Dock-able linear and homodetic di,tri,tetra and pentapeptide library from canonical amino acids:SARS-CoV-2 Mpro as a case study / 药物分析学报

Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity.Although noncanonical residues can always be used,employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening.Towards this goal,the dataset comprising all possible di-,tri-,and tetra-peptide com-binations of the canonical residues has been previously reported.However,with increasing computa-tional power,the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues.Here,we provide both the com-plete and prefiltered libraries of all di-,tri-,tetra-,and penta-peptide sequences from 20 canonical amino acids and their homodetic(N-to-C-terminal)cyclic homologues.The FASTA,simplified molecular-input line-entry system(SMILES),and structure-data file(SDF)-three dimension(3D)libraries can be readily used for screening against protein targets.We also provide a simple method and tool for conducting identity-based filtering.Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns.As a case study,the developed library was screened against severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)main protease to identify po-tential small peptide inhibitors.

The role of lipids and fatty acid metabolism in the development of prostate cancer

The reprogramming of lipid metabolism and signaling pathways is the central aspect of cancer biology. It is hypothesized that tumor cells can alter the lipid spectrum in order to fulfill their metabolic requirements. Furthermore, they can alter potential tumors and suppressive mechanisms in which lipids' involvement is essential. Recently, more attentions have been given on the alteration of lipid metabolism during prostate cancer development, and investigations have shown unique regulation of "de novo" lipid synthesis in cancer cells. Cancer cells often use newer pathways and enzymes to simplify the synthesis of fatty acids, and the newly synthesized lipids affect cellular processes, which impacts cancer cell proliferation and survival outcomes. Herein, we aimed to study the influence of lipid profile alterations on the development of prostate cancer. We found that the total amounts of lipids and phospholipids were increased within tissues from men with the malignant prostate tumor as compared with the benign prostate tissue. Significant changes were also observed in the composition of saturated and unsaturated fatty acids within the malignant tumor tissues. Intensification of lipid peroxidation has also been observed in malignant prostate tumors compared to benign prostate tumors. Collectively, these findings further highlights the fact that lipid and fatty acids play unique regulatory roles in the cellular development of prostate malignant transformation.

Biochemical relationship between leiomyosarcoma and peroxiredoxin-6 expression level: Clinical implications

Uterine leiomyosarcomas are tumors with a heterogeneous genetic profiles that respond very poorly to cytotoxic chemotherapy with aggressive progression. We aimed to show the status of peroxiredoxin 6 as a biomarker in leiomyosarcoma progression.Study included 12 patients diagnosed with "leiomyosarcoma" and 13 patients diagnosed with "myoma" (as control) after histopathological examinations of clinical samples. Peroxiredoxin-6 gene expression and protein levels were evaluated on the tumor preparations (blocks) utilizing ELISA and PCR methods.Peroxiredoxin-6 protein was mainly localized in the cytoplasm of leiomyosarcoma cells, and the expression of peroxiredoxin-6 was significantly increased in cancerous tissues compared to normal myoma tissues (3.33±1.7 vs. 2.03±1.07fold change; P= 0.031). Peroxiredoxin-6 tissue protein levels were also significantly higher in leiomyosarcoma cases (100.54±66.86 vs. 183.72±64.54 pg/µg protein; P= 0.005). Our findings demonstrate that peroxiredoxin-6 plays a vital role in the emergence and development of leiomyosarcoma and that peroxiredoxin-6 level assessments can be used as a biomarker in guiding better prognosis andtreatment plans while managing leiomyosarcoma.

Blood formed elements of the women with uterine tumors as one of the criterion for assessment of severity of the pathology

The indicators for structural analysis of blood formed elements are prominent in the assessment of pathologies, diagnostics and the degree. Therefore, we aimed to evaluate the ongoing alterations that reflect on the structural characteristics of blood formed elements based on the hormonal imbalance among menopausal women with uterine tumors. Blood samples from the women with benign (n=20), malignant (n=20) uterine tumors, and healthy menopausal women (control, n=20) were used. Enzyme-linked Immunosorbent assay (ELISA) kits were used for the quantitative determination of hormones. The blood formed elements ultrastructure observations were conducted using transmission electron microscope. Compared to control (33.8±0.7 pg/mL), estradiol level was higher in benign (45.7±0.9 pg/mL) and malignant (70.7±3.7 pg/mL) cases (P< 0.001). Similar pattern was noted in testosterone levels [control=0.38±0.03 ng/mL, benign=0.55±0.04 ng/mL (P< 0.01), malignant=1.56±0.14 ng/mL (P< 0.001)] was higher in malignant cases. In contrast, progesterone levels were decreased in the disease cases [control=0.93±0.05 ng/mL, benign=0.44±0.003 ng/mL, malignant=0.31±0.02 ng/ml (P< 0.001)]. Assessments of the morphologic structure of erythrocytes revealed pathological forms of erythrocytes (poikilocytosis) in case of benign, as well as in malignant tumors. particularly target cells (codocytes), hamlet cells, teardrop cells (dacrocytes), sickle cell (drepanocytes) erythrocytes. Using ELISA and transmission electron microscopy our results demonstrate that in case of malignant uterine tumor quantitative/structural changes occur in blood formed elements indicating ongoing alterations in hormonal imbalance. Assessing these changes in structural characteristics would be useful in examining uterine pathologies and subsequent treatment plans

Dose-dependent effect of Scolymus hispanicus L. (sevketibostan) on ethylene glycol-induced kidney stone disease in rats

Kidney stone, also known as calcium oxalate nephrolithiasis, is one of the most common diseases worldwide. Calculi usually forms when urine becomes supersaturated with particular calcium salts such as calcium oxalate. In the present study, we investigated the ameliorative potential of the root extract of the Common golden thistle, Scolymus hispanicus L. (SH) on rats with ethylene glycol (EG) induced kidney stone disease. Sprague-Dawley rats, each weighing 250-300 g, were divided into three groups (n=6 per group): (i) Control (C); (ii) EG; and (iii) EG+SH. To induce nephrolithiasis, the rats received 1% of EG with drinking water, while the C group received normal drinking water during the study. SH extract 2 g/kg was added to the treatment from the 4th week onwards in EG+SH group. At the end of each experiment, rats were decapacitated and serum levels of calcium, magnesium, phosphorus, creatinine, aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP) were assessed in all groups at 0, 4, and 8 weeks. Oxalic acid and creatininelevels were measured in urine samples collected at 24 h in metabolic cages. Renal tissues were evaluated histopathologically at the end of the experiment. After 8 weeks, serum creatinine levels were found decreased in the SH group while increased in the EG group. Serum magnesium and AST levels were also found decreased in the EG group, however, SH treatment reversed these values. The SH treatment also increased urinary oxalic acid levels. When the kidney tissue of EG group was examined, there was a high level of crystal/stone, especially in the renal cortex. In kidney tissues of the SH group, only small amounts of crystal/stone were observed. Our experimental findings have demonstrated the ameliorative potential of the aqueous extracts of S. hispanicus roots and shells on EG-induced in the kidney stones in rats. Isolation of active compounds of SH would be desirable to understand the biochemical mechanism behind the process better.

Hormonal status and distribution of the ABO system phenotypic groups in menopausal and postmenopausal women with breast tumors

Breast cancer is one of the most frequent neoplastic diseases within the female population worldwide. Hormonal imbalance and the ABO system group antigens are among the numerous risk-factors which provoke the development of breast benign and malignant tumors. Here, we have investigated the following sex-steroid hormones: estradiol (E2), progesterone (P), testosterone (T)), non-sex hormones (thyroxin (fT4), thyroid-stimulating hormone (TSH) and prolactin (PRL), and the distribution of the ABO system phenotypic groups in the menopausal and postmenopausal women with breast tumors (benign, malignant). Enzyme-linked immunosorbent assay (ELISA) was used for quantitative determination of hormones. The immune-serological methods were used for investigation of the ABO system phenotypic groups. Our present investigations in menopausal and postmenopausal women with breast tumors have revealed significantly higher expression of sex-steroid hormone estradiol, but decreased progesterone, and also significantly increased testosterone levels. Thyroid gland revealed hypofunction, which confirms the decrease of thyroxin, and increase of prolactin and TSH in the blood. According to our findings, carriers of A(II) phenotypic groups showed high risk for breast tumors development in women during both stages, menopausal and postmenopausal.

Oxidative stress causes plasma protein modification.

We investigated the effect of oxidative systems on plasma proteins using Chloramine-T, a source of free radicals. Plasma specimens from 10 healthy volunteers were treated with 40 mmol/L Chloramine-T (1:1 v/v). Total protein and plasma carbonyl levels were evaluated spectrophotometrically. Identification of plasma proteins modifications was performed by SDS-PAGE, protein and lipid electrophoresis. Protein fragmentation was evaluated by HPLC. Total protein levels of oxidised plasmas were significantly lower (4.08 ± 0.12 g/dL) than control (7.86 ± 0.03 g/dL) (P <0.01). Plasma carbonyl levels were higher (1.94 ± 0.38 nmol/mg protein) in oxidised plasma than that of control (0.03 ± 0.01 nmol/mg protein) (P<0.01). Plasma oxidation had no significant effect on the levels of proteins and lipids. Protein fragmentations were detected in oxidised groups compared to those of the control. We conclude that protein modifications have direct effect on the protein functions, which are related to stress agent, its treatment period(s), and the methodology used for evaluating such experimental results.

Determination of oxidant stress in plasma of rheumatoid arthritis and primary osteoarthritis patients.

Determination of oxidant stress in plasma of rheumatoid arthritis (RA) and primary osteoarthritis (POA) patients is important in understanding the pathogenesis of these diseases. In this study, we examined the relationship between oxidant stress and inflammation by measuring protein carbonyl content, thiol levels and plasma protein fractions as the oxidation markers and erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) tests as inflammation markers. Protein carbonyls content was higher in RA and POA patients, as compared to controls (p<0.0001), while the plasma thiol levels in both groups of patients were significantly lower than controls (p<0.0001). Increased levels of proteins under 40 kDa molecular mass were detected in the RA and POA patients compared to that of controls (p<0.0001) both in HPLC and SDS-PAGE analysis. Total protein concentration in plasma of RA patients was higher than the controls (p<0.001), while in POA patients was lower than that of controls (p<0.001). ESR and CRP levels were higher in both the patient groups than the normal group (p<0.001). These results suggested that alterations in the oxidant stress markers could be the cause of inflammation in these diseases. Thus, while working for RA/POA treatment strategies, consideration of the relationship between oxidant stress and inflammation would be worth evaluating.

Screening and partial immunochemical characterization of sulfite oxidase from plant source.

Sulfite oxidase [SO; EC 1.8.3.1] catalyses the physiologically vital oxidation of sulfite to sulfate, the terminal reaction in degradation of sulfur containing amino acids, cysteine and methionine. Sulfite oxidase from vertebrate sources is among the best studied molybdenum enzymes. Existence of SO in plants has been established recently by identification of a cDNA from Arabidopsis thaliana encoding a functional SO. The present study was undertaken to identify herbaceous and woody plants (viz., Azardirachta indica L., Cassia fistula L., Saraca indica L., Spinacea oleracea L., and Syzyzium cumini L.), a relatively less explored source, having significant SO activity and to characterize some of its immuno-biochemical properties. The Syzyzium cumini was chosen to characterize SO as it showed maximum enzyme activity in the crude extract as compared to other plants. Absorption spectra of SO revealed two peaks at 235 and 277 nm, but no distinct peak in the visible region could be observed. Crude extract of all the plants were taken into considerations for immuno-biochemical studies. Despite of significant protein structure-functional similarities between plant and animal SO, no cross-reactivity could be established between the two sources of SO. These data suggested that plants SO, however, differed with regards to their immuno-biochemical properties.

Purification and characterization of sulfite oxidase from goat liver.

Sulfite oxidase (EC 1.8.3.1) catalyzes the physiologically vital oxidation of sulfite to sulfate, the terminal reaction in the degradation of sulfur containing amino acids. Genetic deficiency related to human sulfite oxidase is associated with the severe clinical abnormalities with no effective therapies known, making the enzyme of immense biomedical importance. In the present study, sulfite oxidase was been purified from the goat tissues, a hitherto unexplored source, in particular from the liver, and its physico and biochemical properties were characterized. The liver was chosen as it showed the highest activity, compared to kidney and muscle. The enzyme was purified to homogeneity by salting out, gel filtration and ion-exchange chromatography. It was a dimer (113 kDa) having two identical subunits (56 kDa) and did not contain free sulfhydryl groups. Its spectral analysis showed the presence of heme and molybdenum. circular dichroism (CD) spectra in near and far-UV regions showed the presence of significant amounts of secondary structures (45% alpha helix, 9% beta structure and 26% beta turn and remaining random coil) in the native molecule. The kinetic and hydrodynamic properties of the enzyme were also determined. Results also showed that ferricyanide was 8-times more effective electron acceptor than its physiological acceptor cytochrome c. The limited N-terminal analysis of the enzyme revealed the sequence up to six amino acids Trp-Glu-Pro-Ser-Gly-Ala. Together, these results suggested the liver was a major source of sulfite oxidase in goat and most of its physico-chemical, except secondary structure and amino acid sequence from N-terminal and biological properties were fairly similar to the sulfite oxidase isolated from other mammalian species/organs.

Purification and some properties of buffalo spleen cathepsin Β.

Purification of cathepsin Β from buffalo-spleen, a hitherto unstudied system has been achieved by a simple procedure developed by incorporating suitable modifications in the existing methods for isolation of the enzyme from other sources. The purified enzyme has a molecular weight of 25 KDa and its Stokes radius was found to be 2·24 nm. Effects of several reducing agents, urea and thiol-protease inhibitors such as leupeptin and antipain, have been studied and the data unequivocally support the contention that the buffaloenzyme is similar to cathepsin Β from other tissues with respect to these properties.