Binding site prediction between lysozyme and glucose-regulated protein 78, a hope to fight amyloidosis.

Amyloidosis is an extraordinarily vigorous and heterogeneous group of disorders that causes numerous organ failures due to the precipitation of misfolded proteins. Many of these damaged proteins are discarded before causing any fatal diseases due to the contribution of the protein quality control (PQC) system and its chaperons, including glucose-regulated protein (GRP78). One of the most important enzymatic proteins inside the body is lysozyme, which is reported to have many mutated variants that may cause amyloid fibrils. This study used structural bioinformatics and molecular dynamics simulations to test and suggest binding sites for the human lysozyme protein with GRP78. Multiple sequence alignment (MSA) shows that part of the lysozyme envelope protein (C65-C81 cyclic region) has high similarities (30.77% identity) with the cyclic Pep42. Additionally, the binding between the lysozyme cyclic region (C65-C81) and GRP78 substrate binding domain (SBD) is found favorable. The number and types of interactions vary between each of the mutant isoforms of lysozyme. The more significant the conformational changes in the mutation, the greater its probability of aggregation and the formation of amyloid fibrils. Each mutation leads to different interactions and binding patterns with GRP78. The present computational study suggests a lysozyme-GRP78 binding site, thus paving the way for drug designers to construct suitable carriers that can collect misfolded lysozyme proteins and eliminate them from the body, preventing their aggregation and amyloidogenesis.Communicated by Ramaswamy H. Sarma.

In vivo dose measurements for tangential field-in-field ultra-hypofractionated breast radiotherapy.

INTRODUCTION: Ultra-hypofractionated radiotherapy (UHF-RT) mandates more accuracy in each part of the treatment cycle to maximize cure rates and minimize toxicities. In vivo dosimetry is a direct method for verifying overall treatment accuracy. This study evaluated uncertainties in the delivered dose of Hypofractionated (HF) and UHF Whole Breast Irradiation (WBI) and to analyze the accuracy of the workflow to pave the way for a wide-scale use of UHF-RT. METHODS: Thirty-three breast cancer cases, including 16 HF-WBI and 17 UHF-WBI were treated with 3D conformal Radiotherapy (3D-CRT), where 79 fields were analyzed for dose verification. The measurement point was set at the beam entrance (1.5 cm depth). The expected dose at Dmax was calculated via TPS. Before in vivo measurements, diode detectors were tested and calibrated. We developed initial validation measurements for UHF-RT on an anthropomorphic breast phantom for the first time. RESULTS: For RANDO phantom, the percentage difference between measured and calculated doses showed an average of -0.52 ± 5.4%, in addition to an excellent dose reproducibility within 0.6%. The overall in vivo measurements for studied cases showed that 83.5% of the measured doses were within ±5% and only 1.8% of the measured doses were greater than ±10% of the calculated doses. The percentage accuracy was slightly larger for UHF cohort (84.2%) compared to HF cohort (83.2%). The maximum percentage difference between them was less than 1%. CONCLUSION: Breast in vivo dosimetry is an adequate tool for treatment verification that improves the accuracy of the treatment cycle. UHF-RT may contribute in reducing the long waiting lists, increasing patient convenience, and saving the available resources for breast cancer patients.

Molecular dynamics simulations and MM-GBSA reveal a novel small molecule against Flu A RNA-dependent RNA polymerase.

The interaction between the C-terminal domain (CTD) of the polymerase acidic (PA) component of three Flu A RNA polymerases of different origins and three heptad repeats from human polymerase II CTD was computationally recreated. Then a unique pharmacological library was tested in order to target conserved active site residues in the three RNA-dependent RNA polymerase (RdRps) using a combination of molecular dynamics simulation and molecular docking. Results show that one compound (ZINC66032798) can effectively bind to the desired active site residues in each of the three RdRps. Hence, it may possess an inhibitory action by competing with human polymerase II CTD binding to the same active site of the viruses. The current in silico analysis suggests a promising novel lead to block Flu A RdRp, yet to be confirmed in the wet lab. It decreases the binding affinity of influenza A viruses to human polymerase II by 47.9%, 67.2%, and 28.0%, respectively.Communicated by Ramaswamy H. Sarma.

Dose-enhancement of MCF 7 cell line radiotherapy using silica-iron oxide nanocomposite.

Cancer radiotherapy is one of the most effective regimens of cancer treatments, but cancer cell radioresistance remains a concern. Radiosensitizers can selectively improve the efficacy of radiotherapy and reduce inherent damage. The purpose of this work is to evaluate the effect of silica-coated iron oxide magnetic nanoparticles (SIONPs) as a radiosensitizer and compare their therapeutic effect with that of Iron oxide magnetic nanoparticles (IONPs). IONPs and SIONPs were characterized using several physical techniques such as a transmission electron microscope (TEM) and Vibrating sample magnetometer (VSM). MTT and DNA double-strand breaks (Comet) assays have been used to detect the cytotoxicity, cell viability, and DNA damage of MCF-7 cells, which were treated with different concentrations of prepared nanoparticles and exposed to an X-ray beam. In this study, an efficient radiosensitizer, SIONPs, was successfully prepared and characterized. With 0.5 Gy dose, dose enhancement factor (DEF) values of cells treated with 5 and 10 µg/ml of IONPs were 1 and 1.09, respectively, while those treated with SIONPs at these concentrations had DEF of 1.21 and 1.32, respectively. Results demonstrated that SIONPs provide a potential for improving the radiosensitivity of breast cancer.

Target-filter combination effects on breast tissue characterization using mammographic X-rays: A Monte Carlo simulation study.

BACKGROUND: Characterization of normal and malignant breast tissues using X-ray scattering techniques has shown promising results and applications. OBJECTIVE: To examine possibility of characterizing normal and malignant breast tissues using the scattered photon distribution of polyenergetic beams of 30 kV X-rays. METHODS: A Monte Carlo simulation is upgraded so that it is capable of simulating input mammographic X-ray spectra from different target-filter combinations, tracing photon transport, and producing the distribution of scattered photons. The target-filter combinations include Mo-Mo, Mo-Al, Mo-Rh, Rh-Rh, Rh-Al, W-Rh, and W-Al. Analysis of obtained scattered photon distribution is carried out by comparing the ratio of count under the peak in the momentum transfer region from 0 to 1.55 nm-1, to that in the region from 1.6 to 9.1 nm-1 (covering the regions of scattering from fat and soft tissue, respectively) for breast samples with different percentages of normal tissue (0-100%). RESULTS: Mo-Mo target-filter combination shows a high linear dependence of the count under peak ratio on the percentage of normal tissue in breast samples (R2 = 0.9513). Despite slightly less linear than Mo-Mo, target-filter combinations other than Rh-Rh, W-Rh, and W-Al produce high linear responses (R2 > 0.9)CONCLUSION:Mo-Mo target-filter combination would probably be the most relevant in characterizing normal and malignant breast tissues from their scattered photon distribution.

Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase.

According to the World Health Organization (WHO), SARS-CoV-2 is responsible for more than 5 M deaths and is reported in 223 countries infecting 250+ M people. Despite the current vaccination momentum, thousands of people die every day by COVID-19. Suggesting possible blockers of the viral RNA-dependent RNA polymerase is highly needed for potential effective therapeutics against SARS-CoV-2. This study utilizes combined molecular dynamics simulation and molecular docking to test novel guanosine derivatives against SARS-CoV-2 RdRp. Results reveal the binding potency of nineteen guanosine derivatives against SARS-CoV-2 solved structures. The bulky moieties (hydroxyl or fluorated phenyl moieties) added to the 2' position of the ribose ring positively impacted the binding affinity to RdRp. The current in silico study represents a one-step-ahead for suggesting new possible blockers of SARS-CoV-2 RdRp that are yet to be verified in the wet lab. It offers new potential binders or blockers of RdRp that bind to the protein active site tighter than remdesivir. The latter was approved by the food and drug administration (FDA) for emergency use against COVID-19 last year.

Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective.

Finding a potent inhibitor to the pandemic SARS-CoV-2 is indispensable nowadays. Currently, in-silico methods work as expeditious investigators to screen drugs for possible repurposing or design new ones. Targeting one of the possible SARS-CoV-2 attachment and entry receptors, Glucose-regulated protein 78 (GRP78), is an approach of major interest. Recently, GRP78 was reported as a recognized representative in recognition of the latest variants of SARS-CoV-2. In this work, molecular docking and molecular dynamics simulations were performed on the host cell receptor GRP78. With its many terpenoid compounds, Chaga mushroom was tested as a potential therapeutic against the SARS-CoV-2 receptor, GRP78. Results revealed low binding energies (high affinities) toward the GRP78 substrate-binding domain ß (SBDß) of Chaga mushroom terpenoids. Even the highly specific cyclic peptide Pep42, which selectively targeted GRP78 over cancer cells in vivo, showed lower binding affinity against GRP78 SBDß compared to the binding affinities of terpenoids. These are auspicious results that need to be tested experimentally. Intriguingly, terpenoids work as a double sword as they can be used to interfere with VUI 202,012/01, 501.V2, and B.1.1.248 variants of SARS-CoV-2 spike recognition.

Novel adenosine derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective.

BACKGROUND: SARS-CoV-2 is a newly emerged human coronavirus that severely affected human health and the economy. The viral RNA-dependent RNA polymerase (RdRp) is a crucial protein target to stop virus replication. The adenosine derivative, remdesivir, was authorized for emergency use 10 months ago by the United States FDA against COVID-19 despite its doubtful efficacy against SARS-CoV-2. METHODS: A dozen modifications based on remdesivir are tested against SARS-CoV-2 RdRp using combined molecular docking and dynamics simulation in this work. RESULTS: The results reveal a better binding affinity of 11 modifications compared to remdesivir. Compounds 8, 9, 10, and 11 show the best binding affinities against SARS-CoV-2 RdRp conformations gathered during 100 ns of the Molecular Dynamics Simulation (MDS) run (- 8.13 ± 0.45 kcal/mol, - 8.09 ± 0.67 kcal/mol, - 8.09 ± 0.64 kcal/mol, and - 8.07 ± 0.73 kcal/mol, respectively). CONCLUSIONS: The present study suggests these four compounds as potential SARS-CoV-2 RdRp inhibitors, which need to be validated experimentally.

COVID-19 and Cell Stress.

The present century will undoubtedly be marked with the COVID-19 global health crisis. It is not time yet to talk about the total number of deaths and hospitalizations, as they are enormously growing daily. Understanding the nature of COVID-19-induced pneumonia is vital in order to deal with the associated health complications. Cell stress is an established mechanism known to be associated with infection and cancer. Different proteins crucial for cellular response to stress are reported to be a possible target to stop the infection and to reduce the chemo-resistance in cancer. Heat shock protein (HSP) families of chaperones play an essential role in cells both in normal state and under stress. The upregulation of HSP5A, also termed GRP78 or Bip, is reported in different viral infections. This chapter introduces the current knowledge about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused the COVID-19 pandemic, and cell stress aimed at defining possible strategies to combat the COVID-19 pandemic.

Image quality characteristics of myocardial perfusion SPECT imaging using state-of-the-art commercial software algorithms: evaluation of 10 reconstruction methods.

Myocardial perfusion imaging (MPI) is widely used as standard of care in patients with coronary artery disease. The availability of hybrid SPECT/CT imaging system and associated advanced reconstruction algorithms serve to improve diagnostic accuracy and enhances image quality of MPI. The aim of this work was to evaluate the relative performance of iterative reconstruction algorithms correcting for different combinations of image degrading factors versus filtered back projection on the quality of myocardial perfusion SPECT imaging. A standard cardiac phantom containing myocardial defects of different sizes and compositions was used to simulate myocardial perfusion SPECT/CT clinical studies. A clinically relevant activity was determined to avoid discordance with real data acquisition. Acquisition parameters including time per projection, angular rotation increment, and iterative reconstruction number of iterations and subsets were varied. The reconstruction was carried out applying different algorithms including 10 variants of analytical (e.g FBP) and iterative reconstructions with and without resolution recovery. Typical figures of merit were used to evaluate the image quality of MPI reconstructed with ten different reconstruction methods. OSEM-RR showed remarkable improvement of image quality of MPI in terms of SNR, CNR and defect contrast percentage compared to FBP algorithm. Full correction scheme IR-RR (i.e. IRACSCRR) provides clinically acceptable image quality of MPI compared to FBP.

Is 9-field IMRT superior to 7-field IMRT in the treatment of nasopharyngeal carcinoma?

BACKGROUND: To evaluate the pros and cons of 9-field intensity modulated radiotherapy (IMRT) compared to 7-field IMRT in the treatment of nasopharyngeal carcinoma (NPC). METHODS: Ten NPC patients were treated with 7F-IMRT and 9F-IMRT. A dose prescription of 70 Gy was delivered in 35 fractions to gross planning target volume (PTV1). Plan verification was performed via 2D-array and film dosimetry. Dose-Volume Histogram (DVH) parameters were used to evaluate the quality of IMRT plans. RESULTS: Dose data for the investigated planning techniques obeyed the Radiation Therapy Oncology Group (RTOG) protocol no. 0615. The dose delivered to PTV1 and organs-at-risk (OARs) for 9F-IMRT was significantly better than 7F-IMRT, except for OARs which were at a distance from PTV1, such as eyes, optical nerves, and chiasma. Ninety five percent of PTV1 was covered by more than 95% of the prescribed dose (67.75 ± 1.1 Gy and 68.57 ± 1.2 Gy for 7F-IMRT and 9F-IMRT, respectively). The maximum dose to 1% of brainstem was 50.06 ± 2.7 Gy and 47.75 ± 2.6 Gy for 7F-IMRT and 9F-IMRT, respectively. Dose verification showed good agreement with treatment planning system with a maximum deviation for 2D-array of 2.16% ± 0.86 and 1.73% ± 0.33 for 7F-IMRT and 9F-IMRT, respectively. Similarly, radiochromic film reported maximum dose deviations of 3.38% ± 1.68 and 2.77% ± 1.3, respectively. CONCLUSION: 9F-IMRT provides better homogenous dose to PTV1 and more sparing of OARs over 7F-IMRT for NPC patients, except for OARs which are are a distance from PTV1.

RADIOECOLOGICAL IMPACT AND THE ASSOCIATED HAZARDS DUE TO NORM FROM OIL AND GAS PRODUCTION FACILITY IN THE WESTERN DESERT OF EGYPT.

An oil and gas production facility in the western desert of Egypt was investigated for possible radiation risks due to the routine operation. Radium-226, Radium-228 and Potassium-40 were assessed in the soil samples collected from the adjacent soakaway pond. The average 226Ra, 228Ra and 40K activity concentrations were 881.0 ± 42.0, 966.0 ± 43.0 and 143.0 ± 8.0 Bq kg-1, respectively. Both 226Ra and 228Ra were above the world ranges, while 40K was within the world range. Water samples from the facilities effluent's produced water showed elevated levels of both radium isotopes. The effective doses at three different points on the separator outer surfaces over the period between 1995 and 2014 were assessed. The maximum reading was 5.4 µSv h-1 on 2014. The time has significantly contributed to the enhancement of the effective dose readings. However, they are still within the expected range encountered in similar studies reported by International Atomic Energy Agency (IAEA).

Recognition of gluconeogenic enzymes; Icl1, Fbp1, and Mdh2 by Gid4 ligase: A molecular docking study.

The pro/N-degron pathway is an evolved protein degradation pathway through the ubiquitin-proteasome system. It is a vital pathway to attain protein homeostasis inside the liver cells with varying glucose levels. N-terminal proline exists in more than 300 proteins in Saccharomyces cerevisiae, but only three of them are the gluconeogenic enzymes; isocitrate lyase (Icl1), fructose-1,6-bisphosphatase (Fbp1), and malate dehydrogenase (Mdh2). The present in silico study aims to structurally illustrate the binding of Icl1 enzyme to Gid4 ligase concerning its peers; Fbp1 and Mdh2. Based on the molecular docking scores and interactions, one can attribute the binding stability of Gid4 with degrons, to peptides of length six up to eight from the N-terminal. Moreover, the percent change in the docking score provides a rationale for the unique Gid4-Icl11-4 interaction. The present study provides insights on the binding attitude of Gid4 ligase to degrons of different lengths, so one will consider in designing peptidomimetics to target Gid4 ligase.

Recognition of the gluconeogenic enzyme, Pck1, via the Gid4 E3 ligase: An in silico perspective.

Gluconeogenesis, the reverse process of glycolysis, is a favorable mechanism at conditions of glucose deprivation. Pck1 is a rate-limiting gluconeogenic enzyme, where its deficiency or mutation contributes to serious clinical situations as neonatal hypoglycemia and liver failure. A recent report confirms that Pck1 is a target for proteasomal degradation through its proline residue at the penultimate position, recognized by Gid4 E3 ligase, but with a lack of informative structural details. In this study, we delineate the localized sequence motif, degron, that specifically interact with Gid4 ligase and unravel the binding mode of Pck1 to the Gid4 ligase by using molecular docking and molecular dynamics. The peptide/protein docking HPEPDOCK web server along with molecular dynamic simulations are applied to demonstrate the binding mode and interactions of a Pck1 wild type (SPSK) and mutant (K4V) with the recently solved structure of Gid4 ligase. Results unveil a distinct binding mode of the mutated peptide compared with the wild type despite having comparable binding affinities to Gid4. Moreover, the four-residue peptide is found insufficient for Gid4 binding, while the seven-residue peptide suffices for binding to Gid4. The amino acids S134, K135, and N137 in the loop L1 (between ß1 and ß2) of the Gid4 are essential for the stabilization of the seven-residue peptide in the binding site of the ligase. The presence of Val4 instead of Lys4 smashes the H-bonds that are formed between Lys4 and Gid4 in the wild type peptide, making the peptide prone to bind with the other side of the binding pocket (L4 loop of Gid4). The dynamics of Gid4 L3 loop is affected dramatically once K4V mutant Pck1 peptide is introduced. This opens the door to explore the mutation effects on the binding mode and smooth the path to target protein degradation by design competitive and non-competitive inhibitors.

Plasma membrane proteins: A new probe for the characterization of breast cancer.

This work aimed to characterize normal, benign and malignant excised breast tissues through the analysis of the FTIR spectra of their plasma membrane proteins. Tissue characterization parameters such as peak position, peak intensity, area under the peak, relative peak intensity and relative area under peak were evaluated mainly for protein spectral peaks; 1150 cm-1, Amide I, Amide II, Amide III, and Amide A. The sensitivity, specificity and diagnostic accuracy for each parameter were obtained and Receiver Operating Characteristic (ROC) Curves were plotted. Results showed significant spectral differences between normal and benign tissues compared to malignant tissues at 1536 and 1645 cm-1. The three tissues could be distinguished at 2900 cm-1, where the malignant peak uniquely split into two separate peaks. ROC curves showed that the Amide A peak position yielded a higher accuracy compared to all other investigated characterization parameters. The deconvolution of Amide I revealed the conformational changes in plasma proteins characterizing the transformation to malignancy (a decrease in the percentage of alpha helix accompanied by an increase in the percentage of beta sheets). The use of the present structure-based analysis in conjunction with histopathological examination of excised breast tissues would offer an enhanced characterization that might reduce possible personal diagnostic mistakes.

Magnetic nanoparticles-loaded liposomes as a novel treatment agent for iron deficiency anemia: In vivo study.

Iron deficiency anemia (IDA) is a major worldwide public health problem. This is due to its prevalence among infants, children, adolescents, pregnant and reproductive age women. Ferrous sulfate (FeSO4) is the first line therapy for iron IDA. Unfortunately, it is reported that FeSO4 suffers from low absorption rate in the body and itself exhibits severe side effects. Herein, iron oxide magnetic nanoparticles-loaded liposomes (LMNPs) are prepared, characterized and evaluated as a treatment regimen for IDA in Wistar rats (as an animal model). Iron oxide magnetic nanoparticles (MNPs) are prepared and loaded into liposomes using the thin film hydration method. The size of the prepared formulations is in the range 10-100 nm, thus it can avoid the reticular endothelial system (RES), and increased their blood circulation time. For in vivo assessment, thirty-five Wistar rats are divided into 5 groups (n = 7): negative control group, positive control group, and three groups treated with different iron formulations (FeSO4, MNPs and LMNPs). Anemia is induced in the anemic groups by the bleeding method and then treatment started with different iron compounds administrated orally for 13 days. Hematological parameters are followed up during the treatment period. Results indicate that, in the LMNPs group, the hematological parameters turn to normal values and the histopathological structures of the liver, spleen and kidney remain normal. This proves that liposome increases the bioavailability of MNPs. In conclusion, LMNPs demonstrate superiority as a therapeutic regimen for the treatment of IDA among the tested iron formulations.

Silica-coated iron oxide nanoparticles as a novel nano-radiosensitizer for electron therapy.

AIMS: Conventional radiotherapy is mainly restricted by the low radiation absorption efficiency of tumors tissues and the hypoxic tumor cells radio-resistance. In this paper, novel nano-radiosensitizers, magnetic nanoparticles core coated with silica, were successfully prepared to overcome these limitations. MAIN METHODS: The prepared nanoparticles have been characterized by transmission electron microscope (TEM), Dynamic light scattering (DLS), atomic force microscope (AFM) and vibration sample magnetometer (VSM). MTT cytotoxicity and DNA double-strand breaks (Comet) assays have been used to assess the radio-enhancing effect of iron oxide magnetic nanoparticles (IO-MNPs) and silica-coated iron oxide magnetic nanoparticles (SIO-MNPs) against MCF7 breast cancer cells. MCF7 cells were treated with different concentrations of the prepared nanoformulations and exposed to an electron beam at doses 0, 0.5, 1, 2, 4 Gy. KEY FINDINGS: DLS measurements revealed that the main hydrodynamic diameter of the prepared IO-MNPs and SIO-MNPs was 18.17 ±â€¯4.5 nm and 164.18 ±â€¯16.1 nm, respectively, which was confirmed by TEM micrographs. MTT and comet assays results showed that the radiosensitizing effect of the prepared nanoformulations was dose and concentration dependent. Interestingly, the dose enhancement factor (DEF) for SIO-MNPs was, on average, 1.3-fold greater than that of IO-MNPs. SIGNIFICANCE: Coating of IO-MNPs with silica led to enhance their electron radiosensitization and consequently their therapeutic efficacy. Therefore, SIO-MNPs represent a promising engineered nano-formulation for enhancing breast cancer radiosensitivity.

Novel inhibitors against wild-type and mutated HCV NS3 serine protease: an in silico study.

In 2011, the FDA approved boceprevir as a hepatitis C virus (HCV) NS3 serine protease inhibitor. The sustained virological response rate for treatment with this approved compound is considerably low. Patients have not responded as much as expected to boceprevir therapy. In this in silico study, modified boceprevir compounds are suggested and tested on wild-type HCV NS3 protease and 19 mutated HCV NS3 proteases using molecular docking. Results reveal the superiority of two of the proposed modified compounds to boceprevir. One of which appears to be more potent than boceprevir itself concerning activity against wild-type NS3 and most of the examined mutated NS3 proteases.