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1.
Immunomodulatory peptides-A promising source for novel functional food production and drug discovery.
Pavlicevic, M, Marmiroli, N, Maestri, E
Peptides. 2022;:170696
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Abstract
Immunomodulatory peptides are a complex class of bioactive peptides that encompasses substances with different mechanisms of action. Immunomodulatory peptides could also be used in vaccines as adjuvants which would be extremely desirable, especially in response to pandemics. Thus, immunomodulatory peptides in food of plant origin could be regarded both as valuable suplements of novel functional food preparation and/or as precursors or possible active ingredients for drugs design for treatment variety of conditions arising from impaired function of immune system. Given variety of mechanisms, different tests are required to assess effects of immunomodulatory peptides. Some of those effects show good correlation with in vivo results but others, less so. Certain plant peptides, such as defensins, show both immunomodulatory and antimicrobial effect, which makes them interesting candidates for preparation of functional food and feed, as well as templates for design of synthetic peptides.
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Motixafortide and Pembrolizumab Combined to Nanoliposomal Irinotecan, Fluorouracil, and Folinic Acid in Metastatic Pancreatic Cancer: The COMBAT/KEYNOTE-202 Trial.
Bockorny, B, Macarulla, T, Semenisty, V, Borazanci, E, Feliu, J, Ponz-Sarvise, M, Abad, DG, Oberstein, P, Alistar, A, Muñoz, A, et al
Clinical cancer research : an official journal of the American Association for Cancer Research. 2021;(18):5020-5027
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is largely unresponsive to checkpoint inhibitors. Blockade of the CXCR4/CXCL12 axis increases intratumoral trafficking of activated T cells while restraining immunosuppressive elements. This study evaluates dual blockade of CXCR4 and PD1 with chemotherapy in PDAC. PATIENTS AND METHODS Multicenter, single-arm, phase II study to evaluate the safety and efficacy of motixafortide and pembrolizumab combined with chemotherapy in patients with de novo metastatic PDAC and disease progression on front-line gemcitabine-based therapy (NCT02826486). Subjects received a priming phase of motixafortide daily on days 1-5, followed by repeated cycles of motixafortide twice a week; pembrolizumab every 3 weeks; and nanoliposomal irinotecan, fluorouracil, and leucovorin every 2 weeks (NAPOLI-1 regimen). The primary objective was objective response rate (ORR). Secondary objectives included overall survival (OS), progression-free survival (PFS), disease control rate (DCR), safety, and tolerability. RESULTS A total of 43 patients were enrolled. The ORR according to RECISTv1.1 was 21.1% with confirmed ORR of 13.2%. The DCR was 63.2% with median duration of clinical benefit of 5.7 months. In the intention-to-treat population, median PFS was 3.8 months and median OS was 6.6 months. The triple combination was safe and well tolerated, with toxicity comparable with the NAPOLI-1 regimen. Notably, the incidence of grade 3 or higher neutropenia and infection was 7%, lower than expected for this chemotherapy regimen. CONCLUSIONS Triple combination of motixafortide, pembrolizumab, and chemotherapy was safe and well tolerated, and showed signs of efficacy in a population with poor prognosis and aggressive disease.
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Ultrafast Fluorescence Spectroscopy via Upconversion and Its Applications in Biophysics.
Cao, S, Li, H, Zhao, Z, Zhang, S, Chen, J, Xu, J, Knutson, JR, Brand, L
Molecules (Basel, Switzerland). 2021;(1)
Abstract
In this review, the experimental set-up and functional characteristics of single-wavelength and broad-band femtosecond upconversion spectrophotofluorometers developed in our laboratory are described. We discuss applications of this technique to biophysical problems, such as ultrafast fluorescence quenching and solvation dynamics of tryptophan, peptides, proteins, reduced nicotinamide adenine dinucleotide (NADH), and nucleic acids. In the tryptophan dynamics field, especially for proteins, two types of solvation dynamics on different time scales have been well explored: ~1 ps for bulk water, and tens of picoseconds for "biological water", a term that combines effects of water and macromolecule dynamics. In addition, some proteins also show quasi-static self-quenching (QSSQ) phenomena. Interestingly, in our more recent work, we also find that similar mixtures of quenching and solvation dynamics occur for the metabolic cofactor NADH. In this review, we add a brief overview of the emerging development of fluorescent RNA aptamers and their potential application to live cell imaging, while noting how ultrafast measurement may speed their optimization.
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Conformational changes of GDNF-derived peptide induced by heparin, heparan sulfate, and sulfated hyaluronic acid - Analysis by circular dichroism spectroscopy and molecular dynamics simulation.
Satish, L, Santra, S, Tsurkan, MV, Werner, C, Jana, M, Sahoo, H
International journal of biological macromolecules. 2021;:2144-2150
Abstract
Glial-cell-line-derived neurotrophic factor (GDNF) is a protein that has therapeutic potential in the treatment of Parkinson's disease and other neurodegenerative diseases. The activity of GDNF is highly dependent on the interaction with sulfated glycans which bind at the N-terminus consisting of 19 residues. Herein, we studied the influence of different glycosaminoglycan (i.e., glycan; GAG) molecules on the conformation of a GDNF-derived peptide (GAG binding motif, sixteen amino acid residues at the N-terminus) using both experimental and theoretical studies. The GAG molecules employed in this study are heparin, heparan sulfate, hyaluronic acid, and sulfated hyaluronic acid. Circular dichroism spectroscopy was employed to detect conformational changes induced by the GAG molecules; molecular dynamics simulation studies were performed to support the experimental results. Our results revealed that the sulfated GAG molecules bind strongly with GDNF peptide and induce alpha-helical structure in the peptide to some extent.
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Cell-Penetrating Peptides: Correlation between Peptide-Lipid Interaction and Penetration Efficiency.
Her Choong, F, Keat Yap, B
Chemphyschem : a European journal of chemical physics and physical chemistry. 2021;(5):493-498
Abstract
Cell-penetrating peptides are used in the delivery of peptides and biologics, with some cell-penetrating peptides found to be more efficient than others. The exact mechanism of how they interact with the cell membrane and penetrate it, however, remains unclear. This study attempts to investigate the difference in free energy profiles of three cell-penetrating peptides (TAT, CPP1 and CPP9) with a model lipid bilayer (DOPC) using molecular dynamics pulling simulations with umbrella sampling. Potential mean force (PMF) and free energy barrier between the peptides and DOPC are determined using WHAM analysis and MM-PBSA analysis, respectively. CPP9 is found to have the smallest PMF value, followed by CPP1 and TAT, consistent with the experimental data. YDEGE peptide, however, does not give the highest PMF value, although it is a non-cell-permeable peptide. YDEGE is also found to form water pores, alongside with TAT and CPP9, suggesting that it is difficult to distinguish true water pore formation from artefacts arising from pulling simulations. On the contrary, free energy analysis of the peptide-DOPC complex at the lipid-water interface with MM-PBSA provides results consistent with experimental data with CPP9 having the least interaction with DOPC and lowest free energy barrier, followed by CPP1, TAT and YDEGE. These findings suggest that peptide-lipid interaction at the lipid-water interface has a direct correlation with the penetration efficiency of peptides across the lipid bilayer.
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Mining the Biomarker Potential of the Urine Peptidome: From Amino Acids Properties to Proteases.
Trindade, F, Barros, AS, Silva, J, Vlahou, A, Falcão-Pires, I, Guedes, S, Vitorino, C, Ferreira, R, Leite-Moreira, A, Amado, F, et al
International journal of molecular sciences. 2021;(11)
Abstract
Native biofluid peptides offer important information about diseases, holding promise as biomarkers. Particularly, the non-invasive nature of urine sampling, and its high peptide concentration, make urine peptidomics a useful strategy to study the pathogenesis of renal conditions. Moreover, the high number of detectable peptides as well as their specificity set the ground for the expansion of urine peptidomics to the identification of surrogate biomarkers for extra-renal diseases. Peptidomics further allows the prediction of proteases (degradomics), frequently dysregulated in disease, providing a complimentary source of information on disease pathogenesis and biomarkers. Then, what does urine peptidomics tell us so far? In this paper, we appraise the value of urine peptidomics in biomarker research through a comprehensive analysis of all datasets available to date. We have mined > 50 papers, addressing > 30 different conditions, comprising > 4700 unique peptides. Bioinformatic tools were used to reanalyze peptide profiles aiming at identifying disease fingerprints, to uncover hidden disease-specific peptides physicochemical properties and to predict the most active proteases associated with their generation. The molecular patterns found in this study may be further validated in the future as disease biomarker not only for kidney diseases but also for extra-renal conditions, as a step forward towards the implementation of a paradigm of predictive, preventive and personalized (3P) medicine.
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Comparative Effects of Etelcalcetide and Maxacalcitol on Serum Calcification Propensity in Secondary Hyperparathyroidism: A Randomized Clinical Trial.
Shoji, T, Nakatani, S, Kabata, D, Mori, K, Shintani, A, Yoshida, H, Takahashi, K, Ota, K, Fujii, H, Ueda, S, et al
Clinical journal of the American Society of Nephrology : CJASN. 2021;(4):599-612
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Abstract
BACKGROUND AND OBJECTIVES Vitamin D receptor activators and calcimimetics (calcium-sensing receptor agonists) are two major options for medical treatment of secondary hyperparathyroidism. A higher serum calcification propensity (a shorter T50 value) is a novel surrogate marker of calcification stress and mortality in patients with CKD. We tested a hypothesis that a calcimimetic agent etelcalcetide is more effective in increasing T50 value than a vitamin D receptor activator maxacalcitol. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A randomized, multicenter, open-label, blinded end point trial with active control was conducted in patients with secondary hyperparathyroidism undergoing hemodialysis in Japan. Patients were randomly assigned to receive intravenous etelcalcetide 5 mg thrice weekly (etelcalcetide group) or intravenous maxacalcitol 5 or 10 µg thrice weekly (maxacalcitol group). The primary, secondary, and tertiary outcomes were changes in T50 value, handgrip strength, and score of the Dementia Assessment Sheet for Community-Based Integrated Care System from baseline to 12 months, respectively. RESULTS In total, 425 patients from 23 dialysis centers were screened for eligibility, 326 patients were randomized (etelcalcetide, n=167; control, n=159), and 321 were included in the intention-to-treat analysis (median age, 66 years; 113 women [35%]). The median (interquartile range) of T50 value was changed from 116 minutes (interquartile range, 90-151) to 131 minutes (interquartile range, 102-176) in the maxacalcitol group, whereas it was changed from 123 minutes (interquartile range, 98-174) to 166 minutes (interquartile range, 127-218) in the etelcalcetide group. The increase in T50 value was significantly greater in the etelcalcetide group (difference in change, 20 minutes; 95% confidence interval, 7 to 34 minutes; P=0.004). No significant between-group difference was found in the change in handgrip strength or in the Dementia Assessment Sheet for Community-Based Integrated Care System score. CONCLUSIONS Etelcalcetide was more effective in increasing T50 value than maxacalcitol among patients on hemodialysis with secondary hyperparathyroidism. There was no difference in handgrip strength or cognition between the two drugs. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER VICTORY; UMIN000030636 and jRCTs051180156.
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Probiotics-Derived Peptides and Their Immunomodulatory Molecules Can Play a Preventive Role Against Viral Diseases Including COVID-19.
Manna, S, Chowdhury, T, Chakraborty, R, Mandal, SM
Probiotics and antimicrobial proteins. 2021;(3):611-623
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Abstract
As of recent, the pandemic episode of COVID-19, a severe acute respiratory syndrome brought about by a novel coronavirus (SARS-CoV-2) expanding the pace of mortality, has affected the disease rate profoundly. Invulnerability is the fundamental choice to prevent the ruining event of COVID-19, as the drugs and antibodies are in the phase of preliminary clinical trials. Within this brief period, a few strains of SARS-CoV-2 have been recognized by the vaccine manufacturers, which could be an incorrect guess about the strain that will end up spreading. Since the circulating SARS-CoV-2 strains continue to mutate, immunizations, if at all works, might be for a restricted time. We have not put sufficient time in research to understand the immune responses that correlate with protection as this could help refine vaccines. Here, we have summed up the adequacy of the immunomodulatory component of probiotics for the prevention against viral infections. Furthermore, an in silico data have been provided in support of the "probiotics-derived lipopeptides" role in inactivating spike (S) glycoprotein of SARS-CoV-2 and its host receptor molecule, ACE2. Among well characterized lipopeptides derived from different probiotic strains, subtilisin (Bacillus amyloliquefaciens), curvacin A (Lactobacillus curvatus), sakacin P (Lactobacillus sakei), lactococcin Gb (Lactococcus lactis) was utilized in this study to demonstrate a higher binding proclivity to S-protein of SARS-CoV-2 and human ACE2. The outcome revealed noteworthy capabilities of the lipopeptides, due to their amphiphilic nature, to bind spike protein and receptor molecule, which may act to competitively inhibit the mandatory interaction of SARS-CoV-2 with the host epithelial cell expressing ACE2 for its entry into the cell for reproduction. In the current situation, probiotic treatment alongside chemotherapy may assist in bringing about substantial improvement of the health of COVID-19 patients. At the same time, probiotics may aid towards building up the immune defenses in people to evade COVID-19.
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Extension of the CAVS model to the simulation of helical peptides in a membrane environment.
Shen, H, Wu, Z, Lu, C
Physical chemistry chemical physics : PCCP. 2021;(22):12850-12863
Abstract
Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.
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Investigation of characteristics as endodontic sealer of novel experimental elastin-like polypeptide-based mineral trioxide aggregate.
Kim, HJ, Jang, JH, Kim, SY
Scientific reports. 2021;(1):10537
Abstract
Although mineral trioxide aggregates (MTA) have been adopted as an endodontic sealer because of excellent sealing effect and bioactive property and been modified with improvement of its characteristics, the developed MTA sealers have not yet satisfied all the ideal requirements of endodontic sealers. The aim of this study was to assess the characteristics of elastin-like polypeptide (ELP)-incorporated MTA for use as an endodontic sealer and compare them with those of commercial MTA sealers. Two commercial MTA sealers and three experimental ELP-incorporated MTA sealers with 0.3, 0.4, and 0.5 liquid/powder (L/P) ratio for 10 wt% ELP liquid were evaluated. The push-out bond strength, flow rate, sealer penetrability and wash-out resistance were tested and the sealer-dentin interface was observed using a scanning electron microscope (SEM). Our study revealed the ELP-incorporated MTA sealer, especially in 0.4 L/P ratio, exhibited the higher push-out bond strength and flow rate (P < 0.05), and equal or superior sealer penetration and remarkable wash-out resistance compared to commercial MTA sealers. The groups of ELP-based experimental sealers also exhibited more intimate contact with dentin compared to the commercial MTA sealers. Our research will suggest the possible adoption of the ELP-incorporated MTA as endodontic sealer for clinical use.