In silico identification of potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations

In the present era, there are many efforts trying to face the emerging and successive waves of the COVID-19 pandemic. This has led to considering new and unusual targets for SARS CoV-2. 2′-O-Methyltransferase (nsp16) is a key and attractive target in the SARS CoV-2 life cycle since it is responsible for the viral RNA protection via a cap formation process. In this study, we propose a new potential inhibitor for SARS COV-2 2′-O-methyltransferase (nsp16). A fragment library was screened against the co-crystal structure of the SARS COV-2 2′-O-methyltransferase complexed with Sinefungin (nsp16 – PDB ID: 6WKQ), and consequently the best proposed fragments were linked via a de novo approach to build molecule AP-20. Molecule AP-20 displayed a superior docking score to Sinefungin and reproduced the key interactions in the binding site of 2′-O-methyltransferase. Three molecular dynamic simulations of the 2′-O-methyltransferase apo structure and its complexed forms with AP-20 and Sinefungin were performed for 150 nano-seconds to provide insights on the dynamic nature of such setups and to assess the stability of the proposed AP-20/enzyme complex. AP-20/enzyme complex demonstrated better stability for the ligand–enzyme complex compared to Sinefungin in a respective setup. Furthermore, MM-PBSA binding free energy calculations showed a better profile for AP-20/enzyme complex compared to Sinefungin/enzyme complex emphasizing the potential inhibitory effect of AP-20 on SARS COV-2 2′-O-methyltransferase. We endorse our designed molecule AP-20 to be further explored via experimental evaluations to confront the spread of the emerging COVID-19. Also, in silico ADME profiling has ascribed to AP-20 an excellent safety and metabolic stability profile.

The identification of AP-20 as a potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations.     

Colonoscopy in patients with psoriasis before the initiation of treatment with biological agents

Psoriasis may lead to subsequent colorectal cancer, since chronic systemic inflammation is the common etiologic factor in both psoriasis and colorectal cancer. It is a matter of dispute whether biological agents used in the treatment of psoriasis cause predisposition to colorectal cancer as a result of their immunosuppressive effect. Medical records of psoriasis patients who underwent colonoscopy before biological agents were reviewed. Colonoscopy was performed in all patients who were aged 50 years and older and in patients younger than 50, if they had positive fecal occult blood test results. The study included 95 patients between the age of 34 to 84. Colonoscopy results revealed tubular adenoma in 16 (16.8%) patients, hyperplastic polyps in 7 (7.4%) patients, villous adenoma in 1 (1.1%) patient, and tubulovillous adenoma in 1 (1.1%) patient. Two patients were diagnosed with colon cancer detected by a former colonoscopy, which was recommended by their dermatologist before the biological agent treatment plan. These results revealed that adenomatous polyps which can evolve to colon adenocarcinoma were the most frequent polyp type in patients with psoriasis. We suggest that routine colonoscopy should be performed before the initiation of biological therapy in psoriasis patients who are aged 50 years old and over.     

A Systematic Characterization Approach for Vacuum Bag Only Prepregs towards an Accurate Process Design

Aerospace-grade composite parts can be manufactured using Vacuum Bag Only prepregs through an accurate process design. Quality in the desired part can be realized by following process modeling, process optimization, and validation, which strongly depend on a primary and systematic material characterization methodology of the prepreg system and material constitutive behavior. The present study introduces a systematic characterization approach of a Vacuum Bag Only prepreg by covering the relevant material properties in an integrated manner with the process mechanisms of fluid flow, consolidation, and heat transfer. The characterization recipe is practiced under the categories of (i) resin system, (ii) fiber architecture, and (iii) thermal behavior. First, empirical models are successively developed for the cure-kinetics, glass transition temperature, and viscosity for the resin system. Then, the fiber architecture of the uncured prepreg system is identified with X-ray tomography to obtain the air permeability. Finally, the thermal characteristics of the prepreg and its constituents are experimentally characterized by adopting a novel specimen preparation technique for the specific heat capacity and thermal conductivity. Thus, this systematic approach is designed to provide the material data to process modeling with the motivation of a robust and integrated Vacuum Bag Only process design.     

Arterial elasticity measurement in renal transplant recipients

Arterial distensibility is reduced in chronic kidney disease (CKD) and after kidney transplantation. Pulse counter analysis provides an assessment of compliance or elasticity of the large conduit arteries (C1) and small arteries (C2). Decreased compliance has been shown to be predictive of primary coronary events in CKD patients. The aim of the present study was to compare elasticity measurements in hemodialysis (HD) patients, renal transplant recipients (RTR), and healthy subjects whose coronary angiographies were without lesion. Twenty-three RTRs, 18 HD patients, and 20 healthy subjects were included in the study. Pulse wave analysis was used to determine large and small vessel compliances. The C1 and C2 levels were significantly lower in HD patients compared with recipients and healthy subjects. Recipients showed lower C2 level compared with healthy subjects. There was no difference in C1 and C2 measurements between recipients receiving tacrolimus versus cyclosporine. Transplantation improves large and to some extend small artery elasticities in CKD patients.     

End-to-end microvascular anastomosis in the rat carotid artery using continuous horizontal mattress sutures

This paper reports a continuous horizontal mattress suture technique with advantages such as decreased time for anastomosis, minimized anastomotic leakage, eversion around the vessel edges, and other advantages which the continuous anastomosis technique has. This technique was compared with the classical interrupted and classical continuous suture techniques on a total of 59 Sprague-Dawley rat common carotid arteries: Group 1 (n = 19), interrupted suture technique; Group 2 (n = 20), standard continuous technique, and Group 3 (n = 20), continuous horizontal mattress technique. Early (30 min) and late (21 days) patency rates, anastomosis time, leakage on clamp release, oozing duration, additional sutures needed, and total number of sutures placed were statistically compared between groups. Specimens were taken at the 21st day randomly, and light microscopy (LM), scanning electron microscopy (SEM), and angiographic studies were performed. Results revealed that the continuous mattress suture technique has the advantages of providing a water-tight anastomosis with less suture materials in a shorter time, and minimal intraluminal suture material which can incite thrombosis. On the other hand, a tendency to anastomotic stricture was found to be the sole disadvantage of this technique.     

Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids

Viruses have developed a wide range of strategies to escape from the host cells in which they replicate. For egress some archaeal viruses use a pyramidal structure with sevenfold rotational symmetry. Virus-associated pyramids (VAPs) assemble in the host cell membrane from the virus-encoded protein PVAP and open at the end of the infection cycle. We characterize this unusual supramolecular assembly using a combination of genetic, biochemical, and electron microscopic techniques. By whole-cell electron cryotomography, we monitored morphological changes in virus-infected host cells. Subtomogram averaging reveals the VAP structure. By heterologous expression of PVAP in cells from all three domains of life, we demonstrate that the protein integrates indiscriminately into virtually any biological membrane, where it forms sevenfold pyramids. We identify the protein domains essential for VAP formation in PVAP truncation mutants by their ability to remodel the cell membrane. Self-assembly of PVAP into pyramids requires at least two different, in-plane and out-of-plane, protein interactions. Our findings allow us to propose a model describing how PVAP arranges to form sevenfold pyramids and suggest how this small, robust protein may be used as a general membrane-remodeling system.Release of virus particles from infected cells is the last essential step of the viral replication cycle. In the course of this process, virions face the challenging task of crossing the cell envelope. Viruses have developed an arsenal of diverse strategies to overcome this problem. Most bacterial viruses are lytic and induce lysis of the infected cell with help of the holin-endolysin system (1), whereas others disrupt the host cell envelope via inhibition of the murein biosynthesis pathway (2). The morphological and genomic properties of archaeal viruses (3) suggested that their egress from host cells may have unusual traits that are different from those of bacterial viruses. Indeed, although most archaeal viruses exit cells without lysis, some, in particular the Sulfolobus islandicus rod-shaped virus 2 (SIRV2) and Sulfolobus turreted icosahedral virus (STIV), are lytic and exploit a special mechanism of virion egress (4–8). During the infection cycle of these viruses, pyramidal protrusions with sevenfold rotational symmetry form in the host cell membrane. As the final step of the infection cycle the virus-associated pyramids (VAPs) open outwards along the seams of their seven facets, creating ∼100-nm apertures through which the newly formed virions escape from the host cell (4, 7). VAPs consist of multiple copies of an ∼10-kDa virus-encoded protein, which we term “PVAP” (Protein forming Virus-Associated Pyramids/SIRV2_P98) (7–9). Surprisingly, PVAP assembles into membrane pyramids even when expressed heterologously in archaeal and bacterial expression systems, demonstrating that no other viral proteins are required for VAP formation (7). The mechanism by which VAPs self-assembles in the membrane remains unknown.In the present study we used electron cryotomography to investigate morphological features of SIRV2 replication and the formation of VAPs at different time points after infection. By subtomogram averaging, we determined a 3D map of the VAP. This map, in combination with secondary structure predictions of PVAP and the expression of wild-type (WT) PVAP or a variety of truncation mutants in archaeal, bacterial and eukaryotic cells allows us to propose a model showing how PVAP arranges to form the sevenfold pyramids. These insights are fundamental for understanding how this mechanism can be exploited as a universal tool to engineer the formation and controlled opening of large pores in biological or artificial lipid bilayers.