20,400 results on '"Peptides, Cyclic"'
Search Results
52. A Randomized Trial Evaluating Patient Experience and Preference Between Octreotide Long-Acting Release and Lanreotide for Treatment of Well-Differentiated Neuroendocrine Tumors
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Nitya Raj, Elizabeth Cruz, Sarah O'Shaughnessy, Claudia Calderon, Joanne F. Chou, Marinela Capanu, Olivia Heffernan, April DeMore, Sippy Punn, Tiffany Le, Haley Hauser, Leonard Saltz, and Diane Reidy-Lagunes
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Patient Outcome Assessment ,Neuroendocrine Tumors ,Oncology ,Oncology (nursing) ,Health Policy ,Humans ,Pain ,Octreotide ,Somatostatin ,Peptides, Cyclic - Abstract
PURPOSE: Somatostatin analogs octreotide long-acting release (octLAR) and lanreotide are equally acceptable in National Comprehensive Cancer Network guidelines for neuroendocrine tumors (NETs). Lanreotide is more expensive and given by deep subcutaneous injection, whereas octLAR is given intramuscularly. We evaluated patient preference between these agents in terms of injection site pain. MATERIALS AND METHODS: Randomized, single-blinded study. Patients with NETs received injections every 4 weeks. Arm 1: octLAR × 3, then lanreotide × 3; arm 2: reverse order. Self-reported injection site pain scores (range, 0-10) were obtained after each of the first three injections. Primary end point was comparison of mean pain scores over the first three injections. Secondary end points included patient-reported preference. RESULTS: Fifty-one patients enrolled (26 in arm 1 and 25 arm 2), all evaluable for primary end point. No significant difference was identified in the mean pain score over the first three injections (2.4 ± 1.9 v 1.9 ± 1.5, P = .5). Thirty-four of 51 (67%) patients (15 in arm 1 and 19 in arm 2) completed post-therapy questionnaires and were evaluable for secondary end points. Seven patients (47%) in arm 1 and eight patients (42%) in arm 2 indicated no drug preference at the end of treatment. In the other 19 patients, more patients indicated mild or strong preference for octLAR over lanreotide. CONCLUSION: We found minimal pain with octLAR and lanreotide and no significant pain score differences between the two. Patients indicating a drug preference trended toward favoring octLAR.
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- 2023
53. Optimized Coordination of Uranyl in Engineered Calmodulin Site 1 Provides a Subnanomolar Affinity for Uranyl and a Strong Uranyl versus Calcium Selectivity
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Romain Pardoux, Sandrine Sauge-Merle, Nicolas Bremond, Maria Rosa Beccia, David Lemaire, Christine Battesti, Pascale Delangle, Pier Lorenzo Solari, Philippe Guilbaud, Catherine Berthomieu, Interactions Protéine Métal (IPM), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Département Interfaces pour l'énergie, la Santé et l'Environnement (DIESE), Synchrotron SOLEIL (SOLEIL), Département de recherche sur les procédés pour la mine et le recyclage du combustible (DMRC), and CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN))
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Inorganic Chemistry ,Calmodulin ,Carboxylic Acids ,Uranium ,Calcium ,[CHIM.COOR]Chemical Sciences/Coordination chemistry ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain ,Physical and Theoretical Chemistry ,Ligands ,Peptides, Cyclic - Abstract
As an alpha emitter and chemical toxicant, uranium toxicity in living organisms is driven by its molecular interactions. It is therefore essential to identify main determinants of uranium affinity for proteins. Others and we showed that introducing a phosphoryl group in the coordination sphere of uranyl confers a strong affinity of proteins for uranyl. In this work, using calmodulin site 1 as a template, we modulate the structural organization of a metal-binding loop comprising carboxylate and/or carbonyl ligands and reach affinities for uranyl comparable to that provided by introducing a strong phosphoryl ligand. Shortening the metal binding loop of calmodulin site 1 from 12 to 10 amino acids in CaMΔ increases the uranyl-binding affinity by about 2 orders of magnitude to log
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- 2022
54. Flaxseed Cyclic Peptide [1-9-NαC]-Linusorb B3 (CLA) Improves Oxidative Stability of Flaxseed Oil by Chelating Metal Ions and Intermediate Oxidative Products
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Shilu Deng, Jing Li, Ting Luo, and Zeyuan Deng
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Molecular Docking Simulation ,Oxidative Stress ,Linseed Oil ,Flax ,General Chemistry ,General Agricultural and Biological Sciences ,Peptides, Cyclic ,Antioxidants - Abstract
Oxidative rancidity is a major issue limiting the utilization of flaxseed oil (FSO). Peptides possess an antioxidant effect; however, the flax cyclic peptide, a unique ingredient in FSO, has an obscure influence on the oxidation of FSO. Therefore, this study is aimed to investigate the effects of [1-9-NαC]-linusorb B3 (CLA) on the accelerated oxidation of FSO and the underlying mechanism. We found that CLA increased the antioxidant stability of refined flaxseed oil (RFO), indicated by the improved parameters involved in the oxidation after the addition of CLA. After accelerated oxidation, the acid value (AV) of the RFO was increased by 24.14 times, whereas that of the RFO with CLA (CLA-RFO) increased only by 7.21 times. Similarly, the peroxide value (POV) and
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- 2022
55. Recombineering using RecET-like recombinases from Xenorhabdus and its application in mining of natural products
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Xiyin Huang, Yawei Sun, Siqin Liu, Yaoguang Li, Chen Li, Yunjun Sun, Xuezhi Ding, Liqiu Xia, Yibo Hu, and Shengbiao Hu
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Recombinases ,Biological Products ,Operon ,General Medicine ,Peptides, Cyclic ,Applied Microbiology and Biotechnology ,Xenorhabdus ,Biotechnology - Abstract
Xenorhabdus can produce a large number of secondary metabolites with insecticidal, bacteriostatic, and antitumor activities. Efficient gene editing tools will undoubtedly facilitate the functional genomics research and bioprospecting in Xenorhabdus. In this study, BlastP analysis using the amino acid sequences of Redαβ or RecET recombinases as queries resulted in the identification of an operon (XBJ1_operon 0213) containing RecET-like recombinases encoding genes from the genome of Xenorhabdus bovienii strain SS-2004. Three proteins encoded by this operon was indispensable for full activity of recombineering, namely XBJ1-1173 (RecE-like protein), XBJ1-1172 (RecT-like protein), and XBJ1-1171 (single-strand annealing protein). Using this newly developed recombineering system, a gene cluster responsible for biosynthesis of a novel secondary metabolite (Min16) was identified from X. stockiae HN_xs01 strain. Min16 which exhibited antibacterial and cytotoxic activities was determined to be a cyclopeptide composed of Acyl-Phe-Thr-Phe-Pro-Pro-Leu-Val by using high-resolution mass spectrometry and nuclear magnetic resonance analysis, and was designated as changshamycin. This host-specific recombineering system was proven to be effective for gene editing in Xenorhabdus, allowing for efficient discovery of novel natural products with attractive bioactivities. KEY POINTS: • Screening and identification of efficient gene editing tools from Xenorhabdus • Optimization of the Xenorhabdus electroporation parameters • Discovery of a novel cyclopeptide compound with multiple biological activities.
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- 2022
56. Lanreotide as maintenance therapy after first-line treatment in patients with non-resectable duodeno-pancreatic neuroendocrine tumours: An international double-blind, placebo-controlled randomised phase II trial – Prodige 31 REMINET: An FFCD study
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Côme Lepage, Jean-Marc Phelip, Astrid Lievre, Karine Le-Malicot, Laetitia Dahan, David Tougeron, Christos Toumpanakis, Frédéric Di-Fiore, Catherine Lombard-Bohas, Ivan Borbath, Romain Coriat, Thierry Lecomte, Rosine Guimbaud, Caroline Petorin, Jean-Louis Legoux, Pierre Michel, Jean-Yves Scoazec, Denis Smith, Thomas Walter, Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Oncogenesis, Stress, Signaling (OSS), Université de Rennes (UR)-CRLCC Eugène Marquis (CRLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pontchaillou [Rennes], Hôpital de la Timone [CHU - APHM] (TIMONE), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Royal Free Hospital [London, UK], Communications Cellulaires et Différenciation (CCD), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Hospices Civils de Lyon (HCL), Cliniques Universitaires Saint-Luc [Bruxelles], AP-HP - Hôpital Cochin Broca Hôtel Dieu [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Institut Gustave Roussy (IGR), Département de biologie et pathologie médicales [Gustave Roussy], Hôpital Haut-Lévêque [CHU Bordeaux], CHU Bordeaux [Bordeaux], Amgen, Bristol-Myers Squibb, BMS, Bayer, Merck, Novartis, Roche, Celgene, Sandoz, Advanced Accelerator Applications, AAA, Agence Nationale de la Recherche, ANR: ANR-11-LABX-0021, Ligue Contre le Cancer, Servier, Ipsen, and ANR-11-LABX-0021,Lipstic,Lipoprotéines et santé : prévention et traitement des maladies inflammatoires non vasculaires et du cancer(2011)
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Pancreatic Neoplasms ,Clinical trial ,Neuroendocrine Tumors ,Cancer Research ,Neuroendocrine tumours ,Oncology ,Duodeno-pancreatic ,Maintenance ,Non-resectable ,Humans ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,Somatostatin ,Peptides, Cyclic - Abstract
International audience; Background: Following European guidelines, patients with aggressive metastatic or locally advanced, non-resectable, duodeno-pancreatic (DP) neuroendocrine tumours (NETs) should receive systemic combination chemotherapy until progression. Aggressive disease is defined as progressive and/or symptomatic metastases with or without significant hepatic invasion (>30–50%), and/or bone metastases. Methods: This academic randomised, double-blind, placebo-controlled phase II study aims to evaluate lanreotide autogel 120 mg (LAN) as maintenance treatment after at least 2 months of first-line treatment (L1) in aggressive G1-G2 DP-NET. Patients were randomly assigned in a 1:1 ratio to receive LAN or placebo (PBO), every 28 days, until progression or toxicity. The primary end-point was progression-free survival (PFS) at 6 months. Results: Among the 118 planned patients, 53 were included. Of these, 81.1% had a G2 tumour, and 90.6% had metastatic disease. L1 therapy consisted of chemotherapy (96.8%). Median duration of L1 was 4.6 months (range: 2.0–7.7). At the time of randomisation, 81.1% of patients had stable disease. Median follow-up was 27.0 months (95% CI: 19.5; 31.2). PFS at 6 months was 73.1% (90% CI: 55.3; 86.6) in LAN versus 54.2% (90% CI: 35.8; 71.8) in PBO. Median PFS was 19.4 months (95% CI: 7.6; 32.6) and 7.6 months (95% CI: 3.0; 9.0), respectively. Median overall survival was 41.9 months in PBO and was not reached in LAN. The toxicity profile was mainly grade 1–2 expected toxicities. Conclusions: The encouraging results of lanreotide autogel 120 mg as a maintenance treatment after L1 in aggressive G1/2 DP-NET should be confirmed. Trial registration: NCT02288377 (clinicaltrials.gov). © 2022 The Authors
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- 2022
57. OFP011 Cyclic Peptide as a Multifunctional Agonist for Opioid/Neuropeptide FF Receptors with Improved Blood–Brain Barrier Penetration
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Mengna Zhang, Biao Xu, Ning Li, Run Zhang, Qinqin Zhang, Dan Chen, Syed Faheem Askari Rizvi, Kangtai Xu, Yonghang Shi, Bowen Yu, and Quan Fang
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Analgesics, Opioid ,Receptors, Neuropeptide ,Mice ,Blood-Brain Barrier ,Physiology ,Cognitive Neuroscience ,Receptors, Opioid, mu ,Animals ,Pain ,Cell Biology ,General Medicine ,Peptides, Cyclic ,Biochemistry - Abstract
Mounting evidence indicates that the neuropeptide FF (NPFF) system is involved in the side effects of opioid usage, including antinociceptive tolerance, hyperalgesia, abuse, constipation, and respiratory depression. Our group recently discovered that the multitarget opioid/NPFF receptor agonist DN-9 exhibits peripheral antinociceptive activity. To improve its metabolic stability, antinociceptive potency, and duration, in this study, we designed and synthesized a novel cyclic disulfide analogue of DN-9, OFP011, and examined its bioactivity through
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- 2022
58. A comprehensive review of microorganism‐derived cyclic peptides: Bioactive functions and food safety applications
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Jiaqi Luo, Siyu Liu, Hongyun Lu, Qihe Chen, and Ying Shi
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Meat ,Food Safety ,Food Handling ,Peptides, Cyclic ,Food Science - Abstract
Cyclic peptides possess advanced structural characteristics of stability and play a vital role in medical treatment and agriculture. However, the biological functions of microorganism-derived cyclic peptides (MDCPs) and their applications in food industry were relatively absent. MDCPs are derived from extensive fermented food or soil. In this review, the synthesis approaches and structural characteristics are overviewed, while the interrelationship between bioactivities and functions is emphasized. This review summarizes the bioactivities of MDCPs from in vitro to in vivo, including antimicrobial activities, immune regulation, and antiviral cell activation. Their multiple functions as well as applications during food product processing, packaging, and storage are also comprehensively reviewed. Remarkably, some potential risks and cytotoxicity of MDCPs are also critically discussed. Moreover, future applications of MDCPs in the development of novel food additives and bioengineering materials are organized. Based on this review of native MDCPs, it is noteworthy that expected improvements of synthetic cyclic peptides in bioactive properties present potential valuable applications in future food, including artificial meat.
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- 2022
59. Do Stereochemical Effects Overcome a Charge-Induced Perturbation in Isolated Protonated Cyclo(Tyr-Tyr)?
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Koki Yoshizawa, Keisuke Hirata, Shun-Ichi Ishiuchi, Masaaki Fujii, and Anne Zehnacker
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Diketopiperazines ,Dipeptides ,Physical and Theoretical Chemistry ,Amides ,Peptides, Cyclic - Abstract
Two diastereomers of the protonated diketopiperazine (DKP) dipeptide cyclo(Tyr-Tyr), namely, cyclo(LTyr-LTyr)H
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- 2022
60. Cortistatin-14 Exerts Neuroprotective Effect Against Microglial Activation, Blood-brain Barrier Disruption, and Cognitive Impairment in Sepsis-associated Encephalopathy
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Qiang Wen, Qian Ding, Jinchao Wang, Yanhua Yin, Shangchen Xu, Yuanrong Ju, Hongsheng Ji, and Bin Liu
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Article Subject ,Interleukin-6 ,Tumor Necrosis Factor-alpha ,Interleukin-1beta ,Neuropeptides ,Immunology ,General Medicine ,Peptides, Cyclic ,Disease Models, Animal ,Interferon-gamma ,Mice ,Neuroprotective Agents ,Blood-Brain Barrier ,Sepsis ,Sepsis-Associated Encephalopathy ,Animals ,Cytokines ,Immunology and Allergy ,Cognitive Dysfunction ,Microglia ,Evans Blue - Abstract
Sepsis-associated encephalopathy (SAE) is a life-threatening deterioration of mental status in relation to long-term and disabling cognitive dysfunction that is common in intensive care units worldwide. Cortistatin-14 is a neuropeptide structurally resembling somastostatin, which has been proven to play a crucial role in sepsis. The present study aimed to explore the neuroprotective role of cortistatin-14 in sepsis-associated encephalopathy and its underlying mechanisms in a mouse model. A septic mice model was established using the cecal ligation and puncture (CLP) method. The novel object recognition test (NORT), open field test (OFT), elevated plus maze test (EPMT), and tail suspension test (TST) were used to explore the behavioral performance of the mice. Transmission electron microscopy was used to observe the microstructure of the blood-brain barrier (BBB). Evans Blue staining was used to examine the integrity of the BBB. Immunofluorescence was used to examine the morphology and infiltration of microglia. A multiplex cytokine bead array assay was used to determine cytokine and chemokine levels in mouse serum and brain tissues. NORT revealed that cortistatin treatment improved cognitive impairment in septic mice. OFT, EPMT, and TST indicated that cortistatin-14 relieved the anxiety-related behaviors of CLP mice. In addition, cortistatin-14 treatment decreased the levels of various inflammatory cytokines, including interleukin-1β, interleukin-6, interferon-γ, and tumor necrosis factor-α in both the serum and brain of septic mice. Cortistatin reduced sepsis-induced blood-brain barrier disruption and inhibited microglial activation after the onset of sepsis. Cortistatin exerts neuroprotective effects against SAE and cognitive dysfunction in a CLP-induced mouse model of sepsis.
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- 2022
61. Discovery of Cyclic Peptide Inhibitors Targeting PD-L1 for Cancer Immunotherapy
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John Fetse, Zhen Zhao, Hao Liu, Umar-Farouk Mamani, Bahaa Mustafa, Pratik Adhikary, Mohammed Ibrahim, Yanli Liu, Pratikkumar Patel, Maryam Nakhjiri, Mohammed Alahmari, Guangfu Li, and Kun Cheng
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Neoplasms ,Programmed Cell Death 1 Receptor ,Drug Discovery ,Humans ,Molecular Medicine ,Immunotherapy ,Ligands ,Peptides ,Immune Checkpoint Inhibitors ,Peptides, Cyclic ,B7-H1 Antigen - Abstract
Blockade of the interaction between programmed cell death ligand-1 (PD-L1) and its receptor PD-1 has shown great success in cancer immunotherapy. Peptides possess unique characteristics that give them significant advantages as immune checkpoint inhibitors. However, unfavorable physicochemical properties and proteolytic stability profiles limit the translation of bioactive peptides as therapeutic agents. Studies have revealed that cyclization improves the biological activity and stability of linear peptides. In this study, we report the use of macrocyclization scanning for the discovery of cyclic anti-PD-L1 peptides with improved bioactivity. The cyclic peptides demonstrated up to a 34-fold improvement in the PD-1/PD-L1 blocking activity and significant in vivo anti-tumor activity. Our results demonstrate that macrocyclization scanning is an effective way to improve the serum stability and bioactivity of the anti-PD-L1 linear peptide. This strategy can be employed in the optimization of other bioactive peptides, particularly those for protein-protein interaction modulation.
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- 2022
62. Pegcetacoplan versus eculizumab in patients with paroxysmal nocturnal haemoglobinuria (PEGASUS): 48-week follow-up of a randomised, open-label, phase 3, active-comparator, controlled trial
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Régis Peffault de Latour, Jeff Szer, Ilene C Weitz, Alexander Röth, Britta Höchsmann, Jens Panse, Kensuke Usuki, Morag Griffin, Jean-Jacques Kiladjian, Carlos M de Castro, Hisakazu Nishimori, Temitayo Ajayi, Mohammed Al-Adhami, Pascal Deschatelets, Cedric Francois, Federico Grossi, Antonio M Risitano, Peter Hillmen, de Latour, Régis Peffault, Szer, Jeff, Weitz, Ilene C, Röth, Alexander, Höchsmann, Britta, Panse, Jen, Usuki, Kensuke, Griffin, Morag, Kiladjian, Jean-Jacque, de Castro, Carlos M, Nishimori, Hisakazu, Ajayi, Temitayo, Al-Adhami, Mohammed, Deschatelets, Pascal, Francois, Cedric, Grossi, Federico, Risitano, Antonio M, and Hillmen, Peter
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Adult ,Male ,Medizin ,Hemoglobinuria, Paroxysmal ,Hematology ,Antibodies, Monoclonal, Humanized ,Hemolysis ,Peptides, Cyclic ,Complement Inactivating Agents ,Treatment Outcome ,Quality of Life ,Humans ,Immunologic Factors ,Female ,Fatigue ,Follow-Up Studies - Abstract
Background: In the PEGASUS trial, the complement C3 inhibitor, pegcetacoplan, showed superiority to eculizumab in improving haematological outcomes in adult patients with paroxysmal nocturnal haemoglobinuria and suboptimal response to eculizumab at 16 weeks. The aim of the open-label period was to evaluate the long-term efficacy and safety of pegcetacoplan through to 48 weeks. Methods: PEGASUS was a phase 3, randomised, open-label, active-comparator controlled trial conducted in 44 centres in Australia, Belgium, Canada, France, Germany, Japan, Russia, South Korea, Spain, the UK, and the USA. Eligible participants were aged 18 years or older, had paroxysmal nocturnal haemoglobinuria, and had a haemoglobin concentration of less than 10·50 g/dL after 3 months or longer of stable eculizumab treatment. After a 4-week run-in with eculizumab plus pegcetacoplan, patients were randomly assigned (1:1) by interactive response technology to pegcetacoplan (1080 mg subcutaneously twice weekly) or eculizumab (according to their regimen at enrolment) for 16 weeks and could continue to the open-label period (32 weeks of pegcetacoplan monotherapy [pegcetacoplan-to-pegcetacoplan] or 28 weeks of pegcetacoplan monotherapy [eculizumab-to-pegcetacoplan]). Randomisation was stratified by platelet count and number of previous blood transfusions. The primary endpoint was change from baseline in haemoglobin at week 16, which has previously been reported. The outcomes of the open-label period (week 16 to week 48) are reported here. At 48 weeks, efficacy (including mean haemoglobin concentration and quality of life measured on the Functional Assessment of Chronic Illness Therapy [FACIT]-Fatigue scale) was assessed in the intention-to-treat population and safety was assessed per protocol. This trial was registered with ClinicalTrials.gov, NCT03500549, and has been completed. Findings: Between June 14, 2018, and Nov 14, 2019, 80 patients were randomly assigned to receive treatment with pegcetacoplan (41 patients) or eculizumab (39 patients). Most participants were women (49 [61%]) and 31 (39%) were men; 12 (15%) were Asian, two (3%) were Black, 49 (61%) were White, and 17 (21%) were another race or did not report their race. The open-label period had 77 participants (38 pegcetacoplan-to-pegcetacoplan, 39 eculizumab-to-pegcetacoplan). Patients in the pegcetacoplan-to-pegcetacoplan group maintained high mean haemoglobin concentrations between 16 weeks (11·54 g/dL [SD 1·96]) and 48 weeks (11·30 g/dL [1·77]; p=0·14). Patients in the eculizumab-to-pegcetacoplan group had significantly greater mean haemoglobin concentrations at 48 weeks (11·57 g/dL [2·21]) versus 16 weeks (8·58 g/dL [0·96]; p
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- 2022
63. Applying Promiscuous RiPP Enzymes to Peptide Backbone
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Snigdha, Sarkar, Wenjia, Gu, and Eric W, Schmidt
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Peptides ,Methylation ,Peptides, Cyclic ,Protein Processing, Post-Translational ,Biosynthetic Pathways ,Peptide Hydrolases - Abstract
The methylation of peptide backbone amides is a hallmark of bioactive natural products, and it also greatly modifies the pharmacology of synthetic peptides. Usually, bioactive
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- 2023
64. Optimizing Epitope Conformational Ensembles Using α-Synuclein Cyclic Peptide 'Glycindel' Scaffolds: A Customized Immunogen Method for Generating Oligomer-Selective Antibodies for Parkinson's Disease
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Xubiao Peng, Shawn Ching-Chung Hsueh, Steven S. Plotkin, Adekunle Aina, and Neil R. Cashman
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chemistry.chemical_classification ,Alpha-synuclein ,Physiology ,Protein Conformation ,Cognitive Neuroscience ,In silico ,Parkinson Disease ,Cell Biology ,General Medicine ,Computational biology ,Fibril ,Biochemistry ,Oligomer ,Peptides, Cyclic ,Cyclic peptide ,Epitope ,Antibodies ,chemistry.chemical_compound ,Epitopes ,chemistry ,Human proteome project ,Solvents ,alpha-Synuclein ,Humans ,Conformational ensembles - Abstract
Effectively presenting epitopes on immunogens, in order to raise conformationally selective antibodies through active immunization, is a central problem in treating protein misfolding diseases, particularly neurodegenerative diseases such as Alzheimer’s disease or Parkinson’s disease. We seek to selectively target conformations enriched in toxic, oligomeric propagating species while sparing the healthy forms of the protein that are often more abundant. To this end, we computationally modelled scaffolded epitopes in cyclic peptides by inserting/deleting a variable number of flanking glycines (“glycindels”), to best mimic a misfolding-specific conformation of an epitope of α-synuclein enriched in the oligomer ensemble, as characterized by a region most readily disordered and solvent-exposed in a stressed, partially denatured protofibril. We screen and rank the cyclic peptide scaffolds of α-synuclein in silico based on their ensemble overlap properties with the fibril, oligomer-model, and isolated monomer ensembles. We present experimental data of seeded aggregation that supports nucleation rates consistent with computationally predicted cyclic peptide conformational similarity. We also introduce a method for screening against structured off-pathway targets in the human proteome, by selecting scaffolds with minimal conformational similarity between their epitope and the same solvent-exposed primary sequence in structured human proteins. Different cyclic peptide scaffolds with variable numbers of glycines are predicted computationally to have markedly different conformational ensembles. Ensemble comparison and overlap was quantified by the Jensen-Shannon Divergence, and a new measure introduced here—the embedding depth, which determines the extent to which a given ensemble is subsumed by another ensemble, and which may be a more useful measure in developing immunogens that confer conformational-selectivity to an antibody.Graphical TOC Entry
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- 2023
65. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides
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Karolina Di Remigio Eikås, Maarten T. P. Beerepoot, and Kenneth Ruud
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Circular Dichroism ,Molecular Conformation ,Humans ,Stereoisomerism ,Physical and Theoretical Chemistry ,Oligopeptides ,Peptides, Cyclic ,Anti-Bacterial Agents - Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169−7192 and J. Chem. Theory. Comput. 2019, 15, 2847–2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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- 2022
66. The lipopeptides fengycin and iturin are involved in the anticandidal activity of endophytic Bacillus sp. as determined by experimental and in silico analysis
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S. Banerjee, S. Sen, A. Bhakat, A. Bhowmick, and K. Sarkar
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Molecular Docking Simulation ,Lipopeptides ,Candida albicans ,Bacillus ,Glucan 1,3-beta-Glucosidase ,Peptides, Cyclic ,Applied Microbiology and Biotechnology - Abstract
In this study, an endophytic Bacillus sp. strain (K7) was isolated from the medicinally important ornamental plant, Jasminum officinale. Biochemical analyses were conducted to evaluate the nature of the extracted product, which displayed strong anticandidal activity against Candida albicans (CA) SC5314, as evident from the results obtained in agar-cup diffusion tests, phase-contrast microscopy, scanning electron microscopy and minimum inhibitory concentration assays. After confirming the presence of the gene clusters encoding the lipopeptides iturins and fengycin in the genome of K7, their corresponding molecular ions were identified using MALDI-TOF-MS. 3D structures of the lipopeptides were downloaded from specific databases and molecular docking was performed against a vital CA enzyme, exo-1,3-beta-glucanase, involved in cell wall remodelling, adhesion to polymer materials and biofilm formation. The docking score of iturins was found to be −8·6 and −8·2 kcal mol−1 and for fengycin it was −9·4 kcal mol−1, indicating a strong affinity of these cyclic lipopeptides towards exo-1,3-beta-glucanase. The combined in vitro and in silico anticandidal studies suggested that these secreted lipopeptides from Bacillus sp. may be used as potential therapeutics against opportunistic and complicated infections of CA.
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- 2022
67. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases
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R.H.P. van Neer, P. K. Dranchak, L. Liu, M. Aitha, B. Queme, H. Kimura, T. Katoh, K. P. Battaile, S. Lovell, J. Inglese, and H. Suga
- Subjects
RNA, Transfer ,Peptide Library ,Molecular Medicine ,General Medicine ,Amino Acids ,Peptide Elongation Factor Tu ,Peptides ,Intramolecular Transferases ,Peptides, Cyclic ,Biochemistry - Published
- 2022
68. Changes in hemoglobin and clinical outcomes drive improvements in fatigue, quality of life, and physical function in patients with paroxysmal nocturnal hemoglobinuria: post hoc analyses from the phase III PEGASUS study
- Author
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David Cella, Sujata P. Sarda, Ray Hsieh, Jesse Fishman, Zalmai Hakimi, Kate Hoffman, Mohammed Al-Adhami, Jameel Nazir, Katelyn Cutts, and William R. Lenderking
- Subjects
Hemoglobins ,Hemoglobinuria, Paroxysmal ,Quality of Life ,Humans ,Hematology ,General Medicine ,Peptides, Cyclic ,Fatigue - Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare, chronic, acquired, hematologic, life-threatening disease characterized by thrombosis, impaired bone marrow function, and complement-mediated hemolysis. The PEGASUS phase III clinical trial demonstrated superiority of pegcetacoplan over eculizumab regarding improvements in hemoglobin levels in patients with suboptimal response to prior eculizumab treatment. The objective of this post hoc analysis was to compare the patient-reported outcome (PRO) response rates observed among PEGASUS participants and the relationships between their PRO scores with clinical and hematological parameters. Data from the 16-week randomized, controlled (1:1 to pegcetacoplan or eculizumab) period of the PEGASUS trial included comparisons of weekly PRO measurements taken using the Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F) scale and the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core-30 (EORTC QLQ-C30) scales. A clinically meaningful FACIT-F response was defined as an increase from baseline of ≥5 points. Convergent validity was assessed using conventional threshold correlations between FACIT-F, EORTC QLQ-C30, and laboratory parameters. A clinically meaningful improvement in FACIT-F score was seen in 72.2% of pegcetacoplan-treated patients compared to 22.9% of eculizumab-treated patients. At week 16, the FACIT-F total score correlated with hemoglobin levels (r=0.47, p< 0.0001), absolute reticulocyte count (r=−0.37, pp
- Published
- 2022
69. Inhibition of C3 with pegcetacoplan results in normalization of hemolysis markers in paroxysmal nocturnal hemoglobinuria
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Raymond S M, Wong, Humphrey W H, Pullon, Ismail, Amine, Andrija, Bogdanovic, Pascal, Deschatelets, Cedric G, Francois, Kalina, Ignatova, Surapol, Issaragrisil, Pimjai, Niparuck, Tontanai, Numbenjapon, Eloy, Roman, Jameela, Sathar, Raymond, Xu, Mohammed, Al-Adhami, Lisa, Tan, Eric, Tse, and Federico V, Grossi
- Subjects
Adult ,Hemoglobins ,Clinical Trials, Phase II as Topic ,Complement Inactivating Agents ,Clinical Trials, Phase I as Topic ,Hemoglobinuria, Paroxysmal ,Humans ,Hematology ,General Medicine ,Hemolysis ,Peptides, Cyclic ,Biomarkers - Abstract
Paroxysmal nocturnal hemoglobinuria (PNH) is a rare, acquired hematologic disorder characterized by complement-mediated hemolysis. C5 inhibitors (eculizumab/ravulizumab) control intravascular hemolysis but do not prevent residual extravascular hemolysis. The newly approved complement inhibitor, pegcetacoplan, inhibits C3, upstream of C5, and has the potential to improve control of complement-mediated hemolysis. The PADDOCK and PALOMINO clinical trials assessed the safety and efficacy of pegcetacoplan in complement inhibitor-naïve adults (≥ 18 years) diagnosed with PNH. Patients in PADDOCK (phase 1b open-label, pilot trial) received daily subcutaneous pegcetacoplan (cohort 1: 180 mg up to day 28 [n = 3]; cohort 2: 270–360 mg up to day 365 [n = 20]). PALOMINO (phase 2a, open-label trial) used the same dosing protocol as PADDOCK cohort 2 (n = 4). Primary endpoints in both trials were mean change from baseline in hemoglobin, lactate dehydrogenase, haptoglobin, and the number and severity of treatment-emergent adverse events. Mean baseline hemoglobin levels were below the lower limit of normal in both trials (PADDOCK: 8.38 g/dL; PALOMINO: 7.73 g/dL; normal range: 11.90–18.00 g/dL), increased to within normal range by day 85, and were sustained through day 365 (PADDOCK: 12.14 g/dL; PALOMINO: 13.00 g/dL). In PADDOCK, 3 serious adverse events (SAE) led to study drug discontinuation, 1 of which was deemed likely related to pegcetacoplan and 1 SAE, not deemed related to study drug, led to death. No SAE led to discontinuation/death in PALOMINO. Pegcetacoplan was generally well tolerated and improved hematological parameters by controlling hemolysis, while also improving other clinical PNH indicators in both trials. These trials were registered at www.clinicaltrials.gov (NCT02588833 and NCT03593200).
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- 2022
70. Optimization of Cyclic Peptide Property Using Chromatographic Capacity Factor on Permeability of Passive Cell Membrane and Human Induced Pluripotent Stem Cell-Derived Intestinal Membrane
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Ayahisa Watanabe, Shota Uehara, Takanori Akazawa, and Motohiro Fujiu
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Cell Membrane Permeability ,Cell Membrane ,Induced Pluripotent Stem Cells ,Humans ,Water ,Pharmaceutical Science ,Peptides, Cyclic ,Permeability - Abstract
Cyclic peptides have attracted increasing attention as a privileged class of molecules addressing undruggable targets. Cell permeability of cyclic peptides has remained a challenging issue owing to their molecular properties. Various efficiency metrics have emerged to assess this issue. Among them, the lipophilic permeability efficiency (LPE) metric is the difference between an experimental 1,9-decadiene-water partition coefficient at pH 7.4 (log D
- Published
- 2022
71. The natural bicyclic hexapeptide RA-VII is a novel inhibitor of the eukaryotic translocase eEF2
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Tomohiro Miyoshi, Takaomi Nomura, Koich Takeya, and Toshio Uchiumi
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Eukaryotic Cells ,Peptide Elongation Factor 2 ,Biophysics ,Animals ,Eukaryota ,Guanosine Triphosphate ,Cell Biology ,Peptides, Cyclic ,Molecular Biology ,Biochemistry - Abstract
A cyclic hexapeptide, RA-VII isolated from the Rubiaceae family of plants, has high cytotoxic activity. Although RA-VII has been shown to inhibit protein synthesis in eukaryotic cells, the molecular mode of its action is not clear. Here we investigate the mechanism of the RAVII action on the translation apparatus. Biochemical functional assays showed that RA-VII inhibits poly(U)-dependent polyphenylalanine synthesis in the presence of animal elongation factors eEF1A and eEF2. Furthermore, RAVII prevented eEF2/ribosome-dependent GTPase activity, but not eEF-1A/ribosome-dependent activity. A filter binding assay demonstrated that RA-VII markedly enhances the binding affinity of eEF2 for GTP, but not for GDP, and prevents exchange of GTP in the eEF2-GTP complex, even after addition of a large excess of GTP/GDP. Limited proteolysis experiments indicated that RA-VII prevents the digestion of eEF2 in the presence of either GTP or GMPPCP, but not with GDP. Further footprint analysis and a translocation assay showed that the eEF2•GMPPNP•RA-VII complex binds to the conserved rRNA regions at the factor-binding center of the ribosome and retains the ability to translocate the A site-bound tRNA to the P-site. These results suggest that RA-VII tightly stabilizes the GTP•eEF2 complex structure, which is able to bind to the ribosomal functional site, but seems to suppress normal turnover of eEF2 after translocation. The properties of RA-VII make it a novel ligand for probing the action of eEF2 in the process of translocation on the ribosome.
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- 2022
72. Accessing Diverse Pyridine-Based Macrocyclic Peptides by a Two-Site Recognition Pathway
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Dinh T. Nguyen, Tung T. Le, Andrew J. Rice, Graham A. Hudson, Wilfred A. van der Donk, and Douglas A. Mitchell
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Biological Products ,Colloid and Surface Chemistry ,Pyridines ,Protein Biosynthesis ,General Chemistry ,Peptides ,Peptides, Cyclic ,Protein Processing, Post-Translational ,Biochemistry ,Catalysis ,Biosynthetic Pathways - Abstract
Macrocyclic peptides are sought-after molecular scaffolds for drug discovery, and new methods to access diverse libraries are of increasing interest. Here, we report the enzymatic synthesis of pyridine-based macrocyclic peptides (pyritides) from linear precursor peptides. Pyritides are a recently described class of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are related to the long-known thiopeptide natural products. RiPP precursors typically contain an N-terminal leader region that is physically engaged by the biosynthetic proteins that catalyze modification of the C-terminal core region of the precursor peptide. We demonstrate that pyritide-forming enzymes recognize both the leader region and a C-terminal tripeptide motif, with each contributing to site-selective substrate modification. Substitutions in the core region were well-tolerated and facilitated the generation of a wide range of pyritide analogues, with variations in macrocycle sequence and size. A combination of the pyritide biosynthetic pathway with azole-forming enzymes was utilized to generate a thiazole-containing pyritide (historically known as a thiopeptide) with no similarity in sequence and macrocycle size to the naturally encoded pyritides. The broad substrate scope of the pyritide biosynthetic enzymes serves as a future platform for macrocyclic peptide lead discovery and optimization.
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- 2022
73. CXCR4-targeted theranostics in oncology
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Andreas K. Buck, Sebastian E. Serfling, Thomas Lindner, Heribert Hänscheid, Andreas Schirbel, Stefanie Hahner, Martin Fassnacht, Hermann Einsele, and Rudolf A. Werner
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Adult ,Receptors, CXCR4 ,Lymphoma ,Coordination Complexes ,Hematologic Neoplasms ,Humans ,Radiology, Nuclear Medicine and imaging ,General Medicine ,Precision Medicine ,Multiple Myeloma ,Tomography, X-Ray Computed ,Peptides, Cyclic - Abstract
A growing body of literature reports on the upregulation of C-X-C motif chemokine receptor 4 (CXCR4) in a variety of cancer entities, rendering this receptor as suitable target for molecular imaging and endoradiotherapy in a theranostic setting. For instance, the CXCR4-targeting positron emission tomography (PET) agent [68 Ga]PentixaFor has been proven useful for a comprehensive assessment of the current status quo of solid tumors, including adrenocortical carcinoma or small-cell lung cancer. In addition, [68 Ga]PentixaFor has also provided an excellent readout for hematological malignancies, such as multiple myeloma, marginal zone lymphoma, or mantle cell lymphoma. PET-based quantification of the CXCR4 capacities in vivo allows for selecting candidates that would be suitable for treatment using the theranostic equivalent [177Lu]/[90Y]PentixaTher. This CXCR4-directed theranostic concept has been used as a conditioning regimen prior to hematopoietic stem cell transplantation and to achieve sufficient anti-lymphoma/-tumor activity in particular for malignant tissues that are highly sensitive to radiation, such as the hematological system. Increasing the safety margin, pretherapeutic dosimetry is routinely performed to determine the optimal activity to enhance therapeutic efficacy and to reduce off-target adverse events. The present review will provide an overview of current applications for CXCR4-directed molecular imaging and will introduce the CXCR4-targeted theranostic concept for advanced hematological malignancies.
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- 2022
74. Cyclization and Docking Protocol for Cyclic Peptide–Protein Modeling Using HADDOCK2.4
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Charitou, Vicky, Van Keulen, Siri C., Bonvin, Alexandre M.J.J., Sub NMR Spectroscopy, and NMR Spectroscopy
- Subjects
Molecular Docking Simulation ,Cyclization ,Protein Conformation ,Proteins ,Physical and Theoretical Chemistry ,Peptides, Cyclic ,Software ,Protein Binding ,Computer Science Applications - Abstract
An emerging class of therapeutic molecules are cyclic peptides with over 40 cyclic peptide drugs currently in clinical use. Their mode of action is, however, not fully understood, impeding rational drug design. Computational techniques could positively impact their design, but modeling them and their interactions remains challenging due to their cyclic nature and their flexibility. This study presents a step-by-step protocol for generating cyclic peptide conformations and docking them to their protein target using HADDOCK2.4. A dataset of 30 cyclic peptide-protein complexes was used to optimize both cyclization and docking protocols. It supports peptides cyclized via an N- and C-terminus peptide bond and/or a disulfide bond. An ensemble of cyclic peptide conformations is then used in HADDOCK to dock them onto their target protein using knowledge of the binding site on the protein side to drive the modeling. The presented protocol predicts at least one acceptable model according to the critical assessment of prediction of interaction criteria for each complex of the dataset when the top 10 HADDOCK-ranked single structures are considered (100% success rate top 10) both in the bound and unbound docking scenarios. Moreover, its performance in both bound and fully unbound docking is similar to the state-of-the-art software in the field, Autodock CrankPep. The presented cyclization and docking protocol should make HADDOCK a valuable tool for rational cyclic peptide-based drug design and high-throughput screening.
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- 2022
75. Anti-cyclic citrullinated peptide antibody-positive rheumatoid arthritis caused by bacterial organizing pneumonia in a patient with Sjogren’s syndrome
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Taro Horino, Mitsuharu Yoshida, Satoshi Inotani, Kazuki Anabuki, Hiroshi Ohnishi, Masahiro Komori, Osamu Ichii, and Yoshio Terada
- Subjects
Arthritis, Rheumatoid ,musculoskeletal diseases ,Sjogren's Syndrome ,Humans ,Female ,Pneumonia ,Middle Aged ,skin and connective tissue diseases ,Arthralgia ,Peptides, Cyclic ,Autoantibodies - Abstract
A 58-year-old woman with a history of Sjogren’s syndrome was admitted to our hospital with cough, decreased right lung breath sounds and arthralgia in both thumbs. Chest computed tomography showed consolidation with air bronchogram in the right lung. Levels of anti-cyclic citrullinated peptide antibody and rheumatoid factor levels were significantly elevated. She was diagnosed with rheumatoid arthritis induced by bacterial organizing pneumonia. Treatment with salazosulfapyridine was added for rheumatoid arthritis and arthralgia gradually improved. This case highlights that respiratory infections could lead to anti-cyclic citrullinated peptide antibody-positive rheumatoid arthritis in patients with Sjogren’s syndrome.
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- 2022
76. PREF-NET: a patient preference and experience study of lanreotide autogel administered in the home versus hospital setting among patients with gastroenteropancreatic neuroendocrine tumours in the UK.
- Author
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Khan MS, Cook K, Weickert MO, Davies L, Pritchard DM, Day M, Shah T, Hull D, Caplin M, Back M, Pommie C, and Higgs K
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- Adult, Humans, Middle Aged, Cross-Sectional Studies, Patient Preference, Quality of Life, Hospitals, United Kingdom, Activities of Daily Living, Neuroendocrine Tumors drug therapy, Peptides, Cyclic, Somatostatin analogs & derivatives
- Abstract
Purpose: PREF-NET reported patients' experience of Somatuline® (lanreotide) Autogel® (LAN) administration at home and in hospital among patients with gastroenteropancreatic neuroendocrine tumours (GEP-NETs)., Methods: PREF-NET was a multicentre, cross-sectional study of UK adults (aged ≥ 18 years) with GEP-NETs receiving a stable dose of LAN, which comprised of (1) a quantitative online survey, and (2) qualitative semi-structured interviews conducted with a subgroup of survey respondents. The primary objective was the description of overall patient preference for home versus hospital administration of LAN. Secondary objectives included describing patient-reported opinions on the experience and associated preference for each administration setting, and the impact on healthcare utilisation, societal cost, activities of daily living and health-related quality of life (HRQoL)., Results: In the primary analysis (80 patients; mean age 63.9 years), 98.7% (95% confidence interval [CI]: 96.1-100.0) of patients preferred to receive LAN at home, compared with 1.3% (95% CI: 0.0-3.9) who preferred the hospital setting. Among participants, over half (60.3%) received their injection from a non-healthcare professional. Most patients (79.5% [95% CI: 70.5-88.4]) reported a positive effect on HRQoL after the switch from hospital to home administration. Qualitative interviews (20 patients; mean age 63.6 years) highlighted that patients preferred home administration because it improved overall convenience; saved time and costs; made them feel more comfortable and relaxed, and less stressed; and increased confidence in their ability to self-manage their treatment., Conclusion: Almost all patients preferred to receive LAN treatment at home rather than in hospital with increased convenience and psychological benefits reported as key reasons for this preference., (© 2024. The Author(s).)
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- 2024
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77. Previously Uncharacterized Variants, OCF-E-OCF-J, of the Antifungal Occidiofungin Produced by Burkholderia contaminans MS14.
- Author
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Hansanant N, Cao K, Tenorio A, Joseph T, Ju M, McNally N, Kummari E, Williams M, Cothrell A, Buhrow AR, Shin R, Orugunty R, and Smith L
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- Mice, Animals, Carboxylic Acids, Microbial Sensitivity Tests, Antifungal Agents chemistry, Burkholderia chemistry, Glycopeptides, Peptides, Cyclic
- Abstract
The rise of multidrug resistant fungal infections highlights the need to identify and develop novel antifungal agents. Occidiofungin is a nonribosomally synthesized glycolipopeptide that has a unique mechanism of action, disrupting actin-mediated functions and inducing cellular apoptosis. Antifungal activity has been observed in vitro against various fungal species, including multidrug resistant Candida auris , and in vivo efficacy has been demonstrated in a murine vulvovaginal candidiasis model. Occidiofungin, a cyclic glycolipopeptide, is composed of eight amino acids and in previous studies, an asparagine residue was assigned at position 7 (ASN7). In this study, new structural variants of occidiofungin have been characterized which have aspartic acid (ASP7), glutamine (GLN7), or glutamic acid (GLU7) at position 7. The side chain of the ASP7 variant contains the only terminal carboxylic acid in the peptide and provides a useful site for selective chemical modifications. Analogues were synthesized at the ASP7 position and tested for antifungal activity. These analogues were shown to be more active as compared to the ASP7 variant against a panel of Candida species. The naturally occurring variants of occidiofungin with a side chain containing a carboxylic acid at the seventh amino acid position can be used to develop semisynthetic analogues with enhanced therapeutic properties.
- Published
- 2024
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- View/download PDF
78. Sol-gel Carbowax 20M-zwitterionic ionic liquid composite sorbent-based capsule phase microextraction device combined with HPLC/post-column derivatization for the determination of lanreotide, a human somatostatin analogue in urine.
- Author
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Ntorkou M, Kabir A, Furton KG, Tzanavaras PD, and Zacharis CK
- Subjects
- Humans, Chromatography, High Pressure Liquid methods, Polyethylene Glycols, Spectroscopy, Fourier Transform Infrared, Solid Phase Microextraction methods, Peptides, Cyclic, Limit of Detection, Ionic Liquids chemistry, Somatostatin analogs & derivatives, Liquid Phase Microextraction
- Abstract
In this research, a sol-gel Carbowax 20M-zwitterionic ionic liquid composite sorbent-based capsule phase microextraction (CPME) device was developed in combination with liquid chromatography-post column derivatization for the first ever reported determination of a somatostatin analogue - lanreotide in human urine. The sol-gel Carbowax 20M-zwitterionic ionic liquid composite sorbent was encapsulated in the lumen of a polypropylene capillary tube and characterized by FT-IR spectroscopy and SEM with energy dispersive X-ray spectroscopy (EDS). The main steps of the CPME workflow were optimized to obtain high extraction efficiency for the target analyte. After the separation of the analyte on a C
8 stationary phase, the peptide was derivatized online with o-phthalaldehyde before the fluorescence detection. The main experimental parameters of CPME and the post-column procedures were systematically investigated and optimized. The method was validated in terms of selectivity, linearity, accuracy, precision, limits of detection (LOD), and limits of quantification (LOQ). The relative bias ranged between 88.8 and 115.6 % for the peptide, while the RSD values for repeatability and intermediate precision were less than 14.3 %. The achieved limit of detection (LOD) was 0.2 μΜ while the limit of quantitation (LOQ) was established as 0.9 μΜ. Finally, the sol-gel Carbowax 20M-zwitterionic ionic liquid composite sorbent-based microextraction capsules were found to be reusable for at least 20 extractions. The developed method presented adequate overall performance, and it could be applied in the analysis of selected peptide in human urine samples., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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79. Investigation of periodontitis, halitosis, xerostomia, and serological characteristics of patients with osteoarthritis and rheumatoid arthritis and identification of new biomarkers.
- Author
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Lee YH, Hong SJ, Lee GJ, Shin SI, Hong JY, Chung SW, and Lee YA
- Subjects
- Male, Humans, Female, Adult, Middle Aged, Aged, Anti-Citrullinated Protein Antibodies, Biomarkers, Autoantibodies, Peptides, Cyclic, Halitosis, Arthritis, Rheumatoid complications, Arthritis, Rheumatoid diagnosis, Arthritis, Rheumatoid epidemiology, Osteoarthritis complications, Osteoarthritis diagnosis, Periodontitis complications, Periodontitis diagnosis, Periodontitis epidemiology, Xerostomia, Periodontal Diseases
- Abstract
Rheumatoid arthritis (RA) and osteoarthritis (OA) are two different types of arthritis. Within RA, the subsets between seronegative RA (snRA) and seropositive RA (spRA) represent distinct disease entities; however, identifying clear distinguishing markers between them remains a challenge. This study investigated and compared the oral health conditions in patients with RA and OA to clarify the differences from healthy controls. In addition, we investigated the serological characteristics of the patients, the factors that distinguished patients with RA from those with OA, and the main factors that differentiated between snRA and spRA patients. A total of 161 participants (mean age: 52.52 ± 14.57 years, 32 males and 129 females) were enrolled in this study and categorized as: normal (n = 33), OA (n = 31), and RA (n = 97). Patients with RA were divided into the following two subtypes: snRA (n = 18) and spRA (n = 79). Demographics, oral health, and serological characteristics of these patients were compared. The prevalence of periodontal diseases was significantly higher in patients with OA (100%) and RA (92.8%) than in healthy controls (0.0%). However, the presence of periodontal diseases was not utilized as a distinguishing factor between OA and RA. Xerostomia occurred more frequently in patients with RA (84.5%) than in patients with OA (3.2%) and healthy controls (0.0%) (all p < 0.001). ROC analysis revealed that periodontal disease was a very strong predictor in the diagnosis of OA compared to healthy controls, with an AUC value of 1.00 (p < 0.001). Additionally, halitosis (AUC = 0.746, 95% CI 0.621-0.871, p < 0.001) and female sex (AUC = 0.663, 95% CI 0.529-0.797, p < 0.05) were also significant predictors of OA. The strongest predictors of RA diagnosis compared to healthy controls were periodontal diseases (AUC = 0.964), followed by xerostomia (AUC = 0.923), age (AUC = 0.923), female sex (AUC = 0.660), and halitosis (AUC = 0.615) (all p < 0.05). Significant serological predictors of RA were anti-CCP Ab (AUC = 0.808), and RF (AUC = 0.746) (all p < 0.05). In multiple logistic regression analysis, xerostomia (odds ratio, OR: 8124.88, 95% CI 10.37-6368261.97, p-value = 0.008) and Anti-CCP Ab (OR: 671.33, 95% CI 2.18-207,074.02, p = 0.026) were significant predictors for RA compared to OA. When diagnosing spRA compared to snRA, anti-CCP Ab (AUC = 1.000, p < 0.001) and RF (AUC = 0.910, 95%CI 0.854-0.967, p < 0.001) had outstanding predictive performances. Therefore, clinicians and researchers should thoroughly evaluate the oral status of both OA and RA patients, alongside serological factors, and consider these elements as potential predictors., (© 2024. The Author(s).)
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- 2024
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80. Enhanced Tumor Targeting and Antitumor Activity of Methylated β-Cyclodextrin-Threaded Polyrotaxanes by Conjugating Cyclic RGD Peptides.
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Zhang S, Tamura A, and Yui N
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- Humans, Oligopeptides chemistry, Integrins, Rotaxanes pharmacology, Rotaxanes chemistry, Rotaxanes metabolism, beta-Cyclodextrins chemistry, Neoplasms drug therapy, Peptides, Cyclic
- Abstract
We previously reported that acid-degradable methylated β-cyclodextrins (Me-β-CDs)-threaded polyrotaxanes (Me-PRXs) can induce autophagic cell death through endoplasmic reticulum (ER) stress-related autophagy, even in apoptosis-resistant cells. Hence, Me-PRXs show great potential as anticancer therapeutics. In this study, peptide-supermolecule conjugates were designed to achieve the targeted delivery of Me-PRX to malignant tumors. Arg-Gly-Asp peptides are well-known binding motifs of integrin α
v β3 , which is overexpressed on angiogenic sites and many malignant tumors. The tumor-targeted cyclic Arg-Gly-Asp (cRGD) peptide was orthogonally post-modified to Me-PRX via click chemistry. Surface plasmon resonance (SPR) results indicated that cRGD-Me-PRX strongly binds to integrin αv β3 , whereas non-targeted cyclic Arg-Ala-Glu (cRGE) peptide conjugated to Me-PRX (cRGE-Me-PRX) failed to interact with integrins αv β3 . In vitro, cRGD-Me-PRX demonstrated enhanced cellular internalization and antitumor activity in 4T1 cells than that of unmodified Me-PRX and non-targeted cRGE-Me-PRX, due to its ability to recognize integrin αv β3 . Furthermore, cRGD-Me-PRX accumulated effectively in tumors, leading to antitumor effects, and exhibited excellent biocompatibility and safety in vivo. Therefore, cRGD conjugation to enhance selectivity for integrin αv β3 -positive cancer cells is a promising design strategy for Me-PRXs in antitumor therapy.- Published
- 2024
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- View/download PDF
81. In early rheumatoid arthritis, anticitrullinated peptide antibodies associate with low number of affected joints and rheumatoid factor associates with systemic inflammation.
- Author
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Pertsinidou E, Saevarsdottir S, Manivel VA, Klareskog L, Alfredsson L, Mathsson-Alm L, Hansson M, Cornillet M, Serre G, Holmdahl R, Skriner K, Jakobsson PJ, Westerlind H, Askling J, and Rönnelid J
- Subjects
- Humans, Inflammation, Autoantibodies, Peptides, Cyclic, Immunoglobulin G, Immunoglobulin M, Immunoglobulin A, Rheumatoid Factor, Arthritis, Rheumatoid
- Abstract
Objectives: To investigate how individual rheumatoid arthritis (RA) autoantibodies associate with individual signs and symptoms at the time of RA diagnosis., Methods: IgA, IgG, IgM rheumatoid factor (RF), antibodies against cyclic citrullinated peptide version 2 (anti-CCP2) and 16 individual antibodies against citrullinated protein (ACPA) reactivities were analysed centrally in baseline sera from 1600 patients with RA classified according to the 1987 American College of Rheumatology (ACR) criteria. These results were related to C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), number of swollen and tender joints (SJC and TJC), 28-joint disease activity scores (DAS28 and DAS28CRP), global disease activity evaluated by the patients and Health Assessment Questionnaire, all obtained at baseline., Results: Individually, all autoantibodies except immunoglobulin G (IgG) RF associated with low SJC and TJC and with high ESR. In IgM RF-negative patients, ACPA associated strictly with low number of swollen and tender joints. This association persisted in multiple regression and stratified analyses where IgM and IgA RF instead associated with inflammation expressed as ESR. Among subjects without any ACPA peptide reactivity, there was no association between RF isotypes and ESR. The effect of RF on ESR increased with the number of ACPA reactivities, especially for IgM RF. In patients fulfilling the 1987 ACR criteria without taking RF into account, associations between IgM RF and high ESR, as well as between ACPA and low joint counts, remained., Conclusion: Whereas ACPA associate with low counts of affected joints in early RA, RF associates with elevated measures of systemic inflammation in an ACPA-dependent manner. This latter finding corroborates in vitro models of ACPA and RF in immune complex-induced inflammation. These phenotypic associations are independent of classification criteria., Competing Interests: Competing interests: EP and LM-A are employees at Thermo Fisher Scientific. JA has had or have research agreements with AbbVie, BMS, Eli Lilly, Galapagos, MSD, Pfizer, Roche, Samsung Bioepis and Sanofi, mainly for the national safety monitoring of rheumatology immunomodulators in Sweden (ARTIS). JR has been a member of the Scientific Advisory Board for Thermo Fisher Scientific and for Inova/Werfen and has received consulting fees, speaking fees and/ or honoraria by Thermo Fisher Scientific. RH has received consulting fees from Regor, Lipum AB and Cyxone AB and is the founder of Vacara AB. LK has been a co-ordinator of several IMI-funded projects which included collaborations with Janssen, Pfizer, Sanofi, UCB, GSK and Eli-Lilly. This work has been presented as a poster in a preliminary form at EULAR (June 2019) and to the European Workshop for Rheumatology Research (March 2023)., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2024
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82. A comparison of the performance of 68 Ga-Pentixafor PET/CT versus adrenal vein sampling for subtype diagnosis in primary aldosteronism.
- Author
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Yin X, Ai K, Luo J, Liu W, Ma X, Zhou L, Xiang X, Su X, Wang Y, and Li Y
- Subjects
- Humans, Adrenal Glands metabolism, Gallium Radioisotopes metabolism, Cytochrome P-450 CYP11B2 metabolism, Positron Emission Tomography Computed Tomography, Hyperaldosteronism diagnosis, Hyperaldosteronism surgery, Hyperaldosteronism metabolism, Peptides, Cyclic, Coordination Complexes
- Abstract
Objective: To investigate the diagnostic efficiency and prognostic value of
68 Ga-Pentixafor PET/CT in comparison with adrenal vein sampling (AVS) for functional lateralization in primary aldosteronism (PA). Histology and long-term clinical follow-up normally serve as the gold standard for such diagnosis., Methods: We prospectively recruited 26 patients diagnosed with PA. All patients underwent68 Ga-Pentixafor PET/CT and AVS. Postsurgical biochemical and clinical outcomes of patients with unilateral primary aldosteronism (UPA), as diagnosed by PET/CT or AVS, were assessed by applying standardized Primary Aldosteronism Surgical Outcome (PASO) criteria. Immunohistochemistry (IHC) was performed to detect the expression of aldosterone synthase (CYP11B2) and CXCR4., Results: On total, 19 patients were diagnosed with UPA; of these, 13 patients were lateralized by both PET/CT and AVS, four patients were lateralized by PET-only, and two by AVS-only. Seven subjects with no lateralization on AVS and PET received medical therapy. All patients achieved complete biochemical success except one with nodular hyperplasia lateralized by AVS alone. The consistency between PET/CT and AVS outcomes was 77% (20/26). Moreover, CYP11B2-positive nodules were all CXCR4-positive and showed positive findings on PET. Patients who achieved complete biochemical and clinical success had a higher uptake on PET as well as stronger expression levels of CXCR4 and CYP11B2., Conclusion: Our analysis showed that68 Ga-Pentixafor PET/CT could enable non-invasive diagnosis in most patients with PA and identify additional cases of unilateral and surgically curable PA which could not be classified by AVS.68 Ga-Pentixafor PET/CT should be considered as a first-line test for the future classification of PA., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Yin, Ai, Luo, Liu, Ma, Zhou, Xiang, Su, Wang and Li.)- Published
- 2024
- Full Text
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83. Re: Patel et al.: A cost-effectiveness analysis of pegcetacoplan for the treatment of geographic atrophy. (Ophthalmol Retina. 2024;8:25-31).
- Author
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Shen LL and Del Priore LV
- Subjects
- Humans, Cost-Effectiveness Analysis, Retina, Peptides, Cyclic, Geographic Atrophy diagnosis, Geographic Atrophy drug therapy
- Published
- 2024
- Full Text
- View/download PDF
84. Additional Information About Pegcetacoplan for Treatment of Geographic Atrophy Growth.
- Author
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Bressler NM
- Subjects
- Humans, Peptides, Cyclic, Geographic Atrophy therapy
- Published
- 2024
- Full Text
- View/download PDF
85. Further structural optimization and SAR study of sungsanpin derivatives as cell-invasion inhibitors.
- Author
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Chen S, Zhang K, Zou J, Yu Z, Gai C, Chai X, Zhao Q, and Zou Y
- Subjects
- Humans, Matrix Metalloproteinases, A549 Cells, Peptides, Cyclic, Tissue Inhibitor of Metalloproteinase-1 genetics, Peptides
- Abstract
Metastasis is one of the major causes of death in patients with cancer, and cell invasion plays a fundamental part in this process. Because of the absence of efficacious treatments, caring for these patients is challenging. Recently, we optimized the structure of the naturally occurring lasso peptide sungsanpin. We identified two peptides, octapeptide S3 and cyclic peptide S4, which inhibited invasion into A549 cells effectively. We undertook an alanine scan of S3 to explore the structure-activity relationship. The linear octapeptide S3-4 and cyclic peptide S4-1 exhibited improved inhibition of invasion into A549 cells. We modified S3-4 to obtain S3-4K, which displayed much higher inhibitory activity against invasion into A549 cells than S3-4. Of all peptides tested, S4-1 upregulated significantly mRNA of tissue inhibitor matrix metalloproteinase TIMP-1 and TIMP-2., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
86. Elevated Serum Levels of Zonulin Family Peptides in Anticitrullinated Protein Antibody-Positive At-Risk Individuals Without Arthritis.
- Author
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Hemgren C, Martinsson K, Rooney C, Wetterö J, Mankia K, Emery P, and Kastbom A
- Subjects
- Humans, Prospective Studies, Peptides, Cyclic, Peptides, Autoantibodies, Arthritis, Rheumatoid diagnosis, Haptoglobins, Protein Precursors
- Abstract
Objective: Recent advances imply that early events triggering rheumatoid arthritis (RA) occur at mucosal surfaces. We aimed to evaluate whether intestinal permeability is altered in patients at increased risk of RA, and/or predicts the development of clinical arthritis, by measuring serum zonulin family peptides (ZFP) levels, which are shown to reflect intestinal barrier integrity., Methods: Two independent prospective observational cohorts were studied, including subjects with musculoskeletal symptoms and anticitrullinated protein antibodies (ACPA), but without clinical arthritis at baseline. In Sweden, 82 such at-risk patients were compared to 100 age-matched healthy blood donors. In the UK, 307 at-risk patients were compared to 100 ACPA-negative symptomatic controls. ZFP was measured in baseline sera by enzyme-linked immunoassays., Results: In the Swedish at-risk cohort, ZFP levels were significantly increased in patients compared to controls (mean 41.4 vs 33.6 ng/mL, P < 0.001) and Cox regression analysis showed prognostic value of ZFP for arthritis development (hazard ratio [HZ] 1.04 per ng/mL ZFP increase, 95% CI 1.01-1.07, P = 0.02). Elevated ZFP levels among ACPA-positive at-risk patients compared to symptomatic ACPA-negative controls were confirmed in the UK at-risk cohort (mean 69.7 vs 36.0 ng/mL, P < 0.001), but baseline ZFP were not associated with arthritis development (HR 1.00 per ng/mL ZFP increase, 95% CI 1.00-1.01, P = 0.30)., Conclusion: Serum ZFP levels are elevated in ACPA-positive at-risk patients when compared to both healthy blood donors and symptomatic ACPA-negative controls. Thus, gut barrier function may be of importance in RA-associated autoimmunity. A possible prognostic value of serum ZFP merits further investigation, preferably in larger prospective cohorts., (Copyright © 2024 by the Journal of Rheumatology.)
- Published
- 2024
- Full Text
- View/download PDF
87. Selective targeting of human TET1 by cyclic peptide inhibitors: Insights from biochemical profiling.
- Author
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Šimelis K, Saraç H, Salah E, Nishio K, McAllister TE, Corner TP, Tumber A, Belle R, Schofield CJ, Suga H, and Kawamura A
- Subjects
- Humans, Epigenesis, Genetic, DNA-Binding Proteins metabolism, Mixed Function Oxygenases metabolism, DNA Methylation, Proto-Oncogene Proteins, Peptides, Cyclic, Dioxygenases metabolism
- Abstract
Ten-Eleven Translocation (TET) enzymes are Fe(II)/2OG-dependent oxygenases that play important roles in epigenetic regulation, but selective inhibition of the TETs is an unmet challenge. We describe the profiling of previously identified TET1-binding macrocyclic peptides. TiP1 is established as a potent TET1 inhibitor (IC
50 = 0.26 µM) with excellent selectivity over other TETs and 2OG oxygenases. TiP1 alanine scanning reveals the critical roles of Trp10 and Glu11 residues for inhibition of TET isoenzymes. The results highlight the utility of the RaPID method to identify potent enzyme inhibitors with selectivity over closely related paralogues. The structure-activity relationship data generated herein may find utility in the development of chemical probes for the TETs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that influenced the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)- Published
- 2024
- Full Text
- View/download PDF
88. Chemokine receptor-targeted PET/CT provides superior diagnostic performance in newly diagnosed marginal zone lymphoma patients: a head-to-head comparison with [ 18 F]FDG.
- Author
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Kosmala A, Duell J, Schneid S, Serfling SE, Higuchi T, Weich A, Lapa C, Hartrampf PE, Raderer M, Einsele H, Buck AK, Topp MS, Schlötelburg W, and Werner RA
- Subjects
- Humans, Fluorodeoxyglucose F18, Gallium Radioisotopes, Peptides, Cyclic, Positron-Emission Tomography, Radionuclide Imaging, Coordination Complexes, Positron Emission Tomography Computed Tomography methods
- Abstract
Background: In patients with marginal zone lymphoma (MZL), [
18 F]FDG PET/CT provided inconsistent diagnostic accuracy. C-X-C motif chemokine receptor 4 (CXCR4) is overexpressed in MZL and thus, may emerge as novel theranostic target. We aimed to evaluate the diagnostic performance of CXCR4-targeting [68 Ga]Ga-PentixaFor when compared to [18 F]FDG PET/CT in MZL., Methods: Thirty-two untreated MZL patients (nodal, n = 17; extranodal, n = 13; splenic, n = 2) received [68 Ga]Ga-PentixaFor and [18 F]FDG PET/CT within median 2 days. We performed a visual and quantitative analysis of the total lymphoma volume by measuring maximum/peak standardized uptake values (SUVmax/peak ), and calculating target-to-background ratios (TBR, defined as lesion-based SUVpeak divided by SUVmean from blood pool). Visual comparisons for both radiotracers were carried out for all target lesions (TL), and quantitative analysis of concordant TL evident on both scans. Last, MZL subtype analyses were also conducted., Results: On a patient-based level, [68 Ga]Ga-PentixaFor identified MZL manifestations in 32 (100%) subjects (vs. [18 F]FDG, 25/32 [78.1%]). Of the 256 identified TL, 127/256 (49.6%) manifestations were evident only on CXCR4-directed imaging, while only 7/256 (2.7%) were identified on [18 F]FDG but missed by [68 Ga]Ga-PentixaFor. In the remaining 122/256 (47.7%) concordant TL, [68 Ga]Ga-PentixaFor consistently provided increased metrics when compared to [18 F]FDG: SUVmax , 10.3 (range, 2.53-37.2) vs. 5.72 (2.32-37.0); SUVpeak , 6.23 (1.58-25.7) vs. 3.87 (1.54-27.7); P < 0.01, respectively. Concordant TL TBR on [68 Ga]Ga-PentixaFor (median, 3.85; range, 1.05-16.0) was also approximately 1.8-fold higher relative to [18 F]FDG (median, 2.08; range, 0.81-28.8; P < 0.01). Those findings on image contrast, however, were driven by nodal MZL (P < 0.01), and just missed significance for extranodal MZL (P = 0.06)., Conclusions: In newly diagnosed MZL patients, [68 Ga]Ga-PentixaFor identified more sites of disease when compared to [18 F]FDG, irrespective of MZL subtype. Quantitative PET parameters including TBR were also higher on [68 Ga]Ga-PentixaFor PET/CT, suggesting improved diagnostic read-out using chemokine receptor-targeted imaging., (© 2023. The Author(s).)- Published
- 2024
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- View/download PDF
89. Emerging role of carbonyl-carbonyl interactions in the classification of beta turns.
- Author
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D'Arminio N, Ruggiero V, Pierri G, Marabotti A, and Tedesco C
- Subjects
- Protein Conformation, Peptides, Cyclic, Hydrogen Bonding, Peptides chemistry, Proteins chemistry
- Abstract
Carbonyl-carbonyl interactions in peptides and proteins attracted considerable interest in recent years. Here, we report a survey of carbonyl-carbonyl interactions in cyclic peptides, depsipeptides, peptoids and discuss the relationship between backbone torsion angles and CO∙∙∙CO distances. In general, φ values in the range between -40° and -90° and between 40° and 90° correspond to CO∙∙∙CO distances below 3.22 Å. By extending the analysis of carbonyl-carbonyl interactions in different types of beta turns in proteins, we also highlight the role of direct or reciprocal carbonyl-carbonyl interactions in stabilizing the beta turn conformation for each specific type. We confirmed the new type II beta turn, detected by Dunbrack and coworkers, and named Pa, and detect the presence of a direct carbonyl-carbonyl interaction between the second and third residues of the turn. We also evidenced the existence of another new type II beta turn, named pA (following Dunbrack's notation), which represents the alternative conformation of Pa with opposite φ and ψ values and is characterized by a direct carbonyl-carbonyl interaction between the second and third residues of the turn. Finally, we show that the occurrence of CO∙∙∙CO interactions could be also advocated to explain from a chemical point of view the diversity of turn types., (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)
- Published
- 2024
- Full Text
- View/download PDF
90. An international simulated-use study to assess nurses' preferences between two lanreotide syringes for patients with neuroendocrine tumours or acromegaly (PRESTO 3).
- Author
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Ferone D, Martin W, Williams J, Houchard A, Pommie C, Ribeiro-Oliveira A Jr, and Grossman AB
- Subjects
- Humans, Adult, Syringes, Peptides, Cyclic, Acromegaly drug therapy, Neuroendocrine Tumors, Nurses, Somatostatin analogs & derivatives
- Abstract
Purpose: PRESTO 3 evaluated nurses' preference for the Somatuline® Autogel® syringe versus the Lanreotide Pharmathen syringe after injection-pad testing., Methods: This international simulated-use study included oncology/endocrinology nurses with ≥ 1 years' experience in managing neuroendocrine tumours (NETs) and/or acromegaly. Each nurse tested both syringes twice in a randomised order before completing an electronic survey. The primary objective was to assess overall preference (%, 95% confidence interval [CI]) for the Somatuline Autogel syringe versus the Lanreotide Pharmathen syringe. Secondary objectives included rating syringe performance and ranking the importance of syringe attributes., Results: Ninety-four nurses were enrolled: mean age, 41.0 (SD, 11.5) years. The percentage of nurses stating a preference ("strong" or "slight") for the Somatuline Autogel syringe (86.2% [95% CI 77.5-92.4%]) was significantly higher than 50% (p < 0.0001). Performance rating was significantly higher for the Somatuline Autogel syringe versus Lanreotide Pharmathen syringe for 10 of the 11 attributes tested (p < 0.05). The syringe attributes considered most important when injecting patients in routine clinical practice were "easy to use from preparation to injection" (30.9%) and "comfortable to handle during use from preparation to injection" (16.0%). The attribute most commonly rated as least important was "fast administration from preparation to injection" (26.6%)., Conclusion: Nurses strongly preferred the user experience of the Somatuline Autogel syringe over the Lanreotide Pharmathen syringe. "Ease of use" and "comfortable to handle" were the most important syringe attributes, and performance rating was significantly higher with Somatuline Autogel versus Lanreotide Pharmathen syringe for all but one attribute., (© 2023. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
91. A new class of macrocyclic peptides.
- Author
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Pattanayakanahalli Henjarappa K, Das S, and Mahanta N
- Subjects
- Peptides, Cyclic, Peptides, Macrocyclic Compounds
- Published
- 2024
- Full Text
- View/download PDF
92. Creating large chromosomal segment deletions in Aspergillus flavus by a dual CRISPR/Cas9 system: Deletion of gene clusters for production of aflatoxin, cyclopiazonic acid, and ustiloxin B.
- Author
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Chang PK
- Subjects
- Humans, Aspergillus flavus genetics, Aspergillus flavus metabolism, CRISPR-Cas Systems, Commerce, Internationality, Multigene Family, DNA metabolism, Aflatoxins genetics, Indoles, Peptides, Cyclic
- Abstract
Aspergillus flavus produces hepatocarcinogenic aflatoxin that adversely impacts human and animal health and international trade. A promising means to manage preharvest aflatoxin contamination of crops is biological control, which employs non-aflatoxigenic A. flavus isolates possessing defective aflatoxin gene clusters to outcompete field toxigenic populations. However, these isolates often produce other toxic metabolites. The CRISPR/Cas9 technology has greatly advanced genome editing and gene functional studies. Its use in deleting large chromosomal segments of filamentous fungi is rarely reported. A system of dual CRISPR/Cas9 combined with a 60-nucleotide donor DNA that allowed removal of A. flavus gene clusters involved in production of harmful specialized metabolites was established. It efficiently deleted a 102-kb segment containing both aflatoxin and cyclopiazonic acid gene clusters from toxigenic A. flavus morphotypes, L-type and S-type. It further deleted the 27-kb ustiloxin B gene cluster of a resulting L-type mutant. Overall efficiencies of deletion ranged from 66.6 % to 85.6 % and efficiencies of deletions repaired by a single copy of donor DNA ranged from 50.5 % to 72.7 %. To determine the capacity of this technique, a pigment-screening setup based on absence of aspergillic acid gene cluster was devised. Chromosomal segments of 201 kb and 301 kb were deleted with efficiencies of 57.7 % to 69.2 %, respectively. This system used natural A. flavus isolates as recipients, eliminated a forced-recycling step to produce recipients for next round deletion, and generated maker-free deletants with sequences predefined by donor DNA. The research provides a method for creating genuine atoxigenic biocontrol strains friendly for field trial release., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Inc.)
- Published
- 2024
- Full Text
- View/download PDF
93. The Changing Paradigm of Anti-Citrullinated Protein Antibodies in Rheumatoid Arthritis.
- Author
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Demoruelle MK
- Subjects
- Humans, Autoantibodies, Peptides, Cyclic, Anti-Citrullinated Protein Antibodies, Arthritis, Rheumatoid
- Published
- 2024
- Full Text
- View/download PDF
94. Structure prediction of linear and cyclic peptides using CABS-flex.
- Author
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Badaczewska-Dawid A, Wróblewski K, Kurcinski M, and Kmiecik S
- Subjects
- Peptides chemistry, Protein Conformation, Peptides, Cyclic, Proteins chemistry
- Abstract
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins., (© The Author(s) 2024. Published by Oxford University Press.)
- Published
- 2024
- Full Text
- View/download PDF
95. Bioconversion of waste glycerol into viscosinamide by Pseudomonas fluorescens DR54 and its activity evaluation.
- Author
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Jama D, Łaba W, Kruszelnicki M, Polowczyk I, Lazar Z, and Janek T
- Subjects
- Glycerol, Surface-Active Agents chemistry, Lipopeptides, Lipase, Pseudomonas fluorescens, Peptides, Cyclic
- Abstract
Lipopeptides, derived from microorganisms, are promising surface-active compounds known as biosurfactants. However, the high production costs of biosurfactants, associated with expensive culture media and purification processes, limit widespread industrial application. To enhance the sustainability of biosurfactant production, researchers have explored cost-effective substrates. In this study, crude glycerol was evaluated as a promising and economical carbon source in viscosinamide production by Pseudomonas fluorescens DR54. Optimization studies using the Box - Behnken design and response surface methodology were performed. Optimal conditions for viscosinamide production including glycerol 70.8 g/L, leucine 2.7 g/L, phosphate 3.7 g/L, and urea 9.3 g/L were identified. Yield of viscosinamide production, performed under optimal conditions, reached 7.18 ± 0.17 g/L. Preliminary characterization of viscosinamide involved the measurement of surface tension. The critical micelle concentration of lipopeptide was determined to be 5 mg/L. Furthermore, the interactions between the viscosinamide and lipase from Candida rugosa (CRL) were investigated by evaluating the impact of viscosinamide on lipase activity and measuring circular dichroism. It was observed that the α-helicity of CRL increases with increasing viscosinamide concentration, while the random coil structure decreases., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
96. Total Synthesis of Cyanobactin Natural Product Balgacyclamide B.
- Author
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Torres-Hernandez AX, Desman P, Nguyen T, Hoang V, Zhang Y, Bartels A, and Rafferty RJ
- Subjects
- Parasitic Sensitivity Tests, Trypanosoma brucei rhodesiense, Plasmodium falciparum, Antiparasitic Agents, Leishmania donovani, Peptides, Cyclic
- Abstract
Balgacyclamide A-C are a family of cyanobactin natural products isolated from freshwater cyanobacteria Microcystis aeruginosa. These macrocyclic peptides are characterized by their oxazoline-thiazole core, their 7 or 8 stereocenters, and their antiparasitic activities. Balgacyclamide B is known for its activity towards Plasmodium falciparum chloroquine-resistant strain K1, Trypanosoma brucei rhodesiense, and Leishmania donovani. In this report, the first total synthesis of Balgacyclamide B is described in a 17-steps pathway and a 2 % overall yield. The synthetic pathway toward balgacyclamide B can be adapted for the future syntheses of balgacyclamide A and C. In addition, a brief history background of oxazolines syntheses is shown to emphasize the importance of the cyclization conditions used to interconvert or retain configuration of β-hydroxy amides via dehydrative cyclization., (© 2023 Wiley-VCH GmbH.)
- Published
- 2024
- Full Text
- View/download PDF
97. IgM antibodies against acetylated proteins as a possible starting point of the anti-modified protein antibody response in rheumatoid arthritis.
- Author
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van Wesemael TJ, Reijm S, Kawakami A, Dorjée AL, Stoeken G, Maeda T, Kawashiri SY, Huizinga TWJ, Tamai M, Toes REM, and van der Woude D
- Subjects
- Humans, Immunoglobulin M, Rheumatoid Factor, Autoantibodies, Peptides, Cyclic, Antibody Formation, Arthritis, Rheumatoid
- Abstract
Competing Interests: Competing interests: None declared.
- Published
- 2024
- Full Text
- View/download PDF
98. Oral administration of Bifidobacterium longum ES1 reduces endometrial inflammation in women with recurrent pregnancy loss.
- Author
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Tersigni C, Barbaro G, Castellani R, Onori M, Granieri C, Scambia G, and Di Simone N
- Subjects
- Pregnancy, Female, Humans, Inflammasomes, Interleukin-18, Lipopolysaccharides, Caspase 1, Inflammation drug therapy, Glutens, Bifidobacterium longum, Endometritis, Abortion, Habitual, Peptides, Cyclic
- Abstract
Background: Over-activation of endometrial inflammasome NALP-3 (Nod-like receptor family pyrin domain containing 3) can be found in recurrent pregnancy loss (RPL) women probably due to leaky gut and passage into circulation of lipopolysaccharides (LPS). Leaky gut can be caused by exposure to gluten in RPL women genetically predisposed to celiac disease, positive for Human Leukocyte Antigen (HLA)-DQ2/DQ8 haplotype. Oral administration of Bifidobacterium longum ES1 (GliadinES®) can inactivate gluten peptides toxicity to epithelial gut cells and improve gut barrier., Methods: We investigated by enzyme-linked immunoassay: (a) serum levels of LPS and zonuline (a marker of leaky gut); (b) LPS, NALP-3, caspase-1, interleukine (IL)-1β and IL-18 concentration in endometrial fluids, in untreated women with uncomplicated pregnancies (negative HLA-DQ2/DQ8 haplotype) (n = 22) and in women with unexplained RPL, HLA-DQ2/DQ8 positive (n = 22), before and after daily oral administration for 3 months of GliadinES®., Results: RLP women showed higher serum levels of LPS (p < 0.0001) and higher concentration of LPS (p < 0.0001), NALP-3 (p < 0.01); Caspase-1 (p < 0.0001), IL-1β (p < 0.0001), and IL-18 (p < 0.0001) in endometrial fluids compared to controls. GliadinES® treatment significantly reduced serum levels of both LPS (p < 0.0001) and zonuline (p < 0.01), as well as LPS (p < 0.5), NALP-3 (p < 0.01), Caspase-1 (p < 0.001), IL-1β (p < 0.001), and IL-18 (p < 0.01) concentrations in endometrial fluids of RPL women., Conclusions: RPL women positive for HLA-DQ2/DQ8 haplotype show increased circulating and endometrial levels of LPS and endometrial inflammasome NALP-3 over-activation. Oral administration of GliadinES® can reduce gut permeability, decrease serum levels of LPS and, contextually, improve endometrial inflammation in this specific subset of RPL women., (© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
99. Should ACR/EULAR criteria be revised changing the RF and ACPA scores?
- Author
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Steiner G, Van Hoovels L, Csige D, Gatto M, Iagnocco A, and Szekanecz Z
- Subjects
- Humans, Anti-Citrullinated Protein Antibodies, Immunologic Tests, Sensitivity and Specificity, Peptides, Cyclic, Autoantibodies, Rheumatoid Factor, Arthritis, Rheumatoid diagnosis
- Abstract
Current classification criteria for rheumatoid arthritis (RA) encompass clinical and immunological items and are capable of correctly identifying the majority of symptomatic RA patients. The presence of positive rheumatoid factor (RF) and/or and anti-cyclic citrullinated protein/peptide antibodies (ACPA) gaining increasing importance according to their serological titer eases the recognition of RA, yet the debate is open on whether this scoring system ought to be optimized by hierarchizing ACPA or the combination of ACPA and RF over single positivity, prioritizing specificity over sensitivity. The risk of misdiagnosis and misclassification are often entangled, yet they are not the same. In fact, while ideal diagnosis requires 100% sensitivity and specificity, classification criteria are conceived to gather a homogeneous patient population, favoring specificity over sensitivity. Nevertheless, as they are frequently summoned to support the diagnostic process in clinical practice, issues arise on how comprehensive those should be and on how frequently they should be updated in light of novel acquisitions regarding measurable RA-related abnormalities. In this viewpoint two different views on the topic are confronted, discussing the performance of available criteria and the potentiality and pitfalls of their refinement according to novel data on ACPA and RF contribution and emergence of newly discovered specificities., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
100. Evaluating the use of preparation guides in interteaching versus a quiz alternative.
- Author
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Schena D 2nd, Rosales R, and Soldner JL
- Subjects
- Humans, Feedback, Peptides, Cyclic, Educational Measurement, Students
- Abstract
Interteaching is a behavioral teaching method that has demonstrated efficacy in higher education. Of particular interest is the use of a preparation guide (a guided reading assignment), which is designed to promote engagement in the other areas of the interteaching process. The present study compared the use of a preparation guide completed before the start of class with that of a quiz administered at the start of the class. The quiz was hypothesized to serve as a functional alternative to the preparation guide. A total of 38 undergraduate students enrolled in an Introduction to Psychology course participated in this study. The primary dependent measure was student performance on tests following each condition. The analysis revealed no statistically significant difference between the conditions, F(1, 302) = 0.103, p = .748, though qualitative feedback revealed student preference for preparation guides. Future research is necessary to examine the effects of quizzing while addressing the limitations of this study., (© 2023 Society for the Experimental Analysis of Behavior (SEAB).)
- Published
- 2024
- Full Text
- View/download PDF
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