve the evidence base for the management of IE.

Reduced density of intramembrane particles in erythrocytes of dystrophic chickens

The intramembrane particles in erythrocytes of chickens with hereditary muscular dystrophy and normal controls were compared by the freeze-fracture technique. Reduction of particles in both fracture faces and greater clustering of them was found in dystrophic samples. The concept of a generalized membrane abnormality in dystrophic chickens is supported.

Pyrazinamide resistance of novel mutations in pncA and their dynamic behavior

Pyrazinamide (PZA) is one of the essential anti-mycobacterium drugs, active against non-replicating Mycobacterium tuberculosis (MTB) isolates. PZA is converted into its active state, called pyrazinoic acid (POA), by action of pncA encoding pyrazinamidase (PZase). In the majority of PZA-resistance isolates, pncA harbored mutations in the coding region. In our recent report, we detected a number of novel variants in PZA-resistance (PZAR) MTB isolates, whose resistance mechanisms were yet to be determined. Here we performed several analyses to unveil the PZAR mechanism of R123P, T76P, G150A, and H71R mutants (MTs) through molecular dynamics (MD) simulations. In brief, culture positive MTB isolates were subjected to PZA susceptibility tests using the WHO recommended concentration of PZA (100 μg ml-1). The PZAR samples were screened for mutations in pncA along sensitive isolates through polymerase chain reactions and sequencing. A large number of variants (GeneBank accession no. MH461111), including R123P, T76P, G150A, and H71R, have been spotted in more than 70% of isolates. However, the mechanism of PZAR for mutants (MTs) R123P, T76P, G150A, and H71R was unknown. For the MTs and native PZase structures (WT), thermodynamic properties were compared using molecular dynamics simulations for 100 ns. The MTs structural activity was compared to the WT. Folding effect and pocket volume variations have been detected when comparing between WT and MTs. Geometric matching further confirmed the effect of R123P, T76P, G150A, and H71R mutations on PZase dynamics, making them vulnerable for activating the pro-drug into POA. This study offers a better understanding for management of PZAR TB. The results may be used as alternative diagnostic tools to infer PZA resistance at a structural dynamics level.

Pitfalls in the management of a child with mild haemophilia A and a traumatic hyphaema

A 12-year-old boy presented with a traumatic hyphaema that failed to settle with the standard treatment. Subsequent investigation showed that despite a normal APTT, he had a low factor VIII:C. Treatment with DDAVP precipitated further bleeding despite correction of the fVIII:C to normal, possibly caused by the vasodilation induced by the therapy. Bleeding was effectively treated with recombinant fVIII concentrate. DDAVP may be contraindicated in mild Haemophilia and von Willebrand patients for treatment of traumatic hyphaema.

Investigation of the binding and dynamic features of A.30 variant revealed higher binding of RBD for hACE2 and escapes the neutralizing antibody: A molecular simulation approach

With the emergence of Delta and Omicron variants, many other important variants of SARS-CoV-2, which cause Coronavirus disease-2019, including A.30, are reported to increase the concern created by the global pandemic. The A.30 variant, reported in Tanzania and other countries, harbors spike gene mutations that help this strain to bind more robustly and to escape neutralizing antibodies. The present study uses molecular modelling and simulation-based approaches to investigate the key features of this strain that result in greater infectivity. The protein-protein docking results for the spike protein demonstrated that additional interactions, particularly two salt-bridges formed by the mutated residue Lys484, increase binding affinity, while the loss of key residues at the N terminal domain (NTD) result in a change to binding conformation with monoclonal antibodies, thus escaping their neutralizing effects. Moreover, we deeply studied the atomic features of these binding complexes through molecular simulation, which revealed differential dynamics when compared to wild type. Analysis of the binding free energy using MM/GBSA revealed that the total binding free energy (TBE) for the wild type receptor-binding domain (RBD) complex was -58.25 kcal/mol in contrast to the A.30 RBD complex, which reported -65.59 kcal/mol. The higher TBE for the A.30 RBD complex signifies a more robust interaction between A.30 variant RBD with ACE2 than the wild type, allowing the variant to bind and spread more promptly. The BFE for the wild type NTD complex was calculated to be -65.76 kcal/mol, while the A.30 NTD complex was estimated to be -49.35 kcal/mol. This shows the impact of the reported substitutions and deletions in the NTD of A.30 variant, which consequently reduce the binding of mAb, allowing it to evade the immune response of the host. The reported results will aid the development of cross-protective drugs against SARS-CoV-2 and its variants.

Accuracy of co-morbidity data in patients undergoing abdominal wall hernia repair: a retrospective study

OBJECTIVES

To determine the baseline accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of routinely collected co-morbidity data in patients undergoing abdominal wall hernia repair.

METHODS

All patients aged > 18 who underwent umbilical, para-umbilical, inguinal or incisional hernia repair between 1 January 2015 and 1 November 2016 were identified. All parts of the clinical notes were searched for co-morbidities by two authors independently. The following co-morbidities were considered: hypertension, ischaemic heart disease (IHD), diabetes, asthma, chronic obstructive pulmonary disease (COPD), cerebrovascular disease (CVD), chronic kidney disease (CKD), hypercholesterolemia, obesity and smoking. The co-morbidities data from clinical notes were compared with corresponding data in hospital episode statistics (HES) database to calculate accuracy, sensitivity, specificity, PPV and NPV of HES codes for co-morbidities. To assess the agreement between clinical notes and HES data, we also calculated Cohen's Kappa index value as a more robust measure of agreement.

RESULTS

Overall, 346 patients comprising 3460 co-morbidity codes were included in the study. The overall accuracy of HES codes for all co-morbidities was 77% (Kappa: 0.13). When calculated separately for each co-morbidity, the accuracy was 72% (Kappa: 0.113) for hypertension, 82% (Kappa: 0.232) for IHD, 85% (Kappa: 0.203) for diabetes, 86% (Kappa: 0.287) for asthma, 91% (Kappa: 0.339) for COPD, 92% (Kappa: 0.374) for CVD, 94% (Kappa: 0.424) for CKD, 74% (Kappa: 0.074) for hypercholesterolemia, 71% (Kappa: 0.66) for obesity and 24% (Kappa: 0.005) for smoking. The overall sensitivity, specificity, PPV and NPV of HES codes were 9, 100, 100, and 77%, respectively. The results were consistent when individual co-morbidities were analyzed separately.

CONCLUSIONS

Our results demonstrated that HES co-morbidity codes in patients undergoing abdominal wall hernia repair are specific with good positive predictive value; however, they have substandard accuracy, sensitivity, and negative predictive value. The presence of a relatively large number of false negative or missed cases in HES database explains our findings. Better documentation of co-morbidities in admission clerking proforma may help to improve the quality of source documents for coders, which in turn may improve the accuracy of coding.

Thermophoretic Movement Transport of Reactive Casson Nanofluid on Riga Plate Surface with Nonlinear Thermal Radiation and Uneven Heat Sink/Source

The flow of magnetized Casson nanofluid past a Riga surface is examined in this study. The model scrutinizes the impacts of nonlinear radiative, uneven heat sink/source, thermophoretic movement and chemical reaction. Additionally, model is considered water based nanofluid with nanoparticles CuO (Copper Oxide) and MgO (Magnesium Oxide). The flow mechanics transport through Riga plate is developed using coupled system of higher order equations have been mutated into ordinary order from partial order utilizing established similarity transform. These nonlinear equations are calculated by the usage of through the Galerkin weighted residual method (GWRM) along with Simpson’s one-third rule and procured results are visualized graphically. Verifications of attained numerical outcomes through available literature for limiting case are also presented and found in excellent agreement. Further, the results of engineering physical parameters were also highlighted. More so, the analysis show that an increment in the Casson term causes rise in the temperature profile for CuO and MgO nanofluid and also dominant behavior is noted in case of CuO nanofluid comparing with MgO nanofluid. Furthermore, higher values of volume fraction parameter rises the both velocity profiles f′ (η), g′ (η) for both MgO and CuO nanofluid cases.

Retinopathy of prematurity screening at ≥30 weeks: urinary NTpro-BNP performance

AIM

Urinary N-terminal B-type natriuretic peptide NTproBNP levels are associated with the development of retinopathy of prematurity (ROP) in infants <30 weeks of gestation. The incidence of ROP in more mature infants who meet other ROP screening criteria is very low. We therefore aimed to test whether urinary NTproBNP predicted ROP development in these infants.

METHODS

Prospective observational study in 151 UK infants ≥30 + 0 weeks of gestation but also <32 weeks of gestation and/or <1501 g, to test the hypothesis that urinary NTproBNP levels on day of life (DOL) 14 and 28 were able to predict ROP development.

RESULTS

Urinary NTproBNP concentrations on day 14 and day 28 of life did not differ between infants with and without ROP (medians 144 vs 128 mcg/mL, respectively, p = 0.86 on DOL 14 and medians 117 vs 94 mcg/mL, respectively, p = 0.64 on DOL28).

CONCLUSION

The association previously shown for infants <30 completed weeks between urinary NTproBNP and the development of ROP was not seen in more mature infants. Urinary NTproBNP does not appear helpful in rationalising direct ophthalmoscopic screening for ROP in more mature infants, and may suggest a difference in pathophysiology of ROP in this population.

Comparing one-year outcomes of invasive versus medical management of patients with prior coronary artery bypass graft surgery presenting with non-ST elevation myocardial infarction

Background

Early percutaneous coronary intervention (PCI) has a Class 1A recommendation for patients with non-ST elevation myocardial infarction (NSTEMI). However, the benefits of this invasive approach in patients with previous coronary artery bypass graft (CABG) surgery are uncertain, as these patients have previously been excluded from pivotal trials.

Purpose

We hypothesised that routine invasive management in patients with previous CABG presenting with NSTEMI, but otherwise medically stable, carried similar prognostic outcomes to patients who were medically managed.

Methods

This single centre retrospective observational study screened patients with prior CABG presenting with NSTEMI between January 2015 and December 2019. Patients either underwent coronary angiography with or without PCI at their physician's discretion or received standard acute coronary syndrome (ACS) medical therapy. Follow up time was 365 days from admission date, and clinical, demographic, procedural and outcome data were collected. The primary endpoint was major adverse cardiac events (MACE), a composite of all-cause mortality and rehospitalisation for unstable angina, myocardial infarction, or heart failure.

Results

The study included 267 patients (mean ±SD age: 72±10 years, 82% male), of whom 80.1% (N=214) underwent cardiac catheterisation, and 19.9% (N=53) only received standard ACS medical therapy. Amongst the invasive group, 65.4% (N=140) received PCI. No one was referred for re-do CABG. At 1-year follow up, the primary composite outcome occurred in 18 (13%) patients in the PCI group, 13 (18%) in those managed conservatively following angiography, and in 27 (51%) patients receiving medical therapy only. Cox regression modelling showed no significant difference in the 1-year primary endpoint amongst those having an angiogram who received PCI versus those treated medically after invasive assessment (HR: 0.75 [95% CI: 0.38–1.48; P=0.412]). Previous revascularisation with PCI (HR: 1.90 [CI, 1.11–3.24; P=0.018]) and chronic kidney disease (CKD) (HR: 2.60 [CI, 1.56–4.34; P&lt;0.001]) at any stage, were the most important predictors of poor outcomes in CABG patients with NSTEMI irrespective of management strategy.

Conclusion

Patients with previous CABG who are admitted with NSTEMI who were not considered suitable for invasive angiography experienced significantly higher rates of MACE at 1-year follow up. The presence of CKD or previous PCI were key indicators of poor outcomes irrespective of management strategy. Outcomes amongst those deemed fit enough for invasive angiography were similar irrespective of treatment, suggesting that additional non-invasive testing may help further define which patients would benefit from an invasive strategy.

Funding Acknowledgement

Type of funding sources: None.

A descriptive study of consent documentation

The aim of this study was to observe the error rate in the consent process of a university hospital and to illicit the opinions of the consenting doctors on the process. A prospective observational review of theatre consent forms was performed along with an anonymous survey of non-consultant hospital doctors (NCHD's). No potential risks were documented in 95.3% of the 64 scrutinized consents and late alterations were required in 9%. Respondents to the NCHD survey estimated that they were unsure of the procedure or risks involved in an average of 29% of occasions. Interns admitted to being unsure of the details of the procedure in almost a third (32%) of cases, making them less well informed than their senior colleagues (p=0.024). This study highlights the difficulties encountered by consenting doctors, an issue which may lead to patient dissatisfaction, threaten the efficient running of a surgical unit and potentially expose its staff to avoidable litigation. It also recommends the use of multimedia adjuncts to facilitate both patient and doctor education in the consent process.

Structural basis for the mechanism of interaction of SARS-CoV-2 B.1.640.2 variant RBD with the host receptors hACE2 and GRP78

The inflicted chaos instigated by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) globally continues with the emergence of novel variants. The current global outbreak is aggravated by the manifestation of novel variants, which affect the effectiveness of the vaccine, attachment with hACE2 (human Angiotensin-converting enzyme 2) and immune evasion. Recently, a new variant named University Hospital Institute (IHU) (B.1.640.2) was reported in France in November 2021 and is spreading globally affecting public healthcare. The B.1.640.2 SARS-CoV-2 strain revealed 14 mutations and 9 deletions in spike protein. Thus, it is important to understand how these variations in the spike protein impact the communication with the host. A protein coupling approach along with molecular simulation protocols was used to interpret the variation in the binding of the wild type (WT) and B.1.640.2 variant with hACE2 and Glucose-regulating protein 78 (GRP78) receptors. The initial docking scores revealed a stronger binding of the B.1.640.2-RBD with both the hACE2 and GRP78. To further understand the crucial dynamic changes, we looked at the structural and dynamic characteristics and also explored the variations in the bonding networks between the WT and B.1.640.2-RBD (receptor-binding domain) in association with hACE2 and GRP78, respectively. Our findings revealed that the variant complex demonstrated distinct dynamic properties in contrast to the wild type due to the acquired mutations. Finally, to provide conclusive evidence on the higher binding by the B.1.640.2 variant the TBE was computed for each complex. For the WT with hACE2 the TBE was quantified to be-61.38 ± 0.96 kcal/mol and for B.1.640.2 variant the TBE was estimated to be -70.47 ± 1.00 kcal/mol. For the WT-RBD-GRP78 the TBE -was computed to be 32.32 ± 0.56 kcal/mol and for the B.1.640.2-RBD a TBE of -50.39 ± 0.88 kcal/mol was reported. This show that these mutations are the basis for higher binding and infectivity produced by B.1.640.2 variant and can be targeted for drug designing against it.Communicated by Ramaswamy H. Sarma.