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.

Avaliação da interação entre leveduras isoladas de kombucha e bactérias probióticas / Evaluation of the interaction between isolated kombucha yeasts and probiotic bacteria

Um dos maiores desafios no desenvolvimento de produtos probióticos é entender como os microrganismos interagem entre si e com o hospedeiro. Quando falamos em alimentos fermentados tradicionais, este obstáculo aumenta porque a matriz alimentar já possui um microbioma intrínseco. No entanto, também é conhecido que muitos microrganismos podem interagir e cooperar para sobreviver quando condições de estresse são encontradas. Assim, o objetivo deste trabalho foi isolar leveduras de quatro diferentes kombuchas em distintos momentos fermentativos e verificar a influência que leveduras isoladas de kombucha têm na manutenção da viabilidade da bactéria probiótica Bifidobacterium animalis subsp. lactis HN019 em condições de aerobiose. Meyerozyma guilliermondii, Candida albicans, Rhodotorula mucilaginosa e Pichia membranifaciens foram leveduras encontradas nas kombuchas, das quais as duas últimas favoreceram a manutenção da alta viabilidade de HN019 em cocultura por 14 dias. Observou-se a viabilidade da bactéria acima de 9 log ao longo de todo o experimento, o que não foi observado em monocultura. Ademais, utilizou-se de análise de autoagregação, hidrofobicidade, atividade enzimática de proteases e fosfolipases das leveuras para analisar seu potencial patogênico. Observou-se que R. mucilaginosa demonstrou características semelhantes à Saccharomyces cerevisiae subsp. boulardii, e sua interação benéfica com HN019 reforça a possibilidade de que esta levedura seja uma chave para a inserção da bactéria em uma kombucha probiótica. Análises metabólicas foram realizadas e encontrou-se uma vasta diversidade de dipeptídeos, principalmente os compostos de prolina, durante a cocultura da bactéria com as leveduras. Tais dipeptídeos apresentam importantes mecanismos de ação no controle biológico e quorum sensing de bactérias e leveduras, e supostamente regulam a manutenção das relações mutualísticas entre ambos microrganismo

One of the biggest challenges in the development of probiotic products is to understand how microorganisms interact with each other and with the host. When we talk about traditional fermented foods, this obstacle increases because the food matrix already has an intrinsic microbiome. However, it is also known that many microorganisms can interact and cooperate to survive when stressful situations are encountered. Thus, the objective of this work was to isolate yeasts from four different kombuchas at different fermentation times and to verify the influence that yeasts isolated from kombucha have on maintaining the viability of the probiotic bacterium Bifidobacterium animalis subsp. lactis HN019 under aerobic conditions. Meyerozyma guilliermondii, Candida albicans, Rhodotorula mucilaginosa and Pichia membranifaciens were yeasts found in kombuchas, of which the last two favored the maintenance of HN019 high viability in co-culture for 14 days. Bacteria viability above 9 log was observed throughout the experiment, which was not observed in monoculture. In addition, analysis of autoaggregation, hydrophobicity, enzyme activity of proteases and phospholipases of yeasts was used to analyze their pathogenic potential. It was observed that R. mucilaginosa demonstrated characteristics similar to Saccharomyces cerevisiae subsp. boulardii, and its beneficial interaction with HN019 reinforces the possibility that this yeast is a key to the insertion of the bacterium in a probiotic kombucha. Metabolic analysis were performed and a wide diversity of dipeptides, mainly proline-based, was found during the co-culture of the bacteria with the yeasts. Such dipeptides have important mechanisms of action in the biological control and quorum sensing of bacteria and yeast, and supposedly regulate the maintenance of mutualistic relationships between both microorganism

Systematic screening and structural characterization of dipeptides using offline 2D LC-LTQ-Orbitrap MS:A case study of Cordyceps sinensis / 药物分析学报

Cordyceps sinensis(C.sinensis)is a widely used and highly valuable traditional Chinese medicine.Several dipeptides have been detected in C.sinensis,but current scientific knowledge of its chemical makeup remains limited.In this study,an improved approach that integrates offline two-dimensional liquid chromatography(2D LC)separation,precursor ion list,library screening,and diagnostic ion filtering was established to systematically screen and characterize dipeptides in C.sinensis.Offline 2D LC integrating hydrophilic interaction LC and reverse phase separations was established to eliminate interference and identify the target dipeptides.A library containing the potential 400 dipeptides was created,and a precursor ion list with all theoretical precursor ions was adopted to trigger the MS/MS scan with high sensitivity.To identify dipeptides,the type and connection sequence of amino acids were determined according to the product ions.Ile and Leu residues were differentiated for the first time according to the characteristic ion at m/z 69.07.Ultimately,170 dipeptides were identified or tentatively characterized from C.sinensis,and most are reported for the first time in this species herein.In addition,the identified dipeptides were also applied for discrimination among the three Cordyceps species,and 11 markers were identified.The obtained results provide a deeper understanding of the chemical basis of C.sinensis.

External exposure dose of 177Lu-PSMA-617 to the public in the treatment of prostate cancer / 中华核医学与分子影像杂志

Objective:To estimate the radiation dose (RD) to the public from patients undergoing 177Lu-prostate specific membrane antigen (PSMA)-617 therapy, and provide reference for the formulation of radiation protection measures. Methods:From July 2020 to January 2021, 10 patients with prostate cancer (age (71.1±5.9) years) who received 177Lu-PSMA-617 therapy in the Affiliated Hospital of Southwest Medical University were retrospectively analyzed. According to the different doses of 177Lu-PSMA-617, the patients were divided into the low-dose (5.55-6.29 GBq) group and high-dose (6.70-8.94 GBq) group. Respectively at 5, 30 min and 1, 2, 4, 24, 48, 72, 96, 144 h after intravenous injection of 177Lu-PSMA-617, whole-body initial dose-equivalent rate (DR) was measured with a radiation-survey meter at 0.3, 1.0 and 2.0 m from the patients. The statistics of ROI were analyzed by HERMES, and the corresponding equations were obtained by fitting the curve regression with double exponential function model. On the basis of human social contact model proposed by the National Council on Radiation Protection and Measurements (NCRP), the RD to the public from the patient discharged from the hospital at different times after completing the 177Lu-PSMA-617 injection was estimated. Results:All patients were discharged from the hospital at 72 h after treatment. The initial DR at 0.3, 1.0 and 2.0 m were (12.6±3.3), (4.7±1.2) and (1.6±0.4) μSv/h, respectively, and the RD to the co-sleeping partner, family members and colleagues who were in contact during the day were (999±253), (121±29) and (160±39) μSv, respectively. If the patients were discharged at 48 h after treatment, the RD to the adult family members could be controlled ≤5 mSv, and the RD to colleagues and children could be controlled ≤1 mSv. Starting from the injection of 177Lu-PSMA-617, the restriction duration for co-sleeping partner and colleagues were both 2 d and the restriction duration for children were 2 d (high-dose group) or 1 d (low-dose group). The patients needed to limit the time for public transportation from the 1st to 4th day after treatment, and there was no restriction from the 5th day. Conclusion:According to the current RD restrictions on the public, 177Lu-PSMA-617 is a relatively safe treatment modality for prostate cancer if good safety precautions are taken.

Research progress on chemical constituents and pharmachological activities of Hypericum japonicum / 中草药

The Chinese folk medicinal herb Hypericum japonicum, also known as Tianjihuang or Diercao in Chinese, has been widely used for clearing heat and removing toxin, hemostasis and detumescence, and for the treatment of acute and chronic hepatitis, and gastrointestinal disorders. In recent decades, several main types of chemical constituents such as phloroglucinols, flavonoids, xanthonoids, pyranones, and dipeptides have been reported. Modern pharmacology studies have shown that the extracts or secondary metabolites of the herb possess a variety of bio-activities such as hepatoprotective, antioxidant, anti-tumorous, antiviral, anti-bacterial, and anti-malarial activities as well as effects on cardiovascular diseases. In this paper, we presented the main metabolites and pharmacological activities of the plant in recent 30 years, which should be helpful for the further development and utilization of the herb resources of H. japonicum.

Profiling and identification of aqueous extract of Cordyceps sinensis by ultra-high performance liquid chromatography tandem quadrupole-orbitrap mass spectrometry / 中国天然药物

Characterization of aqueous extract in traditional Chinese medicine (TCM) is challenging due to the poor retention of the analytes on conventional C columns. This study presents a systematic characterization method based on a rapid chromatographic separation (8 min) on a polar-modified C (Waters Cortecs T3) column of aqueous extract of Cordyceps sinensis. UHPLC-HRMS method was used to profile components in both untargeted and targeted manners by full MS/PIL/dd-MS acquisition approach. The components were identified or tentatively identified by reference standards comparison, fragmentation rules elucidation and available databases search. A total of 91 components, including 10 nucleobases, 20 nucleosides, 39 dipeptides, 18 amino acids and derivatives and 4 other components, were characterized from the aqueous extract of C. sinensis. And this was the first time to systematically report the presence of nucleosides and dipeptides in C. sinensis, especially for modified nucleosides. The chemical basis inquiry of this work would be beneficial to mechanism exploration and quality control of C. sinensis and related products. Meanwhile, this work also provided an effective solution for characterization of aqueous extract in TCM.

In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses

OBJECTIVE@#To explore a common B- and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus (HeV) and Nipah virus (NiV).@*METHODS@#Membrane proteins F, G and M of HeV and NiV were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B- and T-cell epitopes that shared maximum identity with HeV and NiV were selected. Stability of the selected epitopes was predicted. Finally, the selected epitopes were subjected to molecular docking simulation with HLA-DR to confirm their antigenic potentiality in silico.@*RESULTS@#One epitope from G proteins, one from M proteins and none from F proteins were selected based on their antigenic potentiality. The epitope from the G proteins was stable whereas that from M was unstable. The M-epitope was made stable by adding flanking dipeptides. The 15-mer G-epitope (VDPLRVQWRNNSVIS) showed at least 66% identity with all NiV and HeV G protein sequences, while the 15-mer M-epitope (GKLEFRRNNAIAFKG) with the dipeptide flanking residues showed 73% identity with all NiV and HeV M protein sequences available in the database. Molecular docking simulation with most frequent MHC class-II (MHC II) and class-I (MHC I) molecules showed that these epitopes could bind within HLA binding grooves to elicit an immune response.@*CONCLUSIONS@#Data in our present study revealed the notion that the epitopes from G and M proteins might be the target for peptide-based subunit vaccine design against HeV and NiV. However, the biochemical analysis is necessary to experimentally validate the interaction of epitopes individually with the MHC molecules through elucidation of immunity induction.

In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses

Objective To explore a common B- and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus (HeV) and Nipah virus (NiV). Methods Membrane proteins F, G and M of HeV and NiV were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B- and T-cell epitopes that shared maximum identity with HeV and NiV were selected. Stability of the selected epitopes was predicted. Finally, the selected epitopes were subjected to molecular docking simulation with HLA-DR to confirm their antigenic potentiality in silico. Results One epitope from G proteins, one from M proteins and none from F proteins were selected based on their antigenic potentiality. The epitope from the G proteins was stable whereas that from M was unstable. The M-epitope was made stable by adding flanking dipeptides. The 15-mer G-epitope (VDPLRVQWRNNSVIS) showed at least 66% identity with all NiV and HeV G protein sequences, while the 15-mer M-epitope (GKLEFRRNNAIAFKG) with the dipeptide flanking residues showed 73% identity with all NiV and HeV M protein sequences available in the database. Molecular docking simulation with most frequent MHC class-II (MHC II) and class-I (MHC I) molecules showed that these epitopes could bind within HLA binding grooves to elicit an immune response. Conclusions Data in our present study revealed the notion that the epitopes from G and M proteins might be the target for peptide-based subunit vaccine design against HeV and NiV. However, the biochemical analysis is necessary to experimentally validate the interaction of epitopes individually with the MHC molecules through elucidation of immunity induction.

Clinical analysis of compound amino acid(15) and dipeptides(2) injection / 药学实践杂志

Objective To investigate the clinical status about the utility of compound amino acid (15) and dipeptides (2) in-jection, and to promote the rational drug use in our hospital .Methods Data from 127 patients who used compound amino acid (15) and dipeptides(2) injection in surgical wards were collected in July 2012.The data about the drug usage method , duration, administra-ted timing, drug combination and the differences in all departments was analyzed .Results Existing problems:62.2% patients used compound amino acid (15) and dipeptides (2) injection by peripheral intravenous infusion , 6.3% patients used more than 14 days and 7.1%patients infused singly.Conclusion Compound amino acid(15) and dipeptides(2) injection had problems of off-label drug use in surgical ward , which need to be improved .

Lipophilic small molecular compounds from human placenta / 国际药学研究杂志

Objective To nvestigate he ipophilic constituents of human placenta. Methods The compounds were separaed and purified by various column chromatography(silica gel,Sephadex LH-20) and heir structures were established by spectroscopic methods and X-ray diffraction analysis. Rusults Twenty-one compounds were solated from human placenta. Their structures were dentified as cyclo(Leu-Ala) (1),cyclo(Leu-Val) (2),cyclo(Leu-Pro) (3),cyclo(Val-Pro) (4),cyclo(Phe-Leu) (5),caffeine(6), uracil(7), thymine (8), 2'-0-methyluridine (9), 2'-deoxyuridine (10), cholesterol (11), 16a-hydroxyprogesterone (12), 16a-hydroxytestosterone(13),estriol(14),20(fi)-hydroxypregn

Expression of Notch3 and Notch intracellular domain in ovarian carcinoma and effect of N-[N-(3,5-difluorophenyl) acetyl-L-alanyl]-S-phenyl glycine t-butyl ester on ovarian carcinoma cell / 中华妇产科杂志

Objective To study the expression and clinical significance of Notch3 and Notch intracellular domain (NICD) in ovarian carcinoma and the effects of N-[N-(3 ,5-difluorophenyl) acetyl-L-alanyl]-S-phenyl glycine t-butyl ester (DAPT), a γ-secretase inhibitor on the proliferation and apoptosis in OVCAR3, A2780 ovarian carcinoma cell lines. Methods Western blot was used to detect the expression of NICD in the tissues from 58 ovarian carcinomas patients and 21 normal ovarie, who were admitted in Peking University First Hospital from July 2006 to June 2009. Immunohistochemistry was also used to detect the expression of Notch3 in these tissues. The relationship with clinical features of ovarian carcinoma was also analyzed. Proliferation of OVCAR3 and A2780 ovarian cancer cells was determined by methyl thiazolyl tetrazolium (MTT) assay, cell cycles and apoptosis and index of proliferation were detected by flow cytometry method. The expression of NICD in OVCAR3 and A2780 cells incubated with DAPT was detected by western blot. Results (1)The expression level of NICD in ovarian carcinomas was significantly higher than that in normal ovarian tissues (1.64 ±0. 19 vs. 0.98 ±0.20;P <0.05). The NICD expression was higher in ovarian cancers with low grade or advanced stage than those in high-middle grade or early stage,respectively (1.90 ± 0. 22 vs. 1.25 ± 0. 21,1.80 ± 0. 21 vs. 1.21 ± 0. 15; all P < 0. 05). The Notch3 protein was stained positively in cytoplasm, nuclear and cell membrane. The expression of Notch3 was higher in ovarian carcinomas than that in normal ovaries [78% (45/58) vs. 24% (5/21); P < 0. 01]. While,there were no stasistical difference in different pathological types, stages, differentiation of ovarian carcinoma. There was no difference between the patients with adjuvant chemotherapy or not. (2)After OVCAR3 and A2780 cells incubated with DAPT 24, 48, 72 hours, NICD expression was significantly lower than that in control group (P < 0. 05). The effects of DAPT inhibited the proliferation and prompted the apoptosis of OVCAR3 and A2780 cells were depended on the concentrations and times. Conclusions Notch3 and NICD may play a key role in the occurrence and progress of ovarian carcinoma. The mechanism of DAPT inhibited the proliferation and prompted the apoptosis of OVCAR3 and A2780 cells may be due to decreased the formation of NICD.

A critical analysis of studies assessing L-ornithine-L-aspartate (LOLA) in hepatic encephalopathy treatment / Uma análise crítica dos estudos de avaliação do L-ornitina-L-aspartato (LOLA) no tratamento da encefalopatia hepática

CONTEXT: Experimental and clinical studies suggest that LOLA may have a favorable influence on hepatic encephalopathy due to the effect on the reduction of ammonia, and improvement of the symptoms and laboratory findings. OBJECTIVES: To evaluate and to critically analyze the efficacy and/or effectiveness results of the use of LOLA when compared to placebo in the treatment of hepatic encephalopathy. DATA SOURCES: LILACS, SciELO, MEDLINE, PubMed database and Cochrane Collaboration Register of Controlled Trials were searched from 1966 to September of 2006. The review has included all the randomized controlled double-blind clinical trials performed in humans in English language. RESULTS: Four studies published between 1993 and 2000 were selected and reviewed. LOLA was showed as being able to reduce hyperammonemia in patients with hepatic encephalopathy, when compared to patients in the placebo group. CONCLUSIONS: Although the trials have shown efficacy of LOLA in reducing hyperammonemia of hepatic encephalopathy, sufficient evidence of a significant beneficial effect of LOLA on patients with hepatic encephalopathy was not found. The studies performed in this area were small, with short follow-up periods and half of them showed low methodological quality.

CONTEXTO: Estudos experimentais e clínicos sugerem que a L-ornitina-L-aspartato pode ter uma influência favorável na encefalopatia hepática em virtude do seu efeito na redução da amônia, e melhora dos sintomas e achados laboratoriais. OBJETIVOS: Avaliar e analisar criticamente os estudos de eficácia e/ou efetividade do uso de L-ornitina-L-aspartato quando comparado com placebo no tratamento da encefalopatia hepática. FONTES DE INFORMAÇÃO: Foram pesquisadas as bases de dados LILACS, SciELO, MEDLINE, PubMed e o Registro de Ensaios Controlados da Colaboração Cochrane no período de 1966 até setembro de 2006. A revisão incluiu todos os ensaios clínicos controlados randomizados, duplo-cego, em seres humanos, no idioma inglês. RESULTADOS: Foram selecionados e revisados quatro estudos publicados entre 1993 e 2000, que mostraram que a L-ornitina-L-aspartato foi capaz de reduzir a hiperamonemia em portadores de encefalopatia hepática, quando comparados ao grupo que utilizou placebo. CONCLUSÕES: Embora os estudos tenham demonstrado eficácia da L-ornitina-L-aspartato em reduzir a hiperamonemia da encefalopatia hepática, não foi encontrada evidência suficiente que a L-ornitina-L-aspartato tenha um efeito clínico benéfico significativo em pacientes com encefalopatia hepática. Os ensaios realizados neste campo foram pequenos com períodos curtos de acompanhamento e a metade deles com baixa qualidade metodológica.

Expression of Notch intracellular domain in cervical cancer and effect of DAPT on cervical cancer cell / 中华妇产科杂志

Objective To study the expression and clinical significance of Notch intracellular domain (NICD) in cervical cancer and the effects of N-[N-(3,5-difluorophenyl)acetyl-L-alanyl]-S-phenyl glycine t-butyl ester (DAPT), a γ-secretase inhibitor on the proliferation and apoptosis of cervical cancer cell lines. Methods Western blot was used to detect the expression of NICD in the tissues of 40 cervical cancers and 21 normal cervix and its relationship with clinical features of cervical cancer was also analyzed. Proliferation of SiHa and HeLa cervical cells was determined by methyl thiazolyl tetrazolium (MTT) assay, cell cycles and apoptosis and index of proliferation were detected by flow cytometry method. The expression of NICD in SiHa and HeLa cells incubated with DAPT was detected by western blot. Results The expression level of NICD in cervical cancers was significantly higher than that of normal cervical tissues (1.237±0.353 vs 0.938±0.105, P<0.05). The NICD expression was higher in cervical cancers with high grade,lymph node involvement and parametrial invasion than that with low-middle grade (1.496±0.540 vs 1.150±0.216), without lymph node involvement (1.419±0.532 vs 1.159±0.210) and no parametrial invasion (1.718±0.710 vs 1.183±0.258), respectively (all P<0.05). The expression of NICD in cervical adenocarcinoma was higher than that of squamous cell cancer (1.463±0.395 vs 1.162±0.187, P<0.05). After SiHa and HeLa cells were incubated with DAPT, NICD expression was significantly lower than that in control (P<0.05). The effects of DAPT inhibited the proliferation and prompted the apoptosis of SiHa and HeLa cells was depended on its concentrations and times. Conclusions NICD may play a key role in the occurrence and progress of cervical cancer. The mechanism of DAPT inhibited the proliferation and prompted the apoptosis of SiHa and HeLa cells may be due to decreased the formation of NICD.